diff --git a/Analysis/BaseCaller/BarcodeClassifier.cpp b/Analysis/BaseCaller/BarcodeClassifier.cpp index 2a6fc9f8..f2107a10 100644 --- a/Analysis/BaseCaller/BarcodeClassifier.cpp +++ b/Analysis/BaseCaller/BarcodeClassifier.cpp @@ -162,6 +162,7 @@ BarcodeClassifier::BarcodeClassifier(OptArgs& opts, BarcodeDatasets& datasets, c printf(" Barcode filter minreads : %d (0 = disabled)\n", barcode_filter_minreads_); printf(" Barcode filter filename : %s\n", barcode_filter_filename_.c_str()); printf(" Generation of XB bam-tag : %s (number of base errors during barcode classification)\n", (barcode_bam_tag_ ? "on" : "off")); + printf(" No-match read group Idx : %d\n", no_barcode_read_group_); if (barcode_ignore_flows_) printf(" Ignoring flows %d to %d for barcode classification.\n",classifier_ignore_flows_[0],classifier_ignore_flows_[1]); printf("\n"); @@ -479,11 +480,11 @@ int BarcodeClassifier::FlowAlignClassification(const ProcessedRead &processed_r // ------------------------------------------------------------------------ int BarcodeClassifier::SignalSpaceClassification(const BasecallerRead& basecaller_read, float& best_distance, int& best_errors, - vector& best_bias, int& filtered_zero_errors) + vector& best_bias, bool& filtered_zero_errors, int& org_read_group) { int best_barcode = -1; best_errors = -1; - filtered_zero_errors = -1; + filtered_zero_errors = false; best_distance = score_cutoff_ + score_separation_; float second_best_distance = 1e20; @@ -531,10 +532,14 @@ int BarcodeClassifier::SignalSpaceClassification(const BasecallerRead& basecall } if (second_best_distance - best_distance < score_separation_) { - if (best_errors == 0) - filtered_zero_errors = barcode_.at(best_barcode).read_group_index; - best_barcode = -1; + if (best_errors == 0){ + filtered_zero_errors = true; + org_read_group = barcode_.at(best_barcode).read_group_index; + } + else + best_barcode = -1; } + return best_barcode; }; @@ -548,23 +553,24 @@ bool BarcodeClassifier::MatchesBarcodeSignal(const BasecallerRead& basecaller_re int best_barcode = -1; int best_errors = -1; - int filtered_zero_errors = -1; + int org_read_group = -1; + bool filtered_zero_errors = false; float best_distance = 0.0; vector best_bias; - best_barcode = SignalSpaceClassification(basecaller_read, best_distance, best_errors, best_bias, filtered_zero_errors); + best_barcode = SignalSpaceClassification(basecaller_read, best_distance, best_errors, best_bias, filtered_zero_errors, org_read_group); - return (best_barcode >= 0); + return (best_barcode >= 0 and org_read_group < 0); }; // ------------------------------------------------------------------------ int BarcodeClassifier::ProportionalSignalClassification(const BasecallerRead& basecaller_read, float& best_distance, int& best_errors, - vector& best_bias, int& filtered_zero_errors) + vector& best_bias, bool& filtered_zero_errors, int& org_read_group) { int best_barcode = -1; best_errors = -1; - filtered_zero_errors = -1; + filtered_zero_errors = false; best_distance = score_cutoff_ + score_separation_; float second_best_distance = 1e20; @@ -610,9 +616,12 @@ int BarcodeClassifier::ProportionalSignalClassification(const BasecallerRead& b } if (second_best_distance - best_distance < score_separation_) { - if (best_errors == 0) - filtered_zero_errors = barcode_.at(best_barcode).read_group_index; - best_barcode = -1; + if (best_errors == 0){ + filtered_zero_errors = true; + org_read_group = barcode_.at(best_barcode).read_group_index; + } + else + best_barcode = -1; } return best_barcode; }; @@ -620,9 +629,9 @@ int BarcodeClassifier::ProportionalSignalClassification(const BasecallerRead& b // ------------------------------------------------------------------------ -bool BarcodeClassifier::AdapterValidation(const BasecallerRead& basecaller_read, int& best_barcode, int& filtered_read_group) +bool BarcodeClassifier::AdapterValidation(const BasecallerRead& basecaller_read, int best_barcode, bool& filtered_read) { - filtered_read_group = -1; + filtered_read = false; // zero means disabled if (adapter_cutoff_ == 0) @@ -650,8 +659,9 @@ bool BarcodeClassifier::AdapterValidation(const BasecallerRead& basecaller_read, } if (residual_2 > num_adapter_flows * adapter_cutoff_) { - filtered_read_group = barcode_[best_barcode].read_group_index; - best_barcode = -1; + filtered_read = true; + //filtered_read_group = barcode_[best_barcode].read_group_index; + //best_barcode = -1; return false; } else @@ -680,12 +690,12 @@ void BarcodeClassifier::ClassifyAndTrimBarcode(int read_index, ProcessedRead &pr case 2: // Minimize L2 distance for score_mode_ == 2 case 3: // Minimize L1 distance for score_mode_ == 3 best_barcode = SignalSpaceClassification(basecaller_read, processed_read.barcode_distance, processed_read.barcode_n_errors, - processed_read.barcode_bias, processed_read.barcode_filt_zero_error); + processed_read.barcode_bias, processed_read.barcode_filt_zero_error, processed_read.org_rg_idx); break; case 4: //L2 for score mode 4 case 5: //L1 for score mode 5 best_barcode = ProportionalSignalClassification(basecaller_read, processed_read.barcode_distance, processed_read.barcode_n_errors, - processed_read.barcode_bias, processed_read.barcode_filt_zero_error); + processed_read.barcode_bias, processed_read.barcode_filt_zero_error, processed_read.org_rg_idx); break; default: // Trivial base space comparison best_barcode = SimpleBaseSpaceClassification(basecaller_read); @@ -698,30 +708,35 @@ void BarcodeClassifier::ClassifyAndTrimBarcode(int read_index, ProcessedRead &pr // -------- Classification done, now accounting ---------- + int x, y; + barcode_mask_.IndexToRowCol (read_index, y, x); + if (best_barcode == -1) { - int x, y; - barcode_mask_.IndexToRowCol (read_index, y, x); barcode_mask_.SetBarcodeId(x, y, 0); if (no_barcode_read_group_ >= 0) processed_read.read_group_index = no_barcode_read_group_; - return; + } + else if (processed_read.barcode_filt_zero_error or processed_read.barcode_adapter_filtered){ + barcode_mask_.SetBarcodeId(x, y, 0); + processed_read.read_group_index = barcode_[best_barcode].read_group_index; + processed_read.org_rg_idx = barcode_[best_barcode].read_group_index; + if (processed_read.barcode_filt_zero_error) + processed_read.barcode_adapter_filtered = false; + } + else { + barcode_mask_.SetBarcodeId(x, y, (uint16_t)barcode_[best_barcode].mask_index); + processed_read.read_group_index = barcode_[best_barcode].read_group_index; + processed_read.barcode_n_errors = max(processed_read.barcode_n_errors, 0); } - const Barcode& bce = barcode_[best_barcode]; - - int x, y; - barcode_mask_.IndexToRowCol (read_index, y, x); - barcode_mask_.SetBarcodeId(x, y, (uint16_t)bce.mask_index); - processed_read.read_group_index = bce.read_group_index; - processed_read.barcode_n_errors = max(processed_read.barcode_n_errors, 0); + if (not trim_barcodes_ or best_barcode == -1) + return; if(barcode_bam_tag_) processed_read.bam.AddTag("XB","i", processed_read.barcode_n_errors); - if (not trim_barcodes_) - return; - // Account for barcode + barcode adapter bases + const Barcode& bce = barcode_[best_barcode]; if (score_mode_ == 0){ processed_read.filter.n_bases_barcode = min(processed_read.filter.n_bases, (int)barcode_[best_barcode].full_barcode.length()); } @@ -741,7 +756,6 @@ void BarcodeClassifier::ClassifyAndTrimBarcode(int read_index, ProcessedRead &pr processed_read.filter.n_bases_prefix = processed_read.filter.n_bases_tag = processed_read.filter.n_bases_barcode; // And now do handle classification and trimming ClassifyAndTrimHandle(read_index, best_barcode, processed_read, basecaller_read, base_to_flow); - } // ------------------------------------------------------------------------ @@ -877,9 +891,9 @@ void BarcodeClassifier::ClassifyAndTrimHandle(int read_index, int best_barcode, int x, y; barcode_mask_.IndexToRowCol (read_index, y, x); barcode_mask_.SetBarcodeId(x, y, 0); - if (no_barcode_read_group_ >= 0){ - processed_read.barcode_handle_filtered = processed_read.read_group_index; - processed_read.read_group_index = no_barcode_read_group_; + if (no_barcode_read_group_ >= 0 and processed_read.org_rg_idx < 0){ + processed_read.barcode_handle_filtered = true; + processed_read.org_rg_idx = processed_read.read_group_index; processed_read.handle_n_errors = 1+handle_cutoff_; } return; @@ -995,7 +1009,7 @@ int BarcodeClassifier::HandleFlowAlign(int best_barcode, ProcessedRead &process // ------------------------------------------------------------------------ -void BarcodeClassifier::Close(BarcodeDatasets& datasets) +void BarcodeClassifier::Close(BarcodeDatasets& datasets, int num_end_barcodes) { // Nothing to do if dataset is not in use // Do not filter control dataset and do not generate output files @@ -1016,6 +1030,7 @@ void BarcodeClassifier::Close(BarcodeDatasets& datasets) datasets.barcode_filters()["classifier_mode"] = (Json::Int64)score_mode_; datasets.barcode_filters()["classifier_cutoff"] = score_cutoff_; datasets.barcode_filters()["classifier_separation"] = score_separation_; + datasets.barcode_filters()["num_end_barcodes"] = num_end_barcodes; if (hamming_dmin_ >=0) datasets.barcode_filters()["hamming_distance"] = hamming_dmin_; @@ -1090,7 +1105,8 @@ void BarcodeClassifier::Close(BarcodeDatasets& datasets) // Filter read groups where a too large proportion of reads failed adapter verification // Likely to be a highly contaminated sample and should not be analyzed - if ((not i_am_filtered) and (not barcode_filter_postpone_) and (not is_control_barcode)) + // Do not apply to dual barcode sets - dual barcodes will filter contamination + if ((not i_am_filtered) and (not barcode_filter_postpone_) and (not is_control_barcode) and num_end_barcodes == 0) { //unsigned int adapter_filtered = (*rg)["barcode_adapter_filtered"].asUInt(); i_am_filtered = (5*adapter_filtered > read_count) ? true : false; @@ -1505,9 +1521,17 @@ void EndBarcodeClassifier::ClassifyAndTrimBarcode(int read_index, ProcessedRead if (best_barcode < 0) { if (not process_as_single) PushReadToNomatch(read_index, processed_read); + // Trim the parts that have been identified + UpdateReadTrimming(processed_read, n_bases_trimmed, ""); return; } processed_read.end_barcode_index = best_barcode; + // If we process as single barcode, or demultiplex an external list + // we add the end barcode sequence to the YK field. + if (process_as_single or demux_barcode_list_) { + my_YK_tag += end_barcodes_.at(best_barcode).barcode_adapter; + my_YK_tag += end_barcodes_.at(best_barcode).barcode_sequence; + } // Move clearly identified barcode contamination to no-match, i.e., // reads where we identified an end barcode and it was the wrong one @@ -1516,19 +1540,6 @@ void EndBarcodeClassifier::ClassifyAndTrimBarcode(int read_index, ProcessedRead PushReadToNomatch(read_index, processed_read); } - // we're done if trimming is not desired - if (not trim_barcodes_) { - processed_read.filter.n_bases_after_barcode_trim = -1; - return; - } - - // If we process as single barcode, or demultiplex an external list - // we add the end barcode sequence to the YK field. - if (process_as_single or demux_barcode_list_) { - my_YK_tag += end_barcodes_.at(best_barcode).barcode_adapter; - my_YK_tag += end_barcodes_.at(best_barcode).barcode_sequence; - } - UpdateReadTrimming(processed_read, n_bases_trimmed, my_YK_tag); }; @@ -1537,6 +1548,11 @@ void EndBarcodeClassifier::ClassifyAndTrimBarcode(int read_index, ProcessedRead void EndBarcodeClassifier::UpdateReadTrimming(ProcessedRead &processed_read, int trim_n_bases, const string& YK_tag) { + if (not trim_barcodes_) { + processed_read.filter.n_bases_after_barcode_trim = -1; + return; + } + // Trim bases from read processed_read.filter.n_bases_after_barcode_trim = max(0, processed_read.filter.n_bases_filtered-trim_n_bases); processed_read.filter.n_bases_filtered = processed_read.filter.n_bases_after_barcode_trim; @@ -1556,9 +1572,10 @@ void EndBarcodeClassifier::PushReadToNomatch(int read_index, ProcessedRead &proc { int x, y; barcode_mask_pointer_->IndexToRowCol (read_index, y, x); - if (nomatch_read_group_ >= 0){ - processed_read.end_barcode_filtered = processed_read.read_group_index; - processed_read.read_group_index = nomatch_read_group_; + if (nomatch_read_group_ >= 0 and processed_read.org_rg_idx < 0){ + processed_read.end_barcode_filtered = true; + processed_read.org_rg_idx = processed_read.read_group_index; + //processed_read.read_group_index = nomatch_read_group_; barcode_mask_pointer_->SetBarcodeId(x, y, 0); } } diff --git a/Analysis/BaseCaller/BarcodeClassifier.h b/Analysis/BaseCaller/BarcodeClassifier.h index f62de499..b3efc0f3 100644 --- a/Analysis/BaseCaller/BarcodeClassifier.h +++ b/Analysis/BaseCaller/BarcodeClassifier.h @@ -69,12 +69,12 @@ class BarcodeClassifier { int FlowAlignClassification(const ProcessedRead &processed_read, const vector& base_to_flow, int& best_errors); int SignalSpaceClassification(const BasecallerRead& basecaller_read, float& best_distance, int& best_errors, - vector& best_bias, int& filtered_zero_errors); + vector& best_bias, bool& filtered_zero_errors, int& org_read_group); int ProportionalSignalClassification(const BasecallerRead& basecaller_read, float& best_distance, int& best_errors, - vector& best_bias, int& filtered_zero_errors); + vector& best_bias, bool& filtered_zero_errors, int& org_read_group); - bool AdapterValidation(const BasecallerRead& basecaller_read, int& best_barcode, int& filtered_read_group); + bool AdapterValidation(const BasecallerRead& basecaller_read, int best_barcode, bool& filtered_read); void ClassifyAndTrimBarcode(int read_index, ProcessedRead &processed_read, const BasecallerRead& basecaller_read, const vector& base_to_flow); @@ -86,7 +86,7 @@ class BarcodeClassifier { Mask* GetBarcodeMaskPointer() { return &barcode_mask_; }; - void Close(BarcodeDatasets& datasets); + void Close(BarcodeDatasets& datasets, int num_end_barcodes); protected: diff --git a/Analysis/BaseCaller/BaseCaller.cpp b/Analysis/BaseCaller/BaseCaller.cpp index 8aad0749..865cfa5d 100644 --- a/Analysis/BaseCaller/BaseCaller.cpp +++ b/Analysis/BaseCaller/BaseCaller.cpp @@ -24,6 +24,9 @@ #include #include #include // Floating point exceptions +#include +#include +#include #include "json/json.h" #include "MaskSample.h" @@ -41,6 +44,7 @@ #include "BarcodeClassifier.h" #include "OrderedDatasetWriter.h" #include "TreephaserSSE.h" +#include "TreephaserVEC.h" #include "PhaseEstimator.h" #include "PerBaseQual.h" #include "BaseCallerFilters.h" @@ -111,8 +115,9 @@ void ReportState(time_t analysis_start_time, const char *my_state) { time_t analysis_current_time; time(&analysis_current_time); - fprintf(stdout, "\n%s: Elapsed: %.1lf minutes, Timestamp: %s\n", my_state, + fprintf(stdout, "\n%s: Elapsed: %.2lf minutes, (%.0lf seconds) Timestamp: %s\n", my_state, difftime(analysis_current_time, analysis_start_time) / 60, + difftime(analysis_current_time, analysis_start_time), ctime (&analysis_current_time)); } @@ -182,8 +187,42 @@ void make_base_to_flow(const vector& sequence,ion::FlowOrder& flow_order, } } +char FileCacherDummy=0; // to keep the access from being optimized away +void *FileCacher(void *ptr) +{ + const char *fname=(const char *)ptr; + struct stat statbuf; + if(stat(fname,&statbuf) != 0){ + printf("FileCacher: Failed to stat %s\n",fname); + return NULL; + } + + int fd = open(fname,O_RDONLY,0); + char cntr=0; + if(fd >= 0){ + char *dst; + if ((dst = (char *)mmap (0, statbuf.st_size, PROT_READ, + MAP_SHARED, fd, 0)) == (char *) 0xffffffffffffffff){ + printf("FileCacher: Failed to mmap %s size %ld\n",fname,statbuf.st_size); + close(fd); + return NULL; + } + + __off_t addr=0; + while(addr < statbuf.st_size){ + cntr+=dst[addr]; + addr += 4096; + } + FileCacherDummy=cntr; + munmap((void *)dst,statbuf.st_size); + //printf("Done caching %s\n",fname); + close(fd); + } + return NULL; +} + // -------------------------------------------------------------------------- -//! @brief Main function for BaseCaller executable Mark: XXX +//! @brief Main function for BaseCaller executable Mark: //! @ingroup BaseCaller @@ -243,6 +282,21 @@ int main (int argc, const char *argv[]) // Sampling options may reset command line arguments & change context bc_params.InitializeSamplingFromOptArgs(opts, bc.read_class_map->NumValidWells()); + + if(bc_params.GetSamplingOpts().calibration_training > 0 or bc_params.GetSamplingOpts().have_calib_panel){ + vector filename_wells=bc_params.GetFiles().filename_wells; + for (unsigned int i=0; iNumEndBarcodes()); + calibration_barcodes.Close(datasets_calibration, 0); if (bc.have_calibration_panel) { datasets.json()["IonControl"]["datasets"] = datasets_calibration.json()["datasets"]; datasets.json()["IonControl"]["read_groups"] = datasets_calibration.read_groups(); @@ -519,8 +578,9 @@ int main (int argc, const char *argv[]) return EXIT_SUCCESS; } +int threadCntr=0; // ---------------------------------------------------------------- -//! @brief Main code for BaseCaller worker thread Mark: XXX +//! @brief Main code for BaseCaller worker thread Mark: //! @ingroup BaseCaller //! @param[in] input Pointer to BaseCallerContext. @@ -528,17 +588,10 @@ void * BasecallerWorker(void *input) { BaseCallerContext& bc = *static_cast(input); - //RawWells wells ("", bc.filename_wells.c_str()); - WellsManager wells_mngr(bc.filename_wells, false); - wells_mngr.SetWellsContext(&bc.flow_order, - bc.keys, - bc.read_class_map, - bc.wells_norm_method, - bc.compress_multi_taps); - - pthread_mutex_lock(&bc.mutex); - wells_mngr.OpenForIncrementalRead(); - pthread_mutex_unlock(&bc.mutex); + pthread_mutex_lock(&bc.load_mutex); + WellsManager *wells_mngrp=new WellsManager(bc.wells_mngr); + WellsManager &wells_mngr=*wells_mngrp; + pthread_mutex_unlock(&bc.load_mutex); int num_flows = bc.flow_order.num_flows(); vector residual(num_flows, 0); @@ -565,12 +618,19 @@ void * BasecallerWorker(void *input) treephaser.SkipRecalDuringNormalization(bc.skip_recal_during_norm); // SSE treephaser definition. XXX -#if defined( __SSE3__ ) - TreephaserSSE treephaser_sse(bc.flow_order, bc.windowSize); - treephaser_sse.SkipRecalDuringNormalization(bc.skip_recal_during_norm); +#if 0 + TreephaserSSE treephaser_vec(bc.flow_order, bc.windowSize); + treephaser_vec.SkipRecalDuringNormalization(bc.skip_recal_during_norm); +#else + + TreephaserVEC treephaser_vec(bc.flow_order, bc.windowSize); + treephaser_vec.SkipRecalDuringNormalization(bc.skip_recal_during_norm); + treephaser_vec.SetBadPathLimit(bc.BadPathLimit); + treephaser_vec.SetManyPathLimit(bc.ManyPathLimit); + treephaser_vec.SetInitalPaths(bc.InitialPaths); + treephaser_vec.SetMaxMetrDiff(bc.MaxMetrDiff); #endif - while (true) { // @@ -587,10 +647,16 @@ void * BasecallerWorker(void *input) } int num_usable_wells = 0; - for (int y = begin_y; y < end_y; ++y) + if(bc.calibration_training or bc.have_calibration_panel){ + num_usable_wells=1; + }else{ + for (int y = begin_y; y < end_y; ++y) for (int x = begin_x; x < end_x; ++x) - if (bc.read_class_map->ClassMatch(x,y, MapOutputWell)) - num_usable_wells++; + if (bc.read_class_map->ClassMatch(x,y, MapOutputWell)) + num_usable_wells++; + if (begin_x == 0) + SaveBaseCallerProgress(10 + (80*begin_y)/bc.chip_subset.GetChipSizeY(), bc.output_directory); + } if (begin_x == 0) printf("\n% 5d/% 5d: ", begin_y, bc.chip_subset.GetChipSizeY()); if (num_usable_wells == 0) printf(" "); @@ -600,8 +666,6 @@ void * BasecallerWorker(void *input) else printf("##"); fflush(NULL); - if (begin_x == 0) - SaveBaseCallerProgress(10 + (80*begin_y)/bc.chip_subset.GetChipSizeY(), bc.output_directory); pthread_mutex_unlock(&bc.mutex); @@ -625,7 +689,7 @@ void * BasecallerWorker(void *input) continue; } - wells_mngr.LoadChunk(begin_y, end_y-begin_y, begin_x, end_x-begin_x, 0, num_flows); + wells_mngr.LoadChunk(begin_y, end_y-begin_y, begin_x, end_x-begin_x, 0, num_flows,&bc.load_mutex); for (int y = begin_y; y < end_y; ++y) for (int x = begin_x; x < end_x; ++x) { // Loop over wells within current region @@ -737,15 +801,16 @@ void * BasecallerWorker(void *input) treephaser.SetModelParameters(cf, ie, dr); // Execute vectorized basecaller version XXX -#if defined( __SSE3__ ) + if (bc.sse_dephaser) { - treephaser_sse.SetAsBs(aPtr, bPtr); // Set/delete recalibration model for this read - treephaser_sse.SetModelParameters(cf, ie); // SSE version has no hook for droop. - if (bc.dephaser == "treephaser-sse") - treephaser_sse.NormalizeAndSolve(read); + treephaser_vec.SetAsBs(aPtr, bPtr); // Set/delete recalibration model for this read + treephaser_vec.SetModelParameters(cf, ie); // SSE version has no hook for droop. + + if (bc.dephaser == "treephaser-vec") + treephaser_vec.NormalizeAndSolve(read); else // bc.dephaser == "treephaser-solve" Solving without normalization - treephaser_sse.SolveRead(read, 0, num_flows); + treephaser_vec.SolveRead(read, 0, num_flows); // Store debug info if desired and calibration enabled if (bc.debug_normalization_bam and bc.histogram_calibration->is_enabled()) @@ -760,10 +825,10 @@ void * BasecallerWorker(void *input) // Generate base_to_flow before ComputeQVmetrics. But not too early, otherwise the sequence is not ready make_base_to_flow(read.sequence,bc.flow_order,base_to_flow,flow_to_base,num_flows); - treephaser_sse.ComputeQVmetrics_flow(read,flow_to_base,bc.flow_predictors_); + treephaser_vec.ComputeQVmetrics_flow(read,flow_to_base,bc.flow_predictors_); compute_base_calls = false; } -#endif + // Use CPP code version if we didn't already use vectorized code if (compute_base_calls){ @@ -992,7 +1057,7 @@ void * BasecallerWorker(void *input) //! New mechanism for dumping potentially useful metrics. if (bc.metric_saver->save_anything() and (is_random_unfiltered or !bc.metric_saver->save_subset_only())) { - pthread_mutex_lock(&bc.mutex); + pthread_mutex_lock(&bc.metric_mutex); bc.metric_saver->SaveRawMeasurements (y,x,read.raw_measurements); bc.metric_saver->SaveAdditiveCorrection (y,x,read.additive_correction); @@ -1008,7 +1073,7 @@ void * BasecallerWorker(void *input) bc.metric_saver->SaveHomopolymerRank (y,x,homopolymer_rank); bc.metric_saver->SaveNeighborhoodNoise (y,x,neighborhood_noise); - pthread_mutex_unlock(&bc.mutex); + pthread_mutex_unlock(&bc.metric_mutex); } @@ -1016,6 +1081,9 @@ void * BasecallerWorker(void *input) // Step 4b. Add flow signal information to ZM tag in BAM record. // + // Push the reads that - at some point in time - where flagged as nomatch into the nomatch BAM + processed_read.PushToNomatch(bc.barcodes->NoBarcodeReadGroup()); + int max_flow = num_flows; if (bc.trim_zm){ if (processed_read.filter.n_bases_filtered > 0) diff --git a/Analysis/BaseCaller/BaseCallerFilters.cpp b/Analysis/BaseCaller/BaseCallerFilters.cpp index 37ab2e06..f9428e94 100644 --- a/Analysis/BaseCaller/BaseCallerFilters.cpp +++ b/Analysis/BaseCaller/BaseCallerFilters.cpp @@ -111,6 +111,27 @@ ReadFilteringHistory::ReadFilteringHistory() adapter_decision = false; } +// Function resets the +void ReadFilteringHistory::UndoBarcodeTrimming() +{ + if (is_filtered) + return; + + // reset 5' trimming to point to after library key + n_bases_prefix = n_bases_barcode = n_bases_tag = n_bases_key; + + // reset 3' trimming point to min of quality trimmer / adapter trimmer / read length + n_bases_filtered = n_bases; + if (n_bases_after_adapter_trim >=0 and n_bases_after_adapter_trim < n_bases_filtered) + n_bases_filtered = n_bases_after_adapter_trim; + if (n_bases_after_quality_trim >= 0 and n_bases_after_quality_trim < n_bases_filtered) + n_bases_filtered = n_bases_after_quality_trim; + + n_bases_after_barcode_trim = -1; + n_bases_after_tag_trim = -1; + n_bases_after_extra_trim = -1; +} + // ---------------------------------------------------------------------------- // Let's not modify the ZD vector @@ -539,7 +560,9 @@ void ReadFilteringStats::SaveToBasecallerJson(Json::Value &json, const string& c json["Filtering"]["BaseDetails"]["final"] = (Json::Int64)num_bases_final_; json["Filtering"]["LibraryReport"]["filtered_polyclonal"] = (Json::Int64)(num_reads_removed_bkgmodel_polyclonal_ + num_reads_removed_polyclonal_); - json["Filtering"]["LibraryReport"]["filtered_primer_dimer"] = (Json::Int64) num_reads_removed_adapter_trim_; + json["Filtering"]["LibraryReport"]["filtered_primer_dimer"] = (Json::Int64)(num_reads_removed_adapter_trim_ + + num_reads_removed_barcode_trim_ + + num_reads_removed_tag_trim_); json["Filtering"]["LibraryReport"]["filtered_low_quality"] = (Json::Int64)( num_reads_removed_bkgmodel_high_ppf_ + num_reads_removed_bkgmodel_keypass_ + @@ -547,10 +570,8 @@ void ReadFilteringStats::SaveToBasecallerJson(Json::Value &json, const string& c num_reads_removed_short_ + num_reads_removed_keypass_ + num_reads_removed_residual_ + - num_reads_removed_barcode_trim_ + num_reads_removed_quality_trim_ + num_reads_removed_quality_filt_ + - num_reads_removed_tag_trim_ + num_reads_removed_extra_trim_); json["Filtering"]["LibraryReport"]["final_library_reads"] = (Json::Int64)num_reads_final_; @@ -1396,18 +1417,24 @@ bool BaseCallerFilters::TrimAdapter_FlowAlign(float& best_metric, int& best_star best_adapter_overlap= -1; int sequence_pos = 0; char adapter_start_base = effective_adapter.at(0); + int numFlows=flow_order_.num_flows(); + int readSize=(int)read.sequence.size(); + const char *seq=&read.sequence[0]; + int EALength=(int)effective_adapter.length(); + const char *eadap=&effective_adapter[0]; - for (int adapter_start_flow = 0; adapter_start_flow < flow_order_.num_flows(); ++adapter_start_flow) { + for (int adapter_start_flow = 0; adapter_start_flow < numFlows; ++adapter_start_flow) { // Only consider start flows that agree with adapter start if (flow_order_[adapter_start_flow] != adapter_start_base) continue; - while (sequence_pos < (int)read.sequence.size() and base_to_flow[sequence_pos] < adapter_start_flow) + while (sequence_pos < readSize and base_to_flow[sequence_pos] < adapter_start_flow) sequence_pos++; - if (sequence_pos >= (int)read.sequence.size()) + + if (sequence_pos >= readSize) break; - else if (sequence_pos>0 and read.sequence.at(sequence_pos-1)==adapter_start_base) + else if (sequence_pos>0 and seq[sequence_pos-1]==adapter_start_base) continue; // Make sure we don't get impossible configurations // Evaluate this starting position @@ -1417,14 +1444,14 @@ bool BaseCallerFilters::TrimAdapter_FlowAlign(float& best_metric, int& best_star int local_sequence_pos = sequence_pos; int local_start_base = sequence_pos; - for (int flow = adapter_start_flow; flow < flow_order_.num_flows(); ++flow) { + for (int flow = adapter_start_flow; flow < numFlows; ++flow) { int base_delta = 0; - while (adapter_pos < (int)effective_adapter.length() and effective_adapter.at(adapter_pos) == flow_order_[flow]) { + while (adapter_pos < EALength and eadap[adapter_pos] == flow_order_[flow]) { adapter_pos++; base_delta--; } - while (local_sequence_pos < (int)read.sequence.size() and base_to_flow[local_sequence_pos] == flow) { + while (local_sequence_pos < readSize and base_to_flow[local_sequence_pos] == flow) { local_sequence_pos++; base_delta++; } @@ -1437,7 +1464,7 @@ bool BaseCallerFilters::TrimAdapter_FlowAlign(float& best_metric, int& best_star local_start_base += base_delta; score_len_flows++; - if (adapter_pos == (int)effective_adapter.length() or local_sequence_pos == (int)read.sequence.size()) + if (adapter_pos == EALength or local_sequence_pos == readSize) break; } @@ -1447,9 +1474,9 @@ bool BaseCallerFilters::TrimAdapter_FlowAlign(float& best_metric, int& best_star if (adapter_pos < trim_adapter_min_match_) // Match too short continue; - if (score_match * 2 * effective_adapter.length() > trim_adapter_cutoff_) // Match too dissimilar + if (score_match * 2 * EALength > trim_adapter_cutoff_) // Match too dissimilar continue; - float final_metric = adapter_pos / (float)effective_adapter.length() - score_match; // The higher the better + float final_metric = adapter_pos / (float)EALength - score_match; // The higher the better if (final_metric > best_metric) { adapter_found = true; diff --git a/Analysis/BaseCaller/BaseCallerParameters.cpp b/Analysis/BaseCaller/BaseCallerParameters.cpp index 6ee842e5..04c036f6 100644 --- a/Analysis/BaseCaller/BaseCallerParameters.cpp +++ b/Analysis/BaseCaller/BaseCallerParameters.cpp @@ -223,6 +223,8 @@ void BaseCallerParameters::PrintHelp() printf (" --compress-multi-taps BOOL Compress the signal from adjacent multi-tap flows [false]\n"); printf (" --num-unfiltered INT number of subsampled unfiltered reads [100000]\n"); printf (" --only-process-unfiltered-set on/off Only save reads that would also go to unfiltered BAMs. [off]\n"); + printf (" --bad-path-limit INT number of bad paths before aborting [10000]\n"); + printf (" --many-path-limit INT number of >=3 path decisions before aborting [10000]\n"); printf ("\n"); printf ("Chip/Block division:\n"); printf (" -r,--rows INT-INT subset of rows to be processed [all rows]\n"); @@ -403,7 +405,7 @@ bool BaseCallerParameters::InitContextVarsFromOptArgs(OptArgs& opts){ char default_run_id[6]; // Create a run identifier from full output directory string ion_run_to_readname (default_run_id, (char*)bc_files.output_directory.c_str(), bc_files.output_directory.length()); context_vars.run_id = opts.GetFirstString ('-', "run-id", default_run_id); - num_threads_ = opts.GetFirstInt ('n', "num-threads", max(2*numCores(), 4)); + num_threads_ = opts.GetFirstInt ('n', "num-threads", max(numCores(), 4)); num_bamwriter_threads_ = opts.GetFirstInt ('-', "num-threads-bamwriter", 0); compress_output_bam_ = opts.GetFirstBoolean('-', "compress-bam", true); @@ -413,7 +415,7 @@ bool BaseCallerParameters::InitContextVarsFromOptArgs(OptArgs& opts){ // Treephaser options #if defined( __SSE3__ ) - context_vars.dephaser = opts.GetFirstString ('-', "dephaser", "treephaser-sse"); + context_vars.dephaser = opts.GetFirstString ('-', "dephaser", "treephaser-vec"); #else context_vars.dephaser = opts.GetFirstString ('-', "dephaser", "treephaser-swan"); #endif @@ -427,6 +429,10 @@ bool BaseCallerParameters::InitContextVarsFromOptArgs(OptArgs& opts){ context_vars.calibrate_TFs = opts.GetFirstBoolean('-', "calibrate-tfs", false); context_vars.trim_zm = opts.GetFirstBoolean('-', "trim-zm", true); context_vars.compress_multi_taps = opts.GetFirstBoolean('-', "compress-multi-taps", false); + context_vars.bad_path_limit = opts.GetFirstInt ('-', "bad-path-limit", 10000); + context_vars.many_path_limit = opts.GetFirstInt ('-', "many-path-limit",10000); + context_vars.InitialPaths = opts.GetFirstInt ('-', "initial-paths",-1); + context_vars.MaxMetrDiff = opts.GetFirstDouble ('-', "max-metr-diff",0.3); context_vars.inline_control = opts.GetFirstBoolean('-', "inline-control", false); if (context_vars.inline_control and not bc_files.inline_control_reference_file.empty()){ @@ -524,7 +530,7 @@ bool BaseCallerParameters::SetBaseCallerContextVars(BaseCallerContext & bc) bc.wells_norm_method = context_vars.wells_norm_method; bc.keynormalizer = context_vars.keynormalizer; bc.dephaser = context_vars.dephaser; - bc.sse_dephaser = (bc.dephaser == "treephaser-sse" or bc.dephaser == "treephaser-solve"); + bc.sse_dephaser = (bc.dephaser == "treephaser-vec" or bc.dephaser == "treephaser-sse" or bc.dephaser == "treephaser-solve"); bc.windowSize = context_vars.windowSize; bc.diagonal_state_prog = context_vars.diagonal_state_prog; bc.skip_droop = context_vars.skip_droop; @@ -532,6 +538,10 @@ bool BaseCallerParameters::SetBaseCallerContextVars(BaseCallerContext & bc) bc.calibrate_TFs = context_vars.calibrate_TFs; bc.trim_zm = context_vars.trim_zm; bc.compress_multi_taps = context_vars.compress_multi_taps; + bc.BadPathLimit = context_vars.bad_path_limit; + bc.ManyPathLimit = context_vars.many_path_limit; + bc.InitialPaths = context_vars.InitialPaths; + bc.MaxMetrDiff = context_vars.MaxMetrDiff; bc.flow_predictors_ = context_vars.flow_predictors_; bc.inline_control = context_vars.inline_control; diff --git a/Analysis/BaseCaller/BaseCallerParameters.h b/Analysis/BaseCaller/BaseCallerParameters.h index 813c3c3b..1427bbe8 100644 --- a/Analysis/BaseCaller/BaseCallerParameters.h +++ b/Analysis/BaseCaller/BaseCallerParameters.h @@ -119,6 +119,10 @@ struct BCcontextVars { // "unclipped" - Normalized and phased but unclipped. string wells_norm_method; //!< Well file normalization method bool compress_multi_taps; //!< Compress the signal from adjacent multi-tap flows + int bad_path_limit; + int many_path_limit; + int InitialPaths; + float MaxMetrDiff; // Treephaser options string keynormalizer; //!< Name of selected key normalization algorithm @@ -167,6 +171,11 @@ struct BaseCallerContext { bool trim_zm; //!< Trim the ZM tag when writing it to the bam file bool compress_multi_taps; //!< Compress the signal from adjacent multi-tap flows bool inline_control; //!< Switch to trigger inline control statistics + int BadPathLimit; //!< number of dead end paths before aborting + int ManyPathLimit; //!< number of >3 path decisions before aborting + int InitialPaths; //!< number of initial paths to explore + float MaxMetrDiff; //!< maximum metric diff to create a new path + // Important outside entities accessed by BaseCaller ion::ChipSubset chip_subset; //!< Chip coordinate & region handling for Basecaller @@ -184,7 +193,9 @@ struct BaseCallerContext { MolecularTagTrimmer *tag_trimmer; //!< Class for tag accounting within read groups // Threaded processing - pthread_mutex_t mutex; //!< Shared read/write mutex for BaseCaller worker threads + pthread_mutex_t mutex; //!< Shared general mutex for BaseCaller worker threads + pthread_mutex_t load_mutex; //!< Shared load mutex for BaseCaller worker threads + pthread_mutex_t metric_mutex; //!< Shared metric mutex for BaseCaller worker threads // Basecalling results saved here OrderedDatasetWriter lib_writer; //!< Writer object for library BAMs @@ -193,7 +204,8 @@ struct BaseCallerContext { set unfiltered_set; //!< Indicates which wells are to be saved to unfiltered BAMs OrderedDatasetWriter unfiltered_writer; //!< Writer object for unfiltered BAMs for a random subset of library reads OrderedDatasetWriter unfiltered_trimmed_writer; //!< Writer object for unfiltered trimmed BAMs for a random subset of library reads - + WellsManager *wells_mngr; + bool SetKeyAndFlowOrder(OptArgs& opts, const char * FlowOrder, const int NumFlows); void ClassifyAndSampleWells(const BCwellSampling & SamplingOpts); diff --git a/Analysis/BaseCaller/OrderedDatasetWriter.cpp b/Analysis/BaseCaller/OrderedDatasetWriter.cpp index 08835c86..6ad94a17 100644 --- a/Analysis/BaseCaller/OrderedDatasetWriter.cpp +++ b/Analysis/BaseCaller/OrderedDatasetWriter.cpp @@ -17,6 +17,49 @@ using namespace std; +// ------------------------------------------------------------------ + +ProcessedRead::ProcessedRead(int default_read_group) +{ + read_group_index = default_read_group; // Needs to be a valid index at startup + is_control_barcode = false; + org_rg_idx = -1; + barcode_n_errors = 0; + barcode_filt_zero_error = false; + barcode_adapter_filtered= false; + barcode_distance = 0.0; + handle_index = -1; + handle_n_errors = 0; + barcode_handle_filtered = false; + end_barcode_index = -1; + end_barcode_filtered = false; + end_bc_n_errors = -1; + end_handle_index = -1; + end_handle_n_errors = -1; + end_adapter_filtered = false; + end_handle_filtered = false; + trimmed_tags.Clear(); +} + +bool ProcessedRead::PushToNomatch(int no_match_index) +{ + // Just return if this is a non-barcoded run + if (no_match_index < 0) + return false; + // Also return if this read was not filtered + if (org_rg_idx < 0) + return false; + + if (org_rg_idx != read_group_index and no_match_index != read_group_index){ + cerr << "WARNING: read group index " << read_group_index << " does not match org_rg_idx " << org_rg_idx + << " or no_match_index " << no_match_index << " for read " << bam.Name << endl; + } + + read_group_index = no_match_index; + filter.UndoBarcodeTrimming(); + + return true; +} // ------------------------------------------------------------------ @@ -31,6 +74,7 @@ OrderedDatasetWriter::OrderedDatasetWriter() compress_bam_ = true; have_handles_ = false; num_bamwriter_threads_ = 0; + no_barcode_read_group_ = -1; pthread_mutex_init(&dropbox_mutex_, NULL); pthread_mutex_init(&write_mutex_, NULL); pthread_mutex_init(&delete_mutex_, NULL); @@ -101,6 +145,9 @@ void OrderedDatasetWriter::Open(const string& base_directory, BarcodeDatasets& d read_group_end_handle_rejected_.assign(num_read_groups_, 0); for (int rg = 0; rg < num_read_groups_; ++rg) { + if (not datasets.read_group(rg).isMember("barcode_name")) + no_barcode_read_group_ = rg; + read_group_name_.at(rg) = datasets.read_group_name(rg); read_group_num_barcode_errors_.at(rg).assign(3,0); read_group_barcode_bias_.at(rg).assign(datasets.GetBCmaxFlows(),0.0); @@ -406,6 +453,13 @@ void OrderedDatasetWriter::PhysicalWriteRegion(int region) if (entry->filter.is_filtered and not save_filtered_reads_) continue; + // In a last filtering step move the surviving start adapter filtered ones to nomatch + // thus avoiding that small primer-dimers trigger the contamination warning + // processed_read.barcode_adapter_filtered + //if (entry->barcode_adapter_filtered >= 0){ + // entry->read_group_index = no_barcode_read_group_; + //} + int target_file_idx = read_group_dataset_.at(entry->read_group_index); if (target_file_idx < 0) // Read group not assigned to a dataset? continue; @@ -437,40 +491,40 @@ void OrderedDatasetWriter::PhysicalWriteRegion(int region) // Barcode No-match accounting // 0-error filtered barcodes - if (entry->barcode_filt_zero_error >= 0){ - read_group_barcode_filt_zero_err_.at(entry->barcode_filt_zero_error)++; - AddOriginalReadGroupTag(entry->bam, read_group_name_.at(entry->barcode_filt_zero_error)+".SB"); + if (entry->barcode_filt_zero_error){ + read_group_barcode_filt_zero_err_.at(entry->org_rg_idx)++; + AddOriginalReadGroupTag(entry->bam, read_group_name_.at(entry->org_rg_idx)+".SB"); } // Account for filtered reads due to barcode adapter rejection - if (entry->barcode_adapter_filtered >= 0){ - read_group_barcode_adapter_rejected_.at(entry->barcode_adapter_filtered)++; - AddOriginalReadGroupTag(entry->bam, read_group_name_.at(entry->barcode_adapter_filtered)+".SA"); + if (entry->barcode_adapter_filtered){ + read_group_barcode_adapter_rejected_.at(entry->org_rg_idx)++; + AddOriginalReadGroupTag(entry->bam, read_group_name_.at(entry->org_rg_idx)+".SA"); } // *** End barcode // No-match accounting - if (entry->end_barcode_filtered >= 0){ - string org_rg = read_group_name_.at(entry->end_barcode_filtered); + if (entry->end_barcode_filtered){ + string org_rg = read_group_name_.at(entry->org_rg_idx); if (entry->filter.adapter_type < 0){ - read_group_no_bead_adapter_.at(entry->end_barcode_filtered)++; + read_group_no_bead_adapter_.at(entry->org_rg_idx)++; AddOriginalReadGroupTag(entry->bam, org_rg); } else if (entry->end_adapter_filtered) { - read_group_end_adapter_rejected_.at(entry->end_barcode_filtered)++; + read_group_end_adapter_rejected_.at(entry->org_rg_idx)++; AddOriginalReadGroupTag(entry->bam, org_rg+".EA"); } else if (entry->end_handle_filtered){ - read_group_end_handle_rejected_.at(entry->end_barcode_filtered)++; + read_group_end_handle_rejected_.at(entry->org_rg_idx)++; AddOriginalReadGroupTag(entry->bam, org_rg+".EH"); } else{ - read_group_end_barcode_rejected_.at(entry->end_barcode_filtered)++; + read_group_end_barcode_rejected_.at(entry->org_rg_idx)++; AddOriginalReadGroupTag(entry->bam, org_rg+".EB"); } if (read_group_end_barcode_counts_.size() >0 and entry->end_barcode_index >=0){ - ++read_group_end_barcode_counts_.at(entry->end_barcode_filtered).at(entry->end_barcode_index); + ++read_group_end_barcode_counts_.at(entry->org_rg_idx).at(entry->end_barcode_index); } } @@ -488,9 +542,9 @@ void OrderedDatasetWriter::PhysicalWriteRegion(int region) read_group_handle_dist_.at(entry->read_group_index).at(entry->handle_index)++; read_group_num_handle_errors_.at(entry->read_group_index).at(entry->handle_n_errors)++; } - else if (entry->barcode_handle_filtered >=0){ - read_group_handle_rejected_.at(entry->barcode_handle_filtered)++; - AddOriginalReadGroupTag(entry->bam, read_group_name_.at(entry->barcode_handle_filtered)+".SH"); + else if (entry->barcode_handle_filtered){ + read_group_handle_rejected_.at(entry->org_rg_idx)++; + AddOriginalReadGroupTag(entry->bam, read_group_name_.at(entry->org_rg_idx)+".SH"); } if (entry->end_handle_index >= 0){ diff --git a/Analysis/BaseCaller/OrderedDatasetWriter.h b/Analysis/BaseCaller/OrderedDatasetWriter.h index ee4fb2ed..200fcfcd 100644 --- a/Analysis/BaseCaller/OrderedDatasetWriter.h +++ b/Analysis/BaseCaller/OrderedDatasetWriter.h @@ -34,6 +34,7 @@ struct ReadFilteringHistory { void GenerateZDVector(vector& zd_vector); // Save filtering history to a vector void CalledRead(int num_bases) { is_called=true; n_bases=num_bases; }; + void UndoBarcodeTrimming(); // Basic information bool is_filtered; //!< true if the read should not be saved @@ -134,44 +135,30 @@ class ReadFilteringStats { //! @ingroup BaseCaller struct ProcessedRead { - ProcessedRead(int default_read_group) { - read_group_index = default_read_group; // Needs to be a valid index at startup - is_control_barcode = false; - barcode_n_errors = 0; - barcode_filt_zero_error = -1; - barcode_adapter_filtered= -1; - barcode_distance = 0.0; - handle_index = -1; - handle_n_errors = 0; - barcode_handle_filtered = -1; - end_barcode_index = -1; - end_barcode_filtered = -1; - end_bc_n_errors = -1; - end_handle_index = -1; - end_handle_n_errors = -1; - end_adapter_filtered = false; - end_handle_filtered = false; - trimmed_tags.Clear(); - } + ProcessedRead(int default_read_group); + + bool PushToNomatch(int no_match_index); + // Variables storing barcode classification results int read_group_index; //!< Read group index, generally based on barcode classification. + int org_rg_idx; //!< Indicator that the read is intended for the nomatch-bam file. Stores original read group index bool is_control_barcode; //!< Identified the read as having a control barcode int barcode_n_errors; //!< Number of base mismatches in barcode sequence. - int barcode_filt_zero_error; //!< Inidcator whether a hard decision match was filtered in signal space. - int barcode_adapter_filtered; //!< Indicator whether barcode adapter was too dissimilar + bool barcode_filt_zero_error; //!< Inidcator whether a hard decision match was filtered in signal space. + bool barcode_adapter_filtered; //!< Indicator whether barcode adapter was too dissimilar float barcode_distance; //!< Distance to assigned barcode in signal space. vector barcode_bias; //!< A bias vector for the assigned barcode. // Front handles int handle_index; //!< Index of assigned handle int handle_n_errors; //!< Number of errors in handle assignment - int barcode_handle_filtered; //!< Read was filtered for not matching any handle + bool barcode_handle_filtered; //!< Read was filtered for not matching any handle // End barcodes int end_barcode_index; //!< In case we demulitplex read groups, the end barcode index. - int end_barcode_filtered; //!< Read was filtered for not matching end barcode + bool end_barcode_filtered; //!< Read was filtered for not matching end barcode int end_bc_n_errors; //!< Number of errors in end barcode assignment bool end_adapter_filtered; //!< Indicator whether barcode adapter was too dissimilar int end_handle_index; //!< Index of assigned handle @@ -254,6 +241,7 @@ class OrderedDatasetWriter { vector read_group_dataset_; //!< Which dataset should a given read group be saved to? vector read_group_name_; int num_read_groups_; + int no_barcode_read_group_; //!< Index of the non-barcoded read group int num_regions_; //!< Total number of regions to expect int num_regions_written_; //!< Number of regions physically written thus far diff --git a/Analysis/BaseCaller/ReadClassMap.h b/Analysis/BaseCaller/ReadClassMap.h index 06ff60b1..49d704a4 100644 --- a/Analysis/BaseCaller/ReadClassMap.h +++ b/Analysis/BaseCaller/ReadClassMap.h @@ -137,6 +137,10 @@ class ReadClassMap { return ClassMatch(y*W+x, type); }; + inline uint16_t getClass(int x, int y) const + { + return (class_map.at(y*W+x)); + } inline bool ClassMatch(int index, ReadClassType type) const { if ( index < 0 || index >= ( W*H ) ) diff --git a/Analysis/BaseCaller/TreephaserSSE.cpp b/Analysis/BaseCaller/TreephaserSSE.cpp index 5093be7d..7f3f8c03 100644 --- a/Analysis/BaseCaller/TreephaserSSE.cpp +++ b/Analysis/BaseCaller/TreephaserSSE.cpp @@ -498,10 +498,10 @@ void TreephaserSSE::advanceState4(PathRec RESTRICT_PTR parent, int end) rNucCpy = _mm_cmpeq_epi32(rNucCpy, rNucIdx); // store max_flow in ad_FlowEnd - _mm_store_si128((__m128i*)ad_FlowEnd, rFlowEnd); + _mm_store_si128((__m128i*)&ad_FlowEnd, rFlowEnd); // four child flows in four 32 bit integers - _mm_store_si128((__m128i*)ad_Idx, rNucIdx); + _mm_store_si128((__m128i*)&ad_Idx, rNucIdx); // changes datatype from int to float without doing any conversion __m128 rParNuc = _mm_castsi128_ps(rNucCpy); @@ -576,7 +576,7 @@ void TreephaserSSE::advanceState4(PathRec RESTRICT_PTR parent, int end) rTemp1i = _mm_cmpeq_epi32(rTemp1i, rI); // filter min frac for nuc homopolymer child paths - rTemp1s = _mm_and_ps(_mm_castsi128_ps(rTemp1i), *((__m128*)ad_MinFrac)); + rTemp1s = _mm_and_ps(_mm_castsi128_ps(rTemp1i), *((__m128*)&ad_MinFrac)); // compares not less than equal to for two _m128i words. Entries will be 0xFFFF... for words where // (kStateWindowCutoff > child->state[flow]). Rest of the words are 0 @@ -649,7 +649,7 @@ void TreephaserSSE::advanceState4(PathRec RESTRICT_PTR parent, int end) if(EXPECTED(ad_Adv == 0)) { // child window start - _mm_store_si128((__m128i*)ad_Beg, rBeg); + _mm_store_si128((__m128i*)&ad_Beg, rBeg); // flow < parent->window_end - 1 while(i < parLast) { @@ -747,7 +747,7 @@ void TreephaserSSE::advanceState4(PathRec RESTRICT_PTR parent, int end) rTemp1s = _mm_or_ps(rTemp1s, rParNuc); rTemp1s = _mm_castsi128_ps(_mm_cmpeq_epi32(_mm_castps_si128(rTemp1s), rI)); rTemp1s = _mm_and_ps(rTemp1s, rAlive); - rTemp1s = _mm_cmpnle_ps(rTemp1s, *((__m128*)ad_MinFrac)); + rTemp1s = _mm_cmpnle_ps(rTemp1s, *((__m128*)&ad_MinFrac)); // child->window_end < max_flow rS = _mm_cmpnle_ps((_mm_castsi128_ps)(rFlowEnd), (_mm_castsi128_ps)(rEnd)); // flow == child->window_end-1 and child->window_end < max_flow and alive > kStateWindowCutoff @@ -805,7 +805,7 @@ void TreephaserSSE::advanceState4(PathRec RESTRICT_PTR parent, int end) rTemp1s = _mm_or_ps(rTemp1s, rParNuc); rTemp1s = _mm_castsi128_ps(_mm_cmpeq_epi32(_mm_castps_si128(rTemp1s), rI)); rTemp1s = _mm_and_ps(rTemp1s, rAlive); - rTemp1s = _mm_cmpnle_ps(rTemp1s, *((__m128*)ad_MinFrac)); + rTemp1s = _mm_cmpnle_ps(rTemp1s, *((__m128*)&ad_MinFrac)); // child->window_end < max_flow rS = _mm_cmpnle_ps((_mm_castsi128_ps)(rFlowEnd), (_mm_castsi128_ps)(rEnd)); // flow == child->window_end-1 and child->window_end < max_flow and alive > kStateWindowCutoff @@ -817,8 +817,8 @@ void TreephaserSSE::advanceState4(PathRec RESTRICT_PTR parent, int end) j += 4; } - rEnd = _mm_min_epi16(rEnd, *((__m128i*)ad_FlowEnd)); - _mm_store_si128((__m128i*)ad_End, rEnd); + rEnd = _mm_min_epi16(rEnd, *((__m128i*)&ad_FlowEnd)); + _mm_store_si128((__m128i*)&ad_End, rEnd); } // This branch is for if one of the child paths has an increase in window_start @@ -846,7 +846,7 @@ void TreephaserSSE::advanceState4(PathRec RESTRICT_PTR parent, int end) __m128i rTemp1i = rBeg; rTemp1i = _mm_or_si128(rTemp1i, _mm_castps_si128(rParNuc)); rTemp1i = _mm_cmpeq_epi32(rTemp1i, rI); - rTemp1s = _mm_and_ps(_mm_castsi128_ps(rTemp1i), *((__m128*)ad_MinFrac)); + rTemp1s = _mm_and_ps(_mm_castsi128_ps(rTemp1i), *((__m128*)&ad_MinFrac)); rTemp1s = _mm_cmpnle_ps(rTemp1s, rS); rBeg = _mm_sub_epi32(rBeg, _mm_castps_si128(rTemp1s)); rTemp1i = rBeg; @@ -890,7 +890,7 @@ void TreephaserSSE::advanceState4(PathRec RESTRICT_PTR parent, int end) // obtain state for child paths thar are incorporating new hp rTemp1s = _mm_and_ps(_mm_castsi128_ps(rTemp1i), rAlive); // child->state[flow] < kStateWindowCutoff - rTemp1s = _mm_cmpnle_ps(rTemp1s, *((__m128*)ad_MinFrac)); + rTemp1s = _mm_cmpnle_ps(rTemp1s, *((__m128*)&ad_MinFrac)); // child->window_end < max_flow rS = _mm_cmpnle_ps((_mm_castsi128_ps)(rFlowEnd), (_mm_castsi128_ps)(rEnd)); // flow == child->window_end-1 and child->window_end < max_flow and alive > kStateWindowCutoff @@ -922,7 +922,7 @@ void TreephaserSSE::advanceState4(PathRec RESTRICT_PTR parent, int end) __m128i rTemp1i = rBeg; rTemp1i = _mm_or_si128(rTemp1i, _mm_castps_si128(rParNuc)); rTemp1i = _mm_cmpeq_epi32(rTemp1i, rI); - rTemp1s = _mm_and_ps(_mm_castsi128_ps(rTemp1i), *((__m128*)ad_MinFrac)); + rTemp1s = _mm_and_ps(_mm_castsi128_ps(rTemp1i), *((__m128*)&ad_MinFrac)); rTemp1s = _mm_cmpnle_ps(rTemp1s, rS); rBeg = _mm_sub_epi32(rBeg, _mm_castps_si128(rTemp1s)); rTemp1i = rBeg; @@ -956,7 +956,7 @@ void TreephaserSSE::advanceState4(PathRec RESTRICT_PTR parent, int end) rTemp1i = _mm_or_si128(rTemp1i, _mm_castps_si128(rParNuc)); rTemp1i = _mm_cmpeq_epi32(rTemp1i, rI); rTemp1s = _mm_and_ps(_mm_castsi128_ps(rTemp1i), rAlive); - rTemp1s = _mm_cmpnle_ps(rTemp1s, *((__m128*)ad_MinFrac)); + rTemp1s = _mm_cmpnle_ps(rTemp1s, *((__m128*)&ad_MinFrac)); // child->window_end < max_flow rS = _mm_cmpnle_ps((_mm_castsi128_ps)(rFlowEnd), (_mm_castsi128_ps)(rEnd)); // flow == child->window_end-1 and child->window_end < max_flow and alive > kStateWindowCutoff @@ -968,9 +968,9 @@ void TreephaserSSE::advanceState4(PathRec RESTRICT_PTR parent, int end) j += 4; } - rEnd = _mm_min_epi16(rEnd, *((__m128i*)ad_FlowEnd)); - _mm_store_si128((__m128i*)ad_Beg, rBeg); - _mm_store_si128((__m128i*)ad_End, rEnd); + rEnd = _mm_min_epi16(rEnd, *((__m128i*)&ad_FlowEnd)); + _mm_store_si128((__m128i*)&ad_Beg, rBeg); + _mm_store_si128((__m128i*)&ad_End, rEnd); } } @@ -1028,9 +1028,139 @@ void TreephaserSSE::SolveRead(BasecallerRead& read, int begin_flow, int end_flow } // ------------------------------------------------- +void TreephaserSSE::sortPaths(int & pathCnt) +{ + if(pathCnt > 3) { + int m = sv_PathPtr[0]->flow; + int i = 1; + do { + int n = sv_PathPtr[i]->flow; + if(m < n) + m = n; + } while(++i < pathCnt); + if((m -= MAX_PATH_DELAY) > 0) { + do { + if(sv_PathPtr[--i]->flow < m) + swap(sv_PathPtr[i], sv_PathPtr[--pathCnt]); + } while(i > 0); + } + } + + while(pathCnt > MAX_PATHS-4) { + float m = sv_PathPtr[0]->flowMetr; + int i = 1; + int j = 0; + do { + float n = sv_PathPtr[i]->flowMetr; + if(m < n) { + m = n; + j = i; + } + } while(++i < pathCnt); + swap(sv_PathPtr[j], sv_PathPtr[--pathCnt]); + } + +} + +float TreephaserSSE::computeParentDist(PathRec RESTRICT_PTR parent, int end_flow) +{ + // XXX Right here we are having a memory overrun: We copied up to parent->flow but use until parent->window_end of calibA and calibB + // Computing squared distance between parent's predicted signal and normalized measurements + float dist = parent->res+(rd_SqNormMeasureSum[parent->window_end]-rd_SqNormMeasureSum[end_flow]); + for(int i = parent->window_start; i < parent->window_end; ++i) { + if((i & 3) == 0) { + if (recalibrate_predictions_) { + dist += sumOfSquaredDiffsFloatSSE_recal((float*)(&(rd_NormMeasure[i])), + (float*)(&(parent->pred[i])), + (float*)(&(parent->calib_A[i])), + (float*)(&(parent->calib_B[i])), + parent->window_end-i); + } else { + dist += sumOfSquaredDiffsFloatSSE((float*)(&(rd_NormMeasure[i])), + (float*)(&(parent->pred[i])), + parent->window_end-i); + } + break; + } + if (recalibrate_predictions_) + dist += Sqr(rd_NormMeasure[i]-parent->pred[i]*parent->calib_A[i]-parent->calib_B[i]); + else + dist += Sqr(rd_NormMeasure[i]-parent->pred[i]); + } + // Finished computing squared distance + return dist; +} + +void TreephaserSSE::CopyPath(PathRec RESTRICT_PTR dest, PathRec RESTRICT_PTR parent, PathRec RESTRICT_PTR child) +{ + dest->flowMetr = (child->flow == 0) ? 0 : ((child->metr + 0.5f*child->flowMetr) / child->flow); + char RESTRICT_PTR p = ad_Buf+child->nuc*4+AD_STATE_OFS; + for(int i = parent->window_start, j = 0, e = child->window_end; i < e; ++i, j += 16) { + dest->state[i] = *((float*)(p+j)); + dest->pred[i] = *((float*)(p+j+(AD_PRED_OFS-AD_STATE_OFS))); + } + if(dest != parent){ + // copy the beginning of the arrays as well + copySSE(dest->pred, parent->pred, parent->window_start << 2); + copySSE(dest->sequence, parent->sequence, parent->sequence_length); + } + + if(state_inphase_enabled_){ + if(dest != parent && child->flow > 0){ + int cpSize = (parent->flow+1)*sizeof(float); + copySSE(dest->state_inphase, parent->state_inphase, cpSize); + } + //extending from parent->state_inphase[parent->flow] to fill the gap + for(int tempInd = parent->flow+1; tempInd < child->flow; tempInd++){ + dest->state_inphase[tempInd] = max(dest->state[child->flow],0.01f); + } + dest->state_inphase[child->flow] = max(dest->state[child->flow],0.01f); + } + + int psl=parent->sequence_length; + dest->sequence_length = psl + 1; + dest->sequence[psl] = flow_order_[child->flow]; + if (psl and dest->sequence[psl] != dest->sequence[psl-1]) + dest->last_hp = 0; + else + dest->last_hp = parent->last_hp; + dest->last_hp++; + + // copy whole vector to avoid memory access to fields that have been written to by (longer) previously discarded paths XXX + // --> Reintroducing memory overrun since it seems to yield better performance + if (recalibrate_predictions_) { + if(dest != parent && child->flow > 0){ + // --- Reverting to old code with memory overrun + int cpSize = (parent->flow+1) << 2; + memcpy(dest->calib_A, parent->calib_A, cpSize); + memcpy(dest->calib_B, parent->calib_B, cpSize); + // --- + //copySSE(dest->calib_A, parent->calib_A, num_flows_*sizeof(float)); + //copySSE(dest->calib_B, parent->calib_B, num_flows_*sizeof(float)); + } + //explicitly fill zeros between parent->flow and dest->flow; + for(int tempInd = parent->flow + 1; tempInd < child->flow; tempInd++){ + dest->calib_A[tempInd] = 1.0f; + dest->calib_B[tempInd] = 0.0f; + } + int hp_length = min(dest->last_hp, MAX_HPXLEN); + dest->calib_A[child->flow] = (*As_).at(child->flow).at(flow_order_.int_at(child->flow)).at(hp_length); + dest->calib_B[child->flow] = (*Bs_).at(child->flow).at(flow_order_.int_at(child->flow)).at(hp_length); + } + if(dest == parent){ + dest->flow = child->flow; + dest->window_start = child->window_start; + dest->window_end = child->window_end; + dest->res = child->res; + dest->metr = child->metr; + dest->dotCnt = child->dotCnt; + } +} bool TreephaserSSE::Solve(int begin_flow, int end_flow) { + uint32_t num_paths=0; + uint32_t gblPathName=0; sumNormMeasures(); PathRec RESTRICT_PTR parent = sv_PathPtr[0]; @@ -1100,35 +1230,7 @@ bool TreephaserSSE::Solve(int begin_flow, int end_flow) do { - if(pathCnt > 3) { - int m = sv_PathPtr[0]->flow; - int i = 1; - do { - int n = sv_PathPtr[i]->flow; - if(m < n) - m = n; - } while(++i < pathCnt); - if((m -= MAX_PATH_DELAY) > 0) { - do { - if(sv_PathPtr[--i]->flow < m) - swap(sv_PathPtr[i], sv_PathPtr[--pathCnt]); - } while(i > 0); - } - } - - while(pathCnt > MAX_PATHS-4) { - float m = sv_PathPtr[0]->flowMetr; - int i = 1; - int j = 0; - do { - float n = sv_PathPtr[i]->flowMetr; - if(m < n) { - m = n; - j = i; - } - } while(++i < pathCnt); - swap(sv_PathPtr[j], sv_PathPtr[--pathCnt]); - } + sortPaths(pathCnt); parent = sv_PathPtr[0]; int parentPathIdx = 0; @@ -1141,225 +1243,140 @@ bool TreephaserSSE::Solve(int begin_flow, int end_flow) break; int parent_flow = parent->flow; - // compute child path flow states, predicted signal,negative and positive penalties - advanceState4(parent, end_flow); + float dist = computeParentDist(parent,end_flow); - int n = pathCnt; - double bestpen = 25.0; - for(int nuc = 0; nuc < 4; ++nuc) { - PathRec RESTRICT_PTR child = sv_PathPtr[n]; - child->flow = min(ad_Idx[nuc], end_flow); - child->window_start = ad_Beg[nuc]; - child->window_end = min(ad_End[nuc], end_flow); + int bestPathIdx = -1; + int childPathIdx = -1; - // Do not attempt to calculate child->last_hp in this loop; bad things happen - if(child->flow >= end_flow or parent->last_hp >= MAX_HPXLEN or parent->sequence_length >= 2*MAX_VALS-10) - continue; + // current best path is parent path + if(bestDist > dist) { + bestPathIdx = parentPathIdx; + parentPathIdx = -1; + } - // pointer in the ad_Buf buffer pointing at the running sum of positive residuals at start of parent window - char RESTRICT_PTR pn = ad_Buf+nuc*4+(AD_NRES_OFS-16)-parent->window_start*16; + // compute child path flow states, predicted signal,negative and positive penalties + advanceState4(parent, end_flow); - // child path metric - float metr = parent->res + *((float*)(pn+child->window_start*16+(AD_PRES_OFS-AD_NRES_OFS))); - // sum of squared residuals for positive residuals for flows < child->flow - float penPar = *((float*)(pn+child->flow*16+(AD_PRES_OFS-AD_NRES_OFS))); + v4i flowV = ad_Idx; + v4i window_startV=ad_Beg; + v4i window_endV={min(ad_End[0], end_flow),min(ad_End[1], end_flow),min(ad_End[2], end_flow),min(ad_End[3], end_flow)}; + v4i dotCntV={0}; + v4f penParV; + v4f penNegV; + v4f metrV = LD_VEC4F(parent->res); + v4f resV; - // sum of squared residuals for negative residuals for flows < child->window_end - float penNeg = *((float*)(pn+child->window_end*16)); + float bestpen = 19.8; - // sum of squared residuals left of child window start - child->res = metr + *((float*)(pn+child->window_start*16)); - - metr += penNeg; + for(int nuc = 0; nuc < 4; ++nuc) { + char RESTRICT_PTR pn = ad_Buf+nuc*4+(AD_NRES_OFS-16)-parent->window_start*16; + metrV[nuc] += *((float*)(pn+ad_Beg[nuc]*16+(AD_PRES_OFS-AD_NRES_OFS))); + penParV[nuc] = *((float*)(pn+ad_Idx[nuc]*16+(AD_PRES_OFS-AD_NRES_OFS))); + penNegV[nuc] = *((float*)(pn+window_endV[nuc]*16)); + resV[nuc] = metrV[nuc] + *((float*)(pn+ad_Beg[nuc]*16)); - // penPar corresponds to penalty1 in DPTreephaser.cpp - penPar += penNeg; - penNeg += penPar; + } + metrV += penNegV; + penParV += penNegV; + penNegV += penParV; - // penalty = penalty1 + (kNegativeMultiplier = 2)*penNeg - if(penNeg >= 20.0) + int useChild[4]={0}; + int usedChildren=0; + int n = pathCnt; + + for(int nuc = 0; nuc < 4; ++nuc) { + + // Do not attempt to calculate child->last_hp in this loop; bad things happen + if(flowV[nuc] >= end_flow or parent->last_hp >= MAX_HPXLEN or parent->sequence_length >= 2*MAX_VALS-10) continue; - if(bestpen > penNeg) - bestpen = penNeg; - else if(penNeg-bestpen >= 0.2) + if(bestpen > penNegV[nuc]) + bestpen = penNegV[nuc]; + else if(penNegV[nuc]-bestpen >= 0.2) continue; // child->path_metric > sum_of_squares_upper_bound - if(metr > bestDist) + if(metrV[nuc] > bestDist) continue; - float newSignal = rd_NormMeasure[child->flow]; + float newSignal = rd_NormMeasure[flowV[nuc]]; // XXX Right here we are having a memory overrun: We copied up to parent->flow but use until parent->window_end // Check 'dot' criterion - if(child->flow < parent->window_end){ + if(flowV[nuc] < parent->window_end){ if (recalibrate_predictions_) - newSignal -= (parent->calib_A[child->flow]*parent->pred[child->flow]+parent->calib_B[child->flow]); + newSignal -= (parent->calib_A[flowV[nuc]]*parent->pred[flowV[nuc]]+parent->calib_B[flowV[nuc]]); else - newSignal -= parent->pred[child->flow]; + newSignal -= parent->pred[flowV[nuc]]; } - newSignal /= *((float*)(pn+child->flow*16+(AD_STATE_OFS-AD_NRES_OFS+16))); - child->dotCnt = 0; + // pointer in the ad_Buf buffer pointing at the running sum of positive residuals at start of parent window + char RESTRICT_PTR pn = ad_Buf+nuc*4+(AD_NRES_OFS-16)-parent->window_start*16; + newSignal /= *((float*)(pn+flowV[nuc]*16+(AD_STATE_OFS-AD_NRES_OFS+16))); if(newSignal < 0.3f) { if(parent->dotCnt > 0) continue; - child->dotCnt = 1; + dotCntV[nuc] = 1; } - // child path survives at this point - child->metr = float(metr); - child->flowMetr = float(penPar); - child->penalty = float(penNeg); - child->nuc = nuc; - ++n; + useChild[nuc]=1; + usedChildren++; } - // XXX Right here we are having a memory overrun: We copied up to parent->flow but use until parent->window_end of calibA and calibB - // Computing squared distance between parent's predicted signal and normalized measurements - float dist = parent->res+(rd_SqNormMeasureSum[parent->window_end]-rd_SqNormMeasureSum[end_flow]); - for(int i = parent->window_start; i < parent->window_end; ++i) { - if((i & 3) == 0) { - if (recalibrate_predictions_) { - dist += sumOfSquaredDiffsFloatSSE_recal((float*)(&(rd_NormMeasure[i])), - (float*)(&(parent->pred[i])), - (float*)(&(parent->calib_A[i])), - (float*)(&(parent->calib_B[i])), - parent->window_end-i); - } else { - dist += sumOfSquaredDiffsFloatSSE((float*)(&(rd_NormMeasure[i])), - (float*)(&(parent->pred[i])), - parent->window_end-i); - } - break; - } - if (recalibrate_predictions_) - dist += Sqr(rd_NormMeasure[i]-parent->pred[i]*parent->calib_A[i]-parent->calib_B[i]); - else - dist += Sqr(rd_NormMeasure[i]-parent->pred[i]); - } - // Finished computing squared distance +// for(int nuc = 0; nuc < 4; ++nuc) { +// if(useChild[nuc]==0) +// continue; +// if(penNegV[nuc]-bestpen >= 0.2f) +// useChild[nuc]=0; +// } - int bestPathIdx = -1; + for(int nuc = 0; nuc < 4; ++nuc) { + if(useChild[nuc]==0) + continue; - // current best path is parent path - if(bestDist > dist) { - bestPathIdx = parentPathIdx; - parentPathIdx = -1; + // child path survives at this point + PathRec RESTRICT_PTR child = sv_PathPtr[n]; + child->flow = flowV[nuc]; + child->window_start = window_startV[nuc]; + child->window_end = window_endV[nuc]; + child->metr = metrV[nuc]; + child->flowMetr = penParV[nuc]; + child->res = resV[nuc]; + child->penalty = penNegV[nuc]; + child->nuc = nuc; + child->dotCnt = dotCntV[nuc]; + ++n; } - int childPathIdx = -1; while(pathCnt < n) { PathRec RESTRICT_PTR child = sv_PathPtr[pathCnt]; // Rule that depends on finding the best nuc if(child->penalty-bestpen >= 0.2f) { sv_PathPtr[pathCnt] = sv_PathPtr[--n]; sv_PathPtr[n] = child; - } - else if((childPathIdx < 0) && (parentPathIdx >= 0)) { + usedChildren--; + } + else + if((childPathIdx < 0) && (parentPathIdx >= 0)) { sv_PathPtr[pathCnt] = sv_PathPtr[--n]; sv_PathPtr[n] = child; childPathIdx = n; } - // this is the child path to be kept else { - if (child->flow) - child->flowMetr = (child->metr + 0.5f*child->flowMetr) / child->flow; - char RESTRICT_PTR p = ad_Buf+child->nuc*4+AD_STATE_OFS; - for(int i = parent->window_start, j = 0, e = child->window_end; i < e; ++i, j += 16) { - child->state[i] = *((float*)(p+j)); - child->pred[i] = *((float*)(p+j+(AD_PRED_OFS-AD_STATE_OFS))); - } - copySSE(child->pred, parent->pred, parent->window_start << 2); - - copySSE(child->sequence, parent->sequence, parent->sequence_length); - - if(state_inphase_enabled_){ - if(child->flow > 0){ - int cpSize = (parent->flow+1)*sizeof(float); - copySSE(child->state_inphase, parent->state_inphase, cpSize); - } - //extending from parent->state_inphase[parent->flow] to fill the gap - for(int tempInd = parent->flow+1; tempInd < child->flow; tempInd++){ - child->state_inphase[tempInd] = max(child->state[child->flow],0.01f); - } - child->state_inphase[child->flow] = max(child->state[child->flow],0.01f); - } - - child->sequence_length = parent->sequence_length + 1; - child->sequence[parent->sequence_length] = flow_order_[child->flow]; - if (parent->sequence_length and child->sequence[parent->sequence_length] != child->sequence[parent->sequence_length-1]) - child->last_hp = 0; - else - child->last_hp = parent->last_hp; - child->last_hp++; - - // copy whole vector to avoid memory access to fields that have been written to by (longer) previously discarded paths XXX - // --> Reintroducing memory overrun since it seems to yield better performance - if (recalibrate_predictions_) { - if(child->flow > 0){ - // --- Reverting to old code with memory overrun - int cpSize = (parent->flow+1) << 2; - memcpy(child->calib_A, parent->calib_A, cpSize); - memcpy(child->calib_B, parent->calib_B, cpSize); - // --- - //copySSE(child->calib_A, parent->calib_A, num_flows_*sizeof(float)); - //copySSE(child->calib_B, parent->calib_B, num_flows_*sizeof(float)); - } - //explicitly fill zeros between parent->flow and child->flow; - for(int tempInd = parent->flow + 1; tempInd < child->flow; tempInd++){ - child->calib_A[tempInd] = 1.0f; - child->calib_B[tempInd] = 0.0f; - } - int hp_length = min(child->last_hp, MAX_HPXLEN); - child->calib_A[child->flow] = (*As_).at(child->flow).at(flow_order_.int_at(child->flow)).at(hp_length); - child->calib_B[child->flow] = (*Bs_).at(child->flow).at(flow_order_.int_at(child->flow)).at(hp_length); - } + CopyPath(child,parent,child); ++pathCnt; +// ++num_paths; } } +// printf("pathCnt=%d ",pathCnt); +// for(int pthNum=0;pthNumwindow_start,sv_PathPtr[pthNum]->window_end,sv_PathPtr[pthNum]->metr,sv_PathPtr[pthNum]->penalty); +// } +// printf("\n"); // In the event, there is no best path, one of the child is copied to the parent if(childPathIdx >= 0) { - PathRec RESTRICT_PTR child = sv_PathPtr[childPathIdx]; - parent_flow = parent->flow; //MJ - parent->flow = child->flow; - parent->window_end = child->window_end; - parent->res = child->res; - parent->metr = child->metr; - (child->flow == 0) ? (parent->flowMetr == 0) : (parent->flowMetr = (child->metr + 0.5f*child->flowMetr) / child->flow); - parent->dotCnt = child->dotCnt; - char RESTRICT_PTR p = ad_Buf+child->nuc*4+AD_STATE_OFS; - for(int i = parent->window_start, j = 0, e = child->window_end; i < e; ++i, j += 16) { - parent->state[i] = *((float*)(p+j)); - parent->pred[i] = *((float*)(p+j+(AD_PRED_OFS-AD_STATE_OFS))); - } - - parent->sequence[parent->sequence_length] = flow_order_[parent->flow]; - if (parent->sequence_length and parent->sequence[parent->sequence_length] != parent->sequence[parent->sequence_length-1]) - parent->last_hp = 0; - parent->last_hp = min(parent->last_hp+1, MAX_HPXLEN); - parent->sequence_length++; - - //update calib_A and calib_B for parent - if (recalibrate_predictions_) { - for(int tempInd = parent_flow + 1; tempInd < child->flow; tempInd++){ - parent->calib_A[tempInd] = 1.0f; - parent->calib_B[tempInd] = 0.0f; - } - parent->calib_A[parent->flow] = (*As_).at(parent->flow).at(flow_order_.int_at(parent->flow)).at(parent->last_hp); - parent->calib_B[parent->flow] = (*Bs_).at(parent->flow).at(flow_order_.int_at(parent->flow)).at(parent->last_hp); - } - - if(state_inphase_enabled_){ - for(int tempInd = parent_flow+1; tempInd < parent->flow; tempInd++){ - parent->state_inphase[tempInd] = parent->state[parent->flow]; - } - parent->state_inphase[parent->flow] = parent->state[parent->flow]; - } - - parent->window_start = child->window_start; + CopyPath(parent,parent,sv_PathPtr[childPathIdx]); parentPathIdx = -1; } @@ -1382,6 +1399,7 @@ bool TreephaserSSE::Solve(int begin_flow, int end_flow) ResetRecalibrationStructures(num_flows_); } +// printf("num_paths=%d num_flows=%d-%d\n",num_paths,begin_flow, end_flow); return false; } diff --git a/Analysis/BaseCaller/TreephaserSSE.h b/Analysis/BaseCaller/TreephaserSSE.h index aca42e2b..a3571b09 100644 --- a/Analysis/BaseCaller/TreephaserSSE.h +++ b/Analysis/BaseCaller/TreephaserSSE.h @@ -8,6 +8,7 @@ #include #include #include "BaseCallerUtils.h" +#include "Vecs.h" #ifdef _WIN32 #define ALIGN(AAlignSize) __declspec(align(AAlignSize)) @@ -140,6 +141,10 @@ class TreephaserSSE { //! @brief Solving a read bool Solve(int begin_flow, int end_flow); //! @brief Normalizing a read + void sortPaths(int & pathCnt); + float computeParentDist(PathRec RESTRICT_PTR parent, int end_flow); + void CopyPath(PathRec RESTRICT_PTR dest, PathRec RESTRICT_PTR parent, PathRec RESTRICT_PTR child); + void WindowedNormalize(BasecallerRead& read, int step); //! @brief Make recalibration changes to predictions explicitly visible void RecalibratePredictions(PathRec *maxPathPtr); @@ -165,11 +170,11 @@ class TreephaserSSE { ALIGN(64) float ft_stepNorms[MAX_STEPS]; - ALIGN(64) float ad_MinFrac[4]; - ALIGN(16) int ad_FlowEnd[4]; - ALIGN(16) int ad_Idx[4]; - ALIGN(16) int ad_End[4]; - ALIGN(16) int ad_Beg[4]; + ALIGN(64) v4f ad_MinFrac; + ALIGN(16) v4i ad_FlowEnd; + ALIGN(16) v4i ad_Idx; + ALIGN(16) v4i ad_End; + ALIGN(16) v4i ad_Beg; ALIGN(16) char ad_Buf[4*MAX_VALS*4*sizeof(float)]; ion::FlowOrder flow_order_; //!< Sequence of nucleotide flows diff --git a/Analysis/BaseCaller/TreephaserVEC.cpp b/Analysis/BaseCaller/TreephaserVEC.cpp index f1754f34..8a98804d 100644 --- a/Analysis/BaseCaller/TreephaserVEC.cpp +++ b/Analysis/BaseCaller/TreephaserVEC.cpp @@ -10,11 +10,10 @@ #include #include -#include "BaseCallerUtils.h" -#include "DPTreephaser.h" - -#define SHUF_PS(reg, mode) _mm_castsi128_ps(_mm_shuffle_epi32(_mm_castps_si128(reg), mode)) +//#define PRINT_DEBUG 1 +//#define DO_DEBUG (dbgX==1080 && dbgY==2133) +#define DFLT_CACHE 0x100000 using namespace std; @@ -22,81 +21,26 @@ ALWAYS_INLINE float Sqr(float val) { return val*val; } -inline void setZeroSSE(void *dst, int size) { - v4i r0 = LD_VEC4I(0); - v4i *dstV=(v4i *)dst; - int lsize=size/16; +#define memcpy_C(d,s,l) memcpy(d,s,l) - while((size & 15) != 0) { - --size; - ((char*)dst)[size] = char(0); - } - while(lsize) { - lsize--; - dstV[lsize]=r0; - } -} +#define memcpy_F(d,s,l) { \ + float *dst=(d); float *src=(s); int size=(l); \ + while (size--) dst[size] = src[size]; } +#define memcpy_4F(d,s,l) { \ + float *dst=(d); float *src=(s); int size=(l); \ + while (size--) dst[size] = src[4*size]; } -inline void setValueSSE(float *buf, float val, int size) { - v4f valV=LD_VEC4F(val); - v4f *bufV=(v4f *)buf; - int lsize=size/4; - int i=0; - for(;i 0) { - count--; - dstV[count] += srcV[count]; - } -} - - // ---------------------------------------------------------------------------- // Constructor used in variant caller -TreephaserSSE::TreephaserSSE() - : flow_order_("TACG", 4), my_cf_(-1.0), my_ie_(-1.0), As_(NULL), Bs_(NULL) +TreephaserVEC::TreephaserVEC() + : flow_order_("TACG", 4), my_cf_(-1.0), my_ie_(-1.0), As_(NULL), Bs_(NULL), + bad_path_limit_(10000), many_path_limit_(10000), + initial_paths_(-1),max_metr_diff_(0.3) { SetNormalizationWindowSize(38); SetFlowOrder(flow_order_); } // Constructor used in Basecaller -TreephaserSSE::TreephaserSSE(const ion::FlowOrder& flow_order, const int windowSize) - : my_cf_(-1.0), my_ie_(-1.0), As_(NULL), Bs_(NULL) +TreephaserVEC::TreephaserVEC(const ion::FlowOrder& flow_order, const int windowSize) + : my_cf_(-1.0), my_ie_(-1.0), As_(NULL), Bs_(NULL), + bad_path_limit_(10000), many_path_limit_(10000), + initial_paths_(-1),max_metr_diff_(0.3) { SetNormalizationWindowSize(windowSize); SetFlowOrder(flow_order); @@ -205,47 +98,19 @@ TreephaserSSE::TreephaserSSE(const ion::FlowOrder& flow_order, const int windowS // ---------------------------------------------------------------- // Initilizes all float variables to NAN so that they cause mayhem if we read out of bounds // and so that valgrind does not complain about uninitialized variables -void TreephaserSSE::InitializeVariables(float init_val) { - - // Initializing the elements of the paths - for (unsigned int path = 0; path <= MAX_PATHS; ++path) { - sv_PathPtr[path]->flow = 0; - sv_PathPtr[path]->window_start = 0; - sv_PathPtr[path]->window_end = 0; - sv_PathPtr[path]->dotCnt = 0; - sv_PathPtr[path]->sequence_length = 0; - sv_PathPtr[path]->last_hp = 0; - sv_PathPtr[path]->nuc = 0; - - sv_PathPtr[path]->res = init_val; - sv_PathPtr[path]->metr = init_val; - sv_PathPtr[path]->flowMetr = init_val; - sv_PathPtr[path]->penalty = init_val; - for (int val=0; valstate[val] = init_val; - sv_PathPtr[path]->pred[val] = init_val; - sv_PathPtr[path]->state_inphase[val] = init_val; - } - for (int val=0; val<(2*MAX_VALS + 12); val++) - sv_PathPtr[path]->sequence[val] = 0; - } +void TreephaserVEC::InitializeVariables() { + // Initializing the other variables of the object for (unsigned int idx=0; idx<4; idx++) { - ad_FlowEnd.A[idx] = 0; - ad_Idx.A[idx] = 0; - ad_End.A[idx] = 0; - ad_Beg.A[idx] = 0; + ad_FlowEnd[idx] = 0; + flow_Buf[idx] = 0; + winEnd_Buf[idx] = 0; + winStart_Buf[idx] = 0; } for (unsigned int val=0; val= 0; --flow) { nextIdx[flow_order_.int_at(flow)] = flow; - ts_NextNuc[0][flow] = (short)(ts_NextNuc4[flow].A[0] = nextIdx[0]); - ts_NextNuc[1][flow] = (short)(ts_NextNuc4[flow].A[1] = nextIdx[1]); - ts_NextNuc[2][flow] = (short)(ts_NextNuc4[flow].A[2] = nextIdx[2]); - ts_NextNuc[3][flow] = (short)(ts_NextNuc4[flow].A[3] = nextIdx[3]); + ts_NextNuc[flow] = nextIdx; } ts_StepCnt = 0; @@ -298,7 +149,6 @@ void TreephaserSSE::SetFlowOrder(const ion::FlowOrder& flow_order) // The initialization of the recalibration fields for all paths is necessary since we are // over-running memory in the use of the recalibration parameters - ResetRecalibrationStructures(MAX_VALS); pm_model_available_ = false; recalibrate_predictions_ = false; @@ -308,7 +158,7 @@ void TreephaserSSE::SetFlowOrder(const ion::FlowOrder& flow_order) // ---------------------------------------------------------------- -void TreephaserSSE::SetModelParameters(double cf, double ie) +void TreephaserVEC::SetModelParameters(double cf, double ie) { if (cf == my_cf_ and ie == my_ie_) return; @@ -317,13 +167,13 @@ void TreephaserSSE::SetModelParameters(double cf, double ie) for(int flow = 0; flow < num_flows_; ++flow) { dist[flow_order_.int_at(flow)] = 1.0; - ts_Transition4[flow].A[0] = ts_Transition[0][flow] = float(dist[0]*(1-ie)); + ts_Transition[flow][0] = float(dist[0]*(1-ie)); dist[0] *= cf; - ts_Transition4[flow].A[1] = ts_Transition[1][flow] = float(dist[1]*(1-ie)); + ts_Transition[flow][1] = float(dist[1]*(1-ie)); dist[1] *= cf; - ts_Transition4[flow].A[2] = ts_Transition[2][flow] = float(dist[2]*(1-ie)); + ts_Transition[flow][2] = float(dist[2]*(1-ie)); dist[2] *= cf; - ts_Transition4[flow].A[3] = ts_Transition[3][flow] = float(dist[3]*(1-ie)); + ts_Transition[flow][3] = float(dist[3]*(1-ie)); dist[3] *= cf; } my_cf_ = cf; @@ -332,15 +182,17 @@ void TreephaserSSE::SetModelParameters(double cf, double ie) // ---------------------------------------------------------------- -void TreephaserSSE::NormalizeAndSolve(BasecallerRead& read) +void TreephaserVEC::NormalizeAndSolve(BasecallerRead& read) { - copySSE(rd_NormMeasure, &read.raw_measurements[0], num_flows_*sizeof(float)); + memcpy_F(rd_NormMeasure, &read.raw_measurements[0], num_flows_); // Disable recalibration during normalization stage if requested if (skip_recal_during_normalization_) recalibrate_predictions_ = false; + Solve(ts_StepBeg[0], ts_StepEnd[0], ts_StepBeg[1], initial_paths_, max_metr_diff_); + WindowedNormalize(read, 0); for(int step = 0; step < ts_StepCnt; ++step) { - bool is_final = Solve(ts_StepBeg[step], ts_StepEnd[step]); + bool is_final = Solve(ts_StepBeg[step], ts_StepEnd[step], ts_StepBeg[step+1], initial_paths_, max_metr_diff_); WindowedNormalize(read, step); if (is_final) break; @@ -351,862 +203,756 @@ void TreephaserSSE::NormalizeAndSolve(BasecallerRead& read) // And turn recalibration back on (if available) for the final solving part EnableRecalibration(); - Solve(ts_StepBeg[ts_StepCnt], ts_StepEnd[ts_StepCnt]); + Solve(ts_StepBeg[ts_StepCnt], ts_StepEnd[ts_StepCnt], ts_StepEnd[ts_StepCnt], -1, max_metr_diff_); - int to_flow = min(sv_PathPtr[MAX_PATHS]->window_end, num_flows_); // Apparently window_end can be larger than num_flows_ - read.sequence.resize(sv_PathPtr[MAX_PATHS]->sequence_length); - copySSE(&read.sequence[0], sv_PathPtr[MAX_PATHS]->sequence, sv_PathPtr[MAX_PATHS]->sequence_length*sizeof(char)); - copySSE(&read.normalized_measurements[0], rd_NormMeasure, num_flows_*sizeof(float)); - setZeroSSE(&read.prediction[0], num_flows_*sizeof(float)); - copySSE(&read.prediction[0], sv_PathPtr[MAX_PATHS]->pred, to_flow*sizeof(float)); - setZeroSSE(&read.state_inphase[0], num_flows_*sizeof(float)); - copySSE(&read.state_inphase[0], sv_PathPtr[MAX_PATHS]->state_inphase, to_flow*sizeof(float)); + int to_flow = min(sv_PathPtr[BEST_PATH]->window_end, num_flows_); // Apparently window_end can be larger than num_flows_ + read.sequence.resize(sv_PathPtr[BEST_PATH]->sequence_length); + memcpy_C(&read.sequence[0], sv_PathPtr[BEST_PATH]->sequence, sv_PathPtr[BEST_PATH]->sequence_length); + memcpy_F(&read.normalized_measurements[0], rd_NormMeasure, num_flows_); + memset_F(&read.prediction[to_flow], 0, num_flows_-to_flow); + memcpy_F(&read.prediction[0], sv_PathPtr[BEST_PATH]->pred, to_flow); + memset_F(&read.state_inphase[to_flow], 0, num_flows_-to_flow); + memcpy_F(&read.state_inphase[0], sv_PathPtr[BEST_PATH]->state_inphase, to_flow); // copy inphase population and reset state_inphase flag if(state_inphase_enabled_){ for (int p = 0; p <= 8; ++p) { - setZeroSSE(&(sv_PathPtr[p]->state_inphase[0]), num_flows_*sizeof(float)); + memset_F(&(sv_PathPtr[p]->state_inphase[0]), 0, num_flows_); } } state_inphase_enabled_ = false; } -// ---------------------------------------------------------------------- - -// advanceStateInPlace is only used for the simulation step. - -void TreephaserSSE::advanceStateInPlace(PathRec RESTRICT_PTR path, int nuc, int end) { - int idx = ts_NextNuc[nuc][path->flow]; - if(idx > end) - idx = end; - if(path->flow != idx) { - path->flow = idx; - idx = path->window_end; - float alive = 0.0f; - float RESTRICT_PTR trans = ts_Transition[nuc]; - const float minFrac = 1e-6f; - int b = path->window_start; - int e = idx--; - int em1 = e-1; - int i = b; - v4i maskL=(v4i){1,2,3,0}; - while(i < idx) { - alive += path->state[i]; - float s = alive * trans[i]; - path->state[i] = s; - alive -= s; - ++i; - if(!(s < minFrac)) - break; - b++; - } - while(/*(i&3) && */(i < em1)) { - alive += path->state[i]; - float s = alive * trans[i]; - path->state[i] = s; - alive -= s; - ++i; - } -#if 0 - int llen=(em1-i)/4; - v4f *psp=(v4f *)&path->state[i]; - v4f *trp=(v4f *)&trans[i]; - for(int j=0;j < llen;j++) { - v4f_u ps,s,t; - ps.V =psp[j]; - t.V = trp[j]; - - - for(int li=0;li<4;li++){ - alive += ps.A[0]; - s.A[0] = alive * t.A[0]; - alive -= s.A[0]; - // shift ps, s, and t to the left - ps.V = __builtin_shuffle (ps, maskL); - s.V = __builtin_shuffle (s, maskL); - t.V = __builtin_shuffle (t, maskL); - } - psp[j] = s.V; - } - i+=4*llen; -#endif - // flow > window start - if(i > b) { - // flow < window end - 1 - while(i < idx) { - alive += path->state[i]; - float s = alive * trans[i]; - path->state[i] = s; - alive -= s; - ++i; - } - alive += path->state[i]; - - // flow >= window end - 1 - while(i < e) { - float s = alive * trans[i]; - path->state[i] = s; - alive -= s; - if((i == (e-1)) && (e < end) && (alive > minFrac)) - path->pred[e++] = 0.0f; - i++; - } - } - // flow = window start(or window end - 1) - else { - alive += path->state[i]; - while(i < em1) { - float s = alive * trans[i]; - path->state[i] = s; - alive -= s; - if((i == b)&& (s < minFrac)) - b++; - else - break; - i++; - } - while(i < em1) { - float s = alive * trans[i]; - path->state[i] = s; - alive -= s; - i++; - } - while(i < e) { - float s = alive * trans[i]; - path->state[i] = s; - alive -= s; - if((i == b)&& (s < minFrac)) - b++; - if((i == (e-1)) && (e < end) && (alive > minFrac)) - path->pred[e++] = 0.0f; - i++; - } - } - path->window_start = b; - path->window_end = e; - } -} - -#define AD_MINFRAC LD_VEC4F(1e-6f) -//// pseudo code: -// for(int li=0;li<4;li++){ -// rAlive[li] += parentState; -// -// if (parent->flow != child->flow or parent->flow == 0) { -// // This nuc begins a new homopolymer -// rS[li] = parent->state[flow]; -// } -// else{ -// rS[li] = transition_base_[nuc][flow] * rAlive[li] -// } -// childState[j] = rS[li]; -// rAlive[li] -= rS[li]; -// -// } -//// pseudo code: -#define advanceI( parentState, j, rParNuc, ts_tr, rAlive, rS) {\ -\ - /*rS = (v4f)((v4i)LD_VEC4F(parentState) & (v4i) rParNuc);*/ \ - /*v4f rTemp1s; = rParNuc;*/ \ - \ - /* add parent state at this flow */ \ - rAlive += LD_VEC4F(parentState); \ - \ - /* one of the entries is 0xFFFF.. where the homopolymer is extended, rest are 0 */ \ - /* keep the parent state for child where parent homopolymer is extended, rest are 0 */ \ - /*rS = (v4f) ((v4i) rS & (v4i) rParNuc); */\ - \ - /* select transitions where this nuc begins a new homopolymer */ \ - /*rTemp1s = rAlive * (v4f) (~(v4i)rParNuc & (v4i)(ts_tr)); */ \ - \ - /* multiply transition probabilities with alive */ \ - /*rTemp1s *= rAlive;*/ \ - \ - /* child state for this flow */ \ - rS = (v4f)((v4i)LD_VEC4F(parentState) & (v4i)rParNuc) + rAlive * (v4f) (~(v4i)rParNuc & (v4i)(ts_tr)); \ - \ - /* storing child states to the buffer */ \ - state_Buf[j].V = rS; \ - \ - /* alive *= transition_flow[nuc&7][flow] from DpTreephaser.cpp */ \ - \ - rAlive -= rS; \ -} -// this one is all about calculating the residual -inline void TreephaserSSE::CalcResidualI(PathRec RESTRICT_PTR parent, - int flow, int j, v4f &rS, v4f rTemp1s_, v4f &rPenNeg, v4f &rPenPos) +void TreephaserVEC::advanceState4 (PathRecV RESTRICT_PTR path, int end) { - v4f rTemp1S=(rTemp1s_); - /* storing child predictions */ - pred_Buf[j].V = rTemp1S; + ALIGN(64)v4f nres2_Buf[MAX_VALS]; + ALIGN(64)v4f pres2_Buf[MAX_VALS]; - /* apply recalibration model paramters to predicted signal if model is available */ - if (recalibrate_predictions_) { - rTemp1S *= LD_VEC4F(parent->calib_A[flow]); - rTemp1S += LD_VEC4F(parent->calib_B[flow]); - } + // child flows or the flow at which child nuc incorporates (corresponds to + // find child flow in AdvanceState() in DPTreephaser.cpp + flow_Buf = (v4i)_mm_min_epi16((__m128i)ts_NextNuc[path->flow], (__m128i)LD_VEC4I(end)); - /* load normalized measurement for the parent */ - rS = LD_VEC4F(rd_NormMeasure[flow]); + // compare parent flow and child flows + v4f rParNuc = (v4f)_mm_cmpeq_epi32((__m128i)LD_VEC4I(path->flow), (__m128i)flow_Buf); - /* residual from normalized and predicted values for this flow */ - rS -= rTemp1S; + // set alive to 0 for all 4 Nuc paths + v4f alive = LD_VEC4F(0); - rTemp1S = rS; - /* find out the negative residual. The number which are -ve have highest bit one and therefore gives */ - /* four ints with 0's in the ones which are not negative */ - rS = (v4f)(_mm_srai_epi32((__m128i)rS,31)); - /*rS = (v4f) (((v4i) rS) >> 31); get the signed bit... */ + // penalties for each nuc corresponding to four childs + v4f rPenNeg = alive; + v4f rPenPos = alive; + nres2_Buf[0]= alive; + pres2_Buf[0]= alive; + //path->pred_Buf[path->window_start]=alive; + const v4f minFrac = LD_VEC4F( 1e-6 ); + + int endi = path->window_end; + int flow = path->window_start; + v4i e =LD_VEC4I(endi); + v4i b =LD_VEC4I(flow); + + + v4i bInc = LD_VEC4I(-1); + v4i eInc = bInc; + int lastNuc=path->nuc; + + v4f *ps=path->state; + v4f *tst=ts_Transition; + v4f *nsb=&nres2_Buf[0]; + v4f *psb=&pres2_Buf[0]; + v4f *pdb=path->pred_Buf; + float *rdn=rd_NormMeasureAdj; + int j=1; + + while (flow < endi) { + // advance + float state=*(float *)&ps[flow][lastNuc]; + alive += state; + v4f s = (v4f)((v4i)LD_VEC4F(state) & (v4i)rParNuc) + + alive * (v4f) (~(v4i)rParNuc & (v4i)tst[flow]); + ps[flow] = s; + alive -= s; + + // check window start + bInc = (bInc & (v4i) (s < minFrac)); + b -= bInc; // minus -1 is the same as +1 + + v4f pred = s + pdb[flow][lastNuc]; + pdb[flow] = pred; + + // compute residuals + v4f res = rdn[flow] - pred; // difference between real signal and prediction + v4i resSel = (v4i) (_mm_srai_epi32 ((__m128i ) res, 31)); // fills with sign bits.. negative residuals are all 1's + res = res*res; + rPenNeg += (v4f) (resSel & (v4i) res); + rPenPos += (v4f) (~resSel & (v4i) res); + nsb[j] = rPenNeg; + psb[j] = rPenPos; - /* squared residual */ - rTemp1S = rTemp1S * rTemp1S; + flow++; + j++; + } - /* select negative residuals */ - rS = (v4f) ((v4i) rS & (v4i) rTemp1S); + b += (v4i) (e == b); // if (window_start==window_end) window_start--; + eInc = eInc & (v4i) (alive > minFrac); + e -= eInc; // minus -1 same as plus 1 + + // flow >= path->window_end + while ((flow < end) && _mm_movemask_ps ((v4f) eInc)) { + v4f s = alive * (v4f) (~(v4i)rParNuc & (v4i)tst[flow]); + ps[flow] = s; + alive -= s; + + v4f pred = s; + pdb[flow] = pred; + v4f res = rdn[flow] - pred; // difference between real signal and prediction + v4i resSel = (v4i) (_mm_srai_epi32 ((__m128i ) res, 31)); // fills with sign bits.. negative residuals are all 1's + res = res*res; + rPenNeg += (v4f) (resSel & (v4i) res); + rPenPos += (v4f) (~resSel & (v4i) res); + nsb[j] = rPenNeg; + psb[j] = rPenPos; + + eInc = eInc & (v4i) (alive > minFrac); + e -= eInc; + flow++; + j++; + } - /* select positive residuals */ - rTemp1S = (v4f) ((v4i) rTemp1S ^ (v4i) rS); + nres_WE=rPenNeg; + pres_WE=rPenPos; - /* add to negative penalty the square of negative residuals */ - rPenNeg += rS; + winStart_Buf = b; + winEnd_Buf = (v4i) _mm_min_epi16 ((__m128i ) e, (__m128i ) LD_VEC4I(end)); - /* add squared residuals to postive penalty */ - rPenPos += rTemp1S; + v4i wsi = winStart_Buf - path->window_start; + v4i fli = flow_Buf - path->window_start; + penNegV=nres_WE; + for (int nuc = 0; nuc < 4; ++nuc) { - /* running sum of negative penalties */ - nres_Buf[j].V = rPenNeg; - /* running sum of positive penalties */ - pres_Buf[j].V = rPenPos; -} + // sum of squared residuals left of child window start + resV[nuc] = nres2_Buf[wsi[nuc]][nuc]; + metrV[nuc] = pres2_Buf[wsi[nuc]][nuc]; -#define CheckWindowStartBase() \ -/* tracking flow from parent->window_start */ \ -v4i rTemp1i = (v4i)rBeg; \ - \ -/* obtain window start for child which doesn't extend parent homopolymer. The one that extends */ \ -/* has all bits for its word as 1 */ \ -rTemp1i = (rTemp1i | (v4i)rParNuc); \ - \ -/* compare parent window start to current flow i. All match except one where parent last hp extends */ \ -rTemp1i = (v4i)_mm_cmpeq_epi32((__m128i)rTemp1i,(__m128i)LD_VEC4I(flow)); \ - \ -/* filter min frac for nuc homopolymer child paths */ \ -v4f rTemp1s = (v4f)(rTemp1i & (v4i)AD_MINFRAC); \ - \ -/* compares not less than equal to for two _m128i words. Entries will be 0xFFFF... for words where */ \ -/* (kStateWindowCutoff > child->state[flow]). Rest of the words are 0 */ \ -rTemp1s = (v4f)_mm_cmpnle_ps(rTemp1s, rS); \ - \ -/* increasing child window start if child state less than state window cut off. */ \ -rBeg = ((v4i)rBeg - (v4i)rTemp1s); - - -#define CheckWindowStart1() { \ -CheckWindowStartBase(); \ -\ -/* this intrinsic gives sign of each word in binary indicating 1 for -ve sign and 0 for +ve */ \ -/* if ad_adv is greater than 0, it indicates increase in child window start for some child path */ \ -ad_Adv = _mm_movemask_ps(rTemp1s); \ -\ -} + // sum of squared residuals left of child->flow + penParV[nuc] = pres2_Buf[fli[nuc]][nuc]; -#define CheckWindowStart2() { \ -CheckWindowStartBase(); \ -\ -rTemp1i = (v4i)_mm_cmpeq_epi32((__m128i)rBeg, (__m128i)rEnd); \ -rBeg += rTemp1i; \ + } + metrV+=path->res; + resV += metrV; + metrV += penNegV; + penParV += penNegV; + penNegV += penParV; + distV = resV + nres_WE + pres_WE; } - -#define CheckWindowEnd() { \ - \ -v4f rTemp1s = (v4f)(LD_VEC4I(-1) + rEnd); \ -rTemp1s = (v4f)((v4i)rTemp1s | (v4i)rParNuc); \ -rTemp1s = (v4f)_mm_cmpeq_epi32((__m128i)rTemp1s, (__m128i)LD_VEC4I(flow)); \ -rTemp1s = (v4f)((v4i)rTemp1s & (v4i)rAlive);\ -rTemp1s = (v4f)_mm_cmpnle_ps(rTemp1s, AD_MINFRAC);\ -/* child->window_end < max_flow */ \ -rS = (v4f)_mm_cmpnle_ps((v4f)rFlowEnd, (v4f)rEnd); \ -/* flow == child->window_end-1 and child->window_end < max_flow and alive > kStateWindowCutoff */ \ -rTemp1s = (v4f)((v4i)rTemp1s & (v4i)rS); \ - \ -/* if non zero than an increase in window end for some child paths */ \ -ad_Adv = _mm_movemask_ps(rTemp1s); \ -/* increases the child window end */ \ -rEnd -= (v4i)rTemp1s; /* - (-1) is the same thing as +1 */ \ +void TreephaserVEC::sumNormMeasures() { + int i = num_flows_; + float sum = 0.0f; + rd_SqNormMeasureSum[i] = 0.0f; + while(--i >= 0) + rd_SqNormMeasureSum[i] = (sum += rd_NormMeasure[i]*rd_NormMeasure[i]); } -void TreephaserSSE::advanceState4(PathRec RESTRICT_PTR parent, int end) -{ - - int idx = parent->flow; - - // max flows - v4i rFlowEnd = LD_VEC4I(end); - // parent flow - v4i rNucCpy = LD_VEC4I(idx); - - // child flows or the flow at which child nuc incorporates (corresponds to - // find child flow in AdvanceState() in DPTreephaser.cpp - v4i rNucIdx = ts_NextNuc4[idx].V; - rNucIdx = (v4i)_mm_min_epi16((__m128i)rNucIdx, (__m128i)rFlowEnd); +// ------------------------------------------------- - // compare parent flow and child flows - rNucCpy = (v4i)_mm_cmpeq_epi32((__m128i)rNucCpy, (__m128i)rNucIdx); +void TreephaserVEC::RecalibratePredictions(PathRecV *maxPathPtr) +{ + // Distort predictions according to recalibration model + int to_flow = min(maxPathPtr->flow, num_flows_); - // store max_flow in ad_FlowEnd - ad_FlowEnd.V = rFlowEnd; + for (int flow=0; flowpred[flow] = + maxPathPtr->pred[flow] * maxPathPtr->calib_A[flow] + + maxPathPtr->calib_B[flow]; + } - // four child flows in four 32 bit integers - ad_Idx.V = rNucIdx; +} - // changes datatype from int to float without doing any conversion - v4f rParNuc = (v4f)(rNucCpy); +void TreephaserVEC::ResetRecalibrationStructures(int num_flows) { + for (int p = 0; p <= 8; ++p) { + memset_F(&(sv_PathPtr[p]->calib_A[0]), 1.0f, num_flows_); + memset_F(&(sv_PathPtr[p]->calib_B[0]), 0, num_flows_); + } +} - // set alive to 0 for all 4 Nuc paths - v4f rAlive = LD_VEC4F(0); +// -------------------------------------------------- - // penalties for each nuc corresponding to four childs - v4f rPenNeg = rAlive; - v4f rPenPos = rAlive; +void TreephaserVEC::SolveRead(BasecallerRead& read, int begin_flow, int end_flow) +{ + memcpy_F(rd_NormMeasure, &(read.normalized_measurements[0]), num_flows_); + memset_F(sv_PathPtr[BEST_PATH]->pred, 0, num_flows_); // Not necessary? + memcpy_C(sv_PathPtr[BEST_PATH]->sequence, &(read.sequence[0]), (int)read.sequence.size()); + sv_PathPtr[BEST_PATH]->sequence_length = read.sequence.size(); + + Solve(begin_flow, end_flow,end_flow,-1,max_metr_diff_ ); + + int to_flow = min(sv_PathPtr[BEST_PATH]->window_end, end_flow); + read.sequence.resize(sv_PathPtr[BEST_PATH]->sequence_length); + memcpy_C(&(read.sequence[0]), sv_PathPtr[BEST_PATH]->sequence, sv_PathPtr[BEST_PATH]->sequence_length); + memset_F(&(read.prediction[0]), 0, num_flows_); + memcpy_F(&(read.prediction[0]), sv_PathPtr[BEST_PATH]->pred, to_flow); +} - int parLast = parent->window_end; - v4i rEnd = LD_VEC4I(parLast); - parLast--; - v4i rBeg = LD_VEC4I(parent->window_start); +// ------------------------------------------------- +PathRecV *TreephaserVEC::sortPaths(int & pathCnt, int &parentPathIdx, int &badPaths, int numActivePaths) +{ +#ifdef PRINT_DEBUG + int commonSeq=0; + if(DO_DEBUG){ + printf("pathCnt=%d \n",pathCnt); + float minMetr=25.0f; + int minFlow=1000; + for(int i = 0; i < pathCnt; ++i){ + if(sv_PathPtr[i]->flow < minFlow) + minFlow=sv_PathPtr[i]->flow; + } + int diff=0; + for(;commonSeqsequence_length && !diff;commonSeq++){ + for(int i = 0; i < pathCnt; ++i){ + if(sv_PathPtr[0]->sequence[commonSeq] != sv_PathPtr[i]->sequence[commonSeq]){ + diff=1; + } + } + } + if(commonSeq) + commonSeq--; + + for(int i = 0; i < pathCnt; ++i){ + sv_PathPtr[i]->sequence[sv_PathPtr[i]->sequence_length]=0; // null-terminate + printf("%s (%d %s %d/%d-%d) sig(%.3f/%.3f) %.3f/%.3f/%.3f\n",(minFlow==sv_PathPtr[i]->flow?"--":" "), + commonSeq,&sv_PathPtr[i]->sequence[commonSeq], + sv_PathPtr[i]->window_start, + sv_PathPtr[i]->flow, + sv_PathPtr[i]->window_end, + sv_PathPtr[i]->pred[sv_PathPtr[i]->flow], + sv_PathPtr[i]->state[sv_PathPtr[i]->flow], + sv_PathPtr[i]->penalty,sv_PathPtr[i]->flowMetr,sv_PathPtr[i]->metr); + } + printf("\n"); + } +#endif - int flow = parent->window_start; - int j = 1; - ad_Adv = 1; - float *parent_CalibA= &parent->calib_A[0]; - float *parent_CalibB= &parent->calib_B[0]; - v4f rS; + int maxPaths = MAX_PATHS-4; + if(numActivePaths > 0) + maxPaths = min(maxPaths,numActivePaths); + if(pathCnt > (maxPaths-1)) { + int m = sv_PathPtr[0]->flow; + int i = 1; + do { + int n = sv_PathPtr[i]->flow; + if(m < n) + m = n; + } while(++i < pathCnt); + if((m -= MAX_PATH_DELAY) > 0) { + do { + if(sv_PathPtr[--i]->flow < m){ +#ifdef PRINT_DEBUG + sv_PathPtr[pathCnt]->sequence[sv_PathPtr[pathCnt]->sequence_length]=0; // null-terminate + printf("Removing path %s too far behind\n",&sv_PathPtr[pathCnt]->sequence[commonSeq]); +#endif + swap(sv_PathPtr[i], sv_PathPtr[--pathCnt]); + } + } while(i > 0); + } + } - // iterate over the flows from parent->window_start to (parent->window_end - 1) - // break this loop if child->window_start does not increase for any of the child paths from - // parent->window_start - while(flow < parLast) { - advanceI(parent->state[flow], j, rParNuc, ts_Transition4[flow].V, rAlive, rS); + while(pathCnt > maxPaths) { + float m = sv_PathPtr[0]->flowMetr; + int i = 1; + int j = 0; + do { + float n = sv_PathPtr[i]->flowMetr; + if(m < n) { + m = n; + j = i; + } + } while(++i < pathCnt); +#ifdef PRINT_DEBUG + if(DO_DEBUG){ + sv_PathPtr[j]->sequence[sv_PathPtr[j]->sequence_length]=0; // null-terminate + printf("%s Removing path %s too many paths\n",(j>= 4?"****":" "),&sv_PathPtr[j]->sequence[commonSeq]); + } +#endif + swap(sv_PathPtr[j], sv_PathPtr[--pathCnt]); + badPaths++; + } + PathRecV *parent = sv_PathPtr[0]; + for(int i = 1; i < pathCnt; ++i){ + if(parent->metr > sv_PathPtr[i]->metr) { + parent = sv_PathPtr[i]; + parentPathIdx = i; + } + } + return (parent); +} - CheckWindowStart1(); - CalcResidualI(parent, flow, j, rS, (LD_VEC4F(parent->pred[flow])+rS),rPenNeg,rPenPos); +float TreephaserVEC::computeParentDist(PathRecV RESTRICT_PTR parent, int end_flow) +{ + // Right here we are having a memory overrun: We copied up to parent->flow but use until parent->window_end of calibA and calibB + // Computing squared distance between parent's predicted signal and normalized measurements + float dist = parent->res+(rd_SqNormMeasureSum[parent->window_end]-rd_SqNormMeasureSum[end_flow]); + dist += sumOfSquaredDiffsFloatSSE((float*)(&(rd_NormMeasureAdj[parent->window_start])), + (float*)(&(parent->pred[parent->window_start])), + parent->window_end-parent->window_start); + return dist; +} - flow++; - j++; - if(ad_Adv == 0) - break; +void TreephaserVEC::CopyPath (PathRecV RESTRICT_PTR dest, PathRecV RESTRICT_PTR parent, + PathRecV RESTRICT_PTR child, int saveFlow, + int &numSaved, int cached_flow, int cached_flow_ws, int cached_flow_seq) +{ + int pws=parent->window_start; + int cws=child->window_start; + int cwe=child->window_end; + int nuc=child->nuc; + int pf=parent->flow; + int cf=child->flow; + int psl=parent->sequence_length; + + memcpy_4F(&dest->pred[pws],&parent->pred_Buf[pws][nuc],cws - pws+1); + + if (state_inphase_enabled_) { + //extending from parent->state_inphase[pf] to fill the gap + for (int tempInd = pf + 1; tempInd < cf; tempInd++) { + dest->state_inphase[tempInd] = max ((float)dest->state[cf][nuc], 0.01f); + } + dest->state_inphase[cf] = max ((float)dest->state[cf][nuc], 0.01f); } - // if none of the child paths has increase in window start. - // this loop is the same as the previous loop, just doesn't check for window start - if(EXPECTED(ad_Adv == 0)) { - - // child window start - ad_Beg.V = rBeg; + dest->sequence_length = psl + 1; + dest->sequence[psl] = flow_order_[cf]; + dest->sequence[dest->sequence_length]=0; - // flow < parent->window_end - 1 - while(flow < parLast) { + if (psl and dest->sequence[psl] != dest->sequence[psl - 1]) + dest->last_hp = 0; + else + dest->last_hp = parent->last_hp; + dest->last_hp++; - advanceI(parent->state[flow], j, rParNuc, ts_Transition4[flow].V, rAlive, rS); + dest->flowMetr = (cf == 0)?0:((child->metr + 0.5f * child->flowMetr) / cf); - CalcResidualI(parent, flow, j, rS, (LD_VEC4F(parent->pred[flow])+rS),rPenNeg,rPenPos); - - flow++; - j++; + if (recalibrate_predictions_) { + //explicitly fill zeros between pf and cf; + for (int tempInd = pf + 1; tempInd < cf; tempInd++) { + dest->calib_A[tempInd] = 1.0f; + dest->calib_B[tempInd] = 0.0f; } + int hp_length = min (dest->last_hp, MAX_HPXLEN); + dest->calib_A[cf] = (*As_).at (cf).at ( + flow_order_.int_at (cf)).at (hp_length); + dest->calib_B[cf] = (*Bs_).at (cf).at ( + flow_order_.int_at (cf)).at (hp_length); + rd_NormMeasureAdj[cf] = (rd_NormMeasure[cf]-dest->calib_B[cf])/dest->calib_A[cf]; + } + { + dest->flow = child->flow; + dest->window_start = child->window_start; + dest->window_end = child->window_end; + dest->res = child->res; + dest->metr = child->metr; + dest->newSignal = child->newSignal; + dest->dist = child->dist; + dest->nuc = child->nuc; + } - // flow = parent->window_end - 1 - { - advanceI(parent->state[flow], j, rParNuc, (v4i) ts_Transition4[flow].V, rAlive, rS); - - CalcResidualI(parent, flow, j, rS, (LD_VEC4F(parent->pred[flow])+rS),rPenNeg,rPenPos); + dest->cached_flow = min(dest->flow,cached_flow); + dest->cached_flow_ws = min(dest->window_start,cached_flow_ws); + dest->cached_flow_seq = min(dest->sequence_length,cached_flow_seq); - CheckWindowEnd(); - flow++; - j++; +#ifdef PRINT_DEBUG + if(DO_DEBUG){ + child->sequence[child->sequence_length]=0; // null-terminate + if (singleChild != 1) + printf("adding child %s\n",child->sequence); } +#endif - // flow >= parent window end - while((flow < end) && (ad_Adv != 0)) { - rS = (v4f)(~(v4i)rParNuc & (v4i)ts_Transition4[flow].V); //_mm_andnot_ps(rTemp1s, ts_Transition4[flow]); - rS *= rAlive; - state_Buf[j].V=rS; - rAlive -= rS; +} - CalcResidualI(parent, flow, j, rS, rS,rPenNeg,rPenPos); +void TreephaserVEC::CopyPathNew (PathRecV RESTRICT_PTR dest, PathRecV RESTRICT_PTR parent, + PathRecV RESTRICT_PTR child, int saveFlow, + int &numSaved, int cached_flow, int cached_flow_ws, int cached_flow_seq) +{ + int dcf = (dest->cached_flow&0xffff); + int dws = (dest->cached_flow_ws&0xffff); + int dseq= (dest->cached_flow_seq&0xffff); + + int pws=parent->window_start; + int cws=child->window_start; + int cwe=child->window_end; + int nuc=child->nuc; + int pf=parent->flow; + int cf=child->flow; + int psl=parent->sequence_length; + int cwemcws=cwe-cws; + int pfmdcf=pf-dcf+1; + + memcpy_4F(&dest->pred[pws],&parent->pred_Buf[pws][nuc],cws - pws+1); + + if (dest != parent) + { + // copy the beginning of the arrays as well + memcpy_4F4(&dest->state[cws][nuc],&parent->state[cws][nuc],cwemcws); + memcpy_F(&dest->pred[dws], &parent->pred[dws], pws - dws); + memcpy_4F4(&dest->pred_Buf[cws][nuc],&parent->pred_Buf[cws][nuc],cwemcws); + memcpy_C(&dest->sequence[dseq], &parent->sequence[dseq], psl - dseq); + } - CheckWindowEnd(); + if (state_inphase_enabled_) { + if (dest != parent) + { + memcpy_F(&dest->state_inphase[dcf], &parent->state_inphase[dcf],pfmdcf); + } - flow++; - j++; + //extending from parent->state_inphase[pf] to fill the gap + for (int tempInd = pf + 1; tempInd < cf; tempInd++) { + dest->state_inphase[tempInd] = max ((float)dest->state[cf][nuc], 0.01f); } + dest->state_inphase[cf] = max ((float)dest->state[cf][nuc], 0.01f); + } - rEnd = (v4i)_mm_min_epi16((__m128i)rEnd, (__m128i)ad_FlowEnd.V); - ad_End.V = rEnd; + dest->sequence_length = psl + 1; + dest->sequence[psl] = flow_order_[cf]; + dest->sequence[dest->sequence_length]=0; + if (psl and dest->sequence[psl] != dest->sequence[psl - 1]) + dest->last_hp = 0; + else + dest->last_hp = parent->last_hp; + dest->last_hp++; - } - // This branch is for if one of the child paths has an increase in window_start - // flow = (parent->window_end - 1) - else { + dest->flowMetr = (cf == 0)?0:((child->metr + 0.5f * child->flowMetr) / cf); + if (recalibrate_predictions_) { + if (dest != parent && cf > 0) { - advanceI(parent->state[flow], j, rParNuc, ts_Transition4[flow].V, rAlive, rS); - - CalcResidualI(parent, flow, j, rS, (LD_VEC4F(parent->pred[flow])+rS),rPenNeg,rPenPos); - - CheckWindowStart2(); - - CheckWindowEnd(); - - flow++; - j++; + memcpy_F(&dest->calib_A[dcf], &parent->calib_A[dcf],pfmdcf); + memcpy_F(&dest->calib_B[dcf], &parent->calib_B[dcf],pfmdcf); } - - // flow >= parent->window_end - while((flow < end) && (ad_Adv != 0)) { - v4f rTemp1s = rParNuc; - rTemp1s = _mm_andnot_ps(rTemp1s, ts_Transition4[flow].V); - rTemp1s *= rAlive; - rS = rTemp1s; - state_Buf[j].V=rS; - rAlive -= rS; - - CheckWindowStart2(); - - CalcResidualI(parent, flow, j, rS, rS,rPenNeg,rPenPos); - - CheckWindowEnd(); - - flow++; - j++; + //explicitly fill zeros between pf and cf; + for (int tempInd = pf + 1; tempInd < cf; tempInd++) { + dest->calib_A[tempInd] = 1.0f; + dest->calib_B[tempInd] = 0.0f; } + int hp_length = min (dest->last_hp, MAX_HPXLEN); + dest->calib_A[cf] = (*As_).at (cf).at ( + flow_order_.int_at (cf)).at (hp_length); + dest->calib_B[cf] = (*Bs_).at (cf).at ( + flow_order_.int_at (cf)).at (hp_length); + rd_NormMeasureAdj[cf] = (rd_NormMeasure[cf]-dest->calib_B[cf])/dest->calib_A[cf]; + } + if(dest != child) + { + dest->flow = child->flow; + dest->window_start = child->window_start; + dest->window_end = child->window_end; + dest->res = child->res; + dest->metr = child->metr; + dest->newSignal = child->newSignal; + dest->dist = child->dist; + dest->nuc = child->nuc; + } - rEnd = (v4i)_mm_min_epi16((__m128i)rEnd, (__m128i)ad_FlowEnd.V); - ad_Beg.V = rBeg; - ad_End.V = rEnd; + dest->saved = parent->saved; + dest->cached_flow = min(dest->flow,cached_flow); + dest->cached_flow_ws = min(dest->window_start,cached_flow_ws); + dest->cached_flow_seq = min(dest->sequence_length,cached_flow_seq); - } -} +#ifdef PRINT_DEBUG + if(DO_DEBUG){ + child->sequence[child->sequence_length]=0; // null-terminate + if (singleChild != 1) + printf("adding child %s\n",child->sequence); + } +#endif -void TreephaserSSE::sumNormMeasures() { - int i = num_flows_; - float sum = 0.0f; - rd_SqNormMeasureSum[i] = 0.0f; - while(--i >= 0) - rd_SqNormMeasureSum[i] = (sum += rd_NormMeasure[i]*rd_NormMeasure[i]); } -// ------------------------------------------------- - -void TreephaserSSE::RecalibratePredictions(PathRec *maxPathPtr) +void +TreephaserVEC::CopyPathDeep (PathRecV RESTRICT_PTR destPath, + PathRecV RESTRICT_PTR srcPath) { - // Distort predictions according to recalibration model - int to_flow = min(maxPathPtr->flow+1, num_flows_); - - for (int flow=0; flowpred[flow] = - maxPathPtr->pred[flow] * maxPathPtr->calib_A[flow] - + maxPathPtr->calib_B[flow]; + memcpy_4F4(&destPath->state[srcPath->window_start][srcPath->nuc], + &srcPath->state[srcPath->window_start][srcPath->nuc], + srcPath->window_end -srcPath->window_start); + memcpy_4F4(&destPath->pred_Buf[srcPath->window_start][srcPath->nuc], + &srcPath->pred_Buf[srcPath->window_start][srcPath->nuc], + srcPath->window_end - srcPath->window_start + 1); + memcpy_F(destPath->pred,srcPath->pred,srcPath->window_end + 1); + memcpy_4F(&destPath->pred[srcPath->window_start], + &destPath->pred_Buf[srcPath->window_start][srcPath->nuc], + srcPath->window_end - srcPath->window_start); + memcpy_C(destPath->sequence,srcPath->sequence,srcPath->sequence_length + 1); + if (state_inphase_enabled_) { + memcpy_F(destPath->state_inphase,srcPath->state_inphase,srcPath->flow + 1); } -} + destPath->sequence_length = srcPath->sequence_length; -void TreephaserSSE::ResetRecalibrationStructures(int num_flows) { - for (int p = 0; p <= 8; ++p) { - setValueSSE(&(sv_PathPtr[p]->calib_A[0]), 1.0f, num_flows_); - setZeroSSE(&(sv_PathPtr[p]->calib_B[0]), num_flows_*sizeof(float)); + if (recalibrate_predictions_) { + memcpy_F(destPath->calib_A,srcPath->calib_A,srcPath->flow + 1); + memcpy_F(destPath->calib_B,srcPath->calib_B,srcPath->flow + 1); } + + destPath->flow = srcPath->flow; + destPath->window_start = srcPath->window_start; + destPath->window_end = srcPath->window_end; + destPath->res = srcPath->res; + destPath->metr = srcPath->metr; + destPath->newSignal = srcPath->newSignal; + destPath->dist = srcPath->dist; + destPath->flowMetr = srcPath->flowMetr; + destPath->nuc = srcPath->nuc; + destPath->penalty = srcPath->penalty; + destPath->last_hp = srcPath->last_hp; + destPath->cached_flow=0; + destPath->cached_flow_seq=0; + destPath->cached_flow_ws=0; } -// -------------------------------------------------- -void TreephaserSSE::SolveRead(BasecallerRead& read, int begin_flow, int end_flow) -{ - copySSE(rd_NormMeasure, &(read.normalized_measurements[0]), num_flows_*sizeof(float)); - setZeroSSE(sv_PathPtr[MAX_PATHS]->pred, num_flows_*sizeof(float)); // Not necessary? - copySSE(sv_PathPtr[MAX_PATHS]->sequence, &(read.sequence[0]), (int)read.sequence.size()*sizeof(char)); - sv_PathPtr[MAX_PATHS]->sequence_length = read.sequence.size(); - - Solve(begin_flow, end_flow); - - int to_flow = min(sv_PathPtr[MAX_PATHS]->window_end, end_flow); - read.sequence.resize(sv_PathPtr[MAX_PATHS]->sequence_length); - copySSE(&(read.sequence[0]), sv_PathPtr[MAX_PATHS]->sequence, sv_PathPtr[MAX_PATHS]->sequence_length*sizeof(char)); - setZeroSSE(&(read.prediction[0]), num_flows_*sizeof(float)); - copySSE(&(read.prediction[0]), sv_PathPtr[MAX_PATHS]->pred, to_flow*sizeof(float)); -} // ------------------------------------------------- - -bool TreephaserSSE::Solve(int begin_flow, int end_flow) +bool TreephaserVEC::Solve(int begin_flow, int end_flow, int saveFlow, int numActivePaths, float maxMetrDiff) { sumNormMeasures(); - PathRec RESTRICT_PTR parent = sv_PathPtr[0]; - PathRec RESTRICT_PTR best = sv_PathPtr[MAX_PATHS]; + PathRecV RESTRICT_PTR parent = sv_PathPtr[0]; + PathRecV RESTRICT_PTR best = sv_PathPtr[BEST_PATH]; - parent->flow = 0; - parent->window_start = 0; - parent->window_end = 1; - parent->res = 0.0f; - parent->metr = 0.0f; - parent->flowMetr = 0.0f; - parent->dotCnt = 0; - parent->state[0] = 1.0f; - parent->sequence_length = 0; - parent->last_hp = 0; - parent->pred[0] = 0.0f; - parent->state_inphase[0] = 1.0f; + + for(int flow=begin_flow;flow 0) { - - static const int char_to_nuc[8] = {-1, 0, -1, 1, 3, -1, -1, 2}; - - for (int base = 0; base < best->sequence_length; ++base) { - parent->sequence_length++; - parent->sequence[base] = best->sequence[base]; - if (base and parent->sequence[base] != parent->sequence[base-1]) - parent->last_hp = 0; - parent->last_hp++; - if (parent->last_hp > MAX_HPXLEN) { // Safety to not overrun recalibration array - parent->last_hp = MAX_HPXLEN; - } - - advanceStateInPlace(parent, char_to_nuc[best->sequence[base]&7], num_flows_); - if (parent->flow >= num_flows_) - break; - int to_flow = min(parent->window_end, end_flow); - sumVectFloatSSE(&parent->pred[parent->window_start], &parent->state[parent->window_start], to_flow-parent->window_start); -// for(int k = parent->window_start; k < to_flow; ++k) { -// if((k & 3) == 0) { -// sumVectFloatSSE(&parent->pred[k], &parent->state[k], to_flow-k); -// break; -// } -// parent->pred[k] += parent->state[k]; -// } - // Recalibration part of the initial simulation: log coefficients for simulation part - if(recalibrate_predictions_) { - parent->calib_A[parent->flow] = (*As_).at(parent->flow).at(flow_order_.int_at(parent->flow)).at(parent->last_hp); - parent->calib_B[parent->flow] = (*Bs_).at(parent->flow).at(flow_order_.int_at(parent->flow)).at(parent->last_hp); - } - if (parent->flow >= begin_flow) - break; - } - - // No point solving the read if we simulated the whole thing. - if(parent->window_end < begin_flow or parent->flow >= num_flows_) { - sv_PathPtr[MAX_PATHS] = parent; - sv_PathPtr[0] = best; - return true; + int found=0; + + if(sv_PathPtr[SAVED_PATHS]->flow > 0){ + int pth=0; + for(;pthflow > 0 && + memcmp(sv_PathPtr[SAVED_PATHS+pth]->sequence, + sv_PathPtr[BEST_PATH]->sequence, + sv_PathPtr[SAVED_PATHS+pth]->sequence_length)==0){ + + best=sv_PathPtr[SAVED_PATHS+pth]; + sv_PathPtr[SAVED_PATHS+pth]=parent; + sv_PathPtr[0]=best; + parent=best; + found=1; + break; + } + } } - parent->res = sumOfSquaredDiffsFloatSSE( - (float*)rd_NormMeasure, (float*)parent->pred, parent->window_start); - } - best->window_end = 0; - best->sequence_length = 0; + if(!found) return true; - do { + parent->res = sumOfSquaredDiffsFloatSSE( + (float*)rd_NormMeasure, (float*)parent->pred, parent->window_start); + }else{ + for(int i=0;icalib_A[0]=1.0; + sv_PathPtr[i]->calib_B[0]=0; - if(pathCnt > 3) { - int m = sv_PathPtr[0]->flow; - int i = 1; - do { - int n = sv_PathPtr[i]->flow; - if(m < n) - m = n; - } while(++i < pathCnt); - if((m -= MAX_PATH_DELAY) > 0) { - do { - if(sv_PathPtr[--i]->flow < m) - swap(sv_PathPtr[i], sv_PathPtr[--pathCnt]); - } while(i > 0); - } + memset(sv_PathPtr[i]->pred,0,num_flows_*sizeof(sv_PathPtr[i]->pred[0])); } + parent->flow = 0; + parent->window_start = 0; + parent->window_end = 1; + parent->res = 0.0f; + parent->metr = 0.0f; + parent->flowMetr = 0.0f; + parent->newSignal = 1.0f; + parent->state[0] = LD_VEC4F(1.0f); + parent->sequence_length = 0; + parent->last_hp = 0; + parent->pred[0] = 0.0f; + parent->pred_Buf[0]=LD_VEC4F(0); + parent->state_inphase[0] = 1.0f; + parent->nuc=0; - while(pathCnt > MAX_PATHS-4) { - float m = sv_PathPtr[0]->flowMetr; - int i = 1; - int j = 0; - do { - float n = sv_PathPtr[i]->flowMetr; - if(m < n) { - m = n; - j = i; - } - } while(++i < pathCnt); - swap(sv_PathPtr[j], sv_PathPtr[--pathCnt]); - } + } - parent = sv_PathPtr[0]; - int parentPathIdx = 0; - for(int i = 1; i < pathCnt; ++i) - if(parent->metr > sv_PathPtr[i]->metr) { - parent = sv_PathPtr[i]; - parentPathIdx = i; - } - if(parent->metr >= 1000.0f) - break; - int parent_flow = parent->flow; - - // compute child path flow states, predicted signal,negative and positive penalties - advanceState4(parent, end_flow); - - int n = pathCnt; - double bestpen = 25.0; - for(int nuc = 0; nuc < 4; ++nuc) { - PathRec RESTRICT_PTR child = sv_PathPtr[n]; - - child->flow = min(ad_Idx.A[nuc], end_flow); - child->window_start = ad_Beg.A[nuc]; - child->window_end = min(ad_End.A[nuc], end_flow); - - // Do not attempt to calculate child->last_hp in this loop; bad things happen - if(child->flow >= end_flow or parent->last_hp >= MAX_HPXLEN or parent->sequence_length >= 2*MAX_VALS-10) - continue; - - // pointer in the ad_Buf buffer pointing at the running sum of positive residuals at start of parent window - //char RESTRICT_PTR pn = ad_Buf+nuc*4+(AD_NRES_OFS-16)-parent->window_start*16; - int cwsIdx=child->window_start-parent->window_start; - int cfIdx =child->flow-parent->window_start; - int cweIdx=child->window_end-parent->window_start; - - // child path metric - float metr = parent->res + pres_Buf[cwsIdx].A[nuc];//*((float RESTRICT_PTR)(pn+child->window_start*16+(AD_PRES_OFS-AD_NRES_OFS))); - - // sum of squared residuals for positive residuals for flows < child->flow - float penPar = pres_Buf[cfIdx].A[nuc];//*((float RESTRICT_PTR)(pn+child->flow*16+(AD_PRES_OFS-AD_NRES_OFS))); - - // sum of squared residuals for negative residuals for flows < child->window_end - float penNeg = nres_Buf[cweIdx].A[nuc];//*((float RESTRICT_PTR)(pn+child->window_end*16)); - - // sum of squared residuals left of child window start - child->res = metr + nres_Buf[cwsIdx].A[nuc];//*((float RESTRICT_PTR)(pn+child->window_start*16)); - - metr += penNeg; - - // penPar corresponds to penalty1 in DPTreephaser.cpp - penPar += penNeg; - penNeg += penPar; - - // penalty = penalty1 + (kNegativeMultiplier = 2)*penNeg - if(penNeg >= 20.0) - continue; - - if(bestpen > penNeg) - bestpen = penNeg; - else if(penNeg-bestpen >= 0.2) - continue; - - // child->path_metric > sum_of_squares_upper_bound - if(metr > bestDist) - continue; - - float newSignal = rd_NormMeasure[child->flow]; - - // XXX Right here we are having a memory overrun: We copied up to parent->flow but use until parent->window_end - // Check 'dot' criterion - if(child->flow < parent->window_end){ - if (recalibrate_predictions_) - newSignal -= (parent->calib_A[child->flow]*parent->pred[child->flow]+parent->calib_B[child->flow]); - else - newSignal -= parent->pred[child->flow]; - } - newSignal /= state_Buf[cfIdx+1].A[nuc];// *((float RESTRICT_PTR)(ad_Buf+nuc*4+AD_STATE_OFS + (child->flow-parent->window_start)*16)); - child->dotCnt = 0; - if(newSignal < 0.3f) { - if(parent->dotCnt > 0) - continue; - child->dotCnt = 1; - } - // child path survives at this point - child->metr = float(metr); - child->flowMetr = float(penPar); - child->penalty = float(penNeg); - child->nuc = nuc; - ++n; - } + for(int i=1;iflow=0; // mark as invalid for restart + //sv_PathPtr[i]->window_end = 1; + sv_PathPtr[i]->sequence_length = 0; + sv_PathPtr[i]->cached_flow=DFLT_CACHE; + sv_PathPtr[i]->cached_flow_ws=DFLT_CACHE; + sv_PathPtr[i]->cached_flow_seq=DFLT_CACHE; + } + sv_PathPtr[0]->cached_flow=DFLT_CACHE; + sv_PathPtr[0]->cached_flow_ws=DFLT_CACHE; + sv_PathPtr[0]->cached_flow_seq=DFLT_CACHE; - // XXX Right here we are having a memory overrun: We copied up to parent->flow but use until parent->window_end of calibA and calibB - // Computing squared distance between parent's predicted signal and normalized measurements - float dist = parent->res+(rd_SqNormMeasureSum[parent->window_end]-rd_SqNormMeasureSum[end_flow]); - if (recalibrate_predictions_) { - int i=parent->window_start; - dist += sumOfSquaredDiffsFloatSSE_recal((float RESTRICT_PTR)(&(rd_NormMeasure[i])), - (float RESTRICT_PTR)(&(parent->pred[i])), - (float RESTRICT_PTR)(&(parent->calib_A[i])), - (float RESTRICT_PTR)(&(parent->calib_B[i])), - parent->window_end-i); - } else { - int i=parent->window_start; - dist += sumOfSquaredDiffsFloatSSE((float RESTRICT_PTR)(&(rd_NormMeasure[i])), - (float RESTRICT_PTR)(&(parent->pred[i])), - parent->window_end-i); - } - // Finished computing squared distance - int bestPathIdx = -1; + parent->dist=computeParentDist(parent,end_flow); + parent->saved=0; + int badPaths=0; + int manyPaths=0; - // current best path is parent path - if(bestDist > dist) { - bestPathIdx = parentPathIdx; - parentPathIdx = -1; - } + do { + int parentPathIdx=0; + int childPathIdx=-1; + float bestpen = 19.8; + parent=sv_PathPtr[0]; + if(pathCnt>1) + parent = sortPaths(pathCnt,parentPathIdx,badPaths,numActivePaths); + else + badPaths=0; + + int pf=parent->flow; + int pws=parent->window_start; + int pseq=parent->sequence_length; + int numChild=0; + if(!(parent->last_hp >= MAX_HPXLEN or parent->sequence_length >= 2*MAX_VALS-10)){ + advanceState4(parent, end_flow); - int childPathIdx = -1; - while(pathCnt < n) { - PathRec RESTRICT_PTR child = sv_PathPtr[pathCnt]; - // Rule that depends on finding the best nuc - if(child->penalty-bestpen >= 0.2f) { - sv_PathPtr[pathCnt] = sv_PathPtr[--n]; - sv_PathPtr[n] = child; - } - else if((childPathIdx < 0) && (parentPathIdx >= 0)) { - sv_PathPtr[pathCnt] = sv_PathPtr[--n]; - sv_PathPtr[n] = child; - childPathIdx = n; + for(int nuc = 0; nuc < 4; ++nuc) { + bestpen = min(bestpen,(float)penNegV[nuc]); } - // this is the child path to be kept - else { - if (child->flow) - child->flowMetr = (child->metr + 0.5f*child->flowMetr) / child->flow; - //char RESTRICT_PTR p = ad_Buf+child->nuc*4+AD_STATE_OFS; - { - int len=child->window_end-parent->window_start; - copySSE_4th(&child->state[parent->window_start],&state_Buf[1].A[child->nuc],len); - copySSE_4th(&child->pred[parent->window_start],&pred_Buf[1].A[child->nuc],len); - } -// for(int i = parent->window_start, j = 1, e = child->window_end; i < e; ++i, j ++) { -// child->state[i] = state_Buf[j].A[child->nuc];//*((float*)(ad_Buf+child->nuc*4+AD_STATE_OFS + j)); -// child->pred[i] = pred_Buf[j].A[child->nuc]; //*((float*)(ad_Buf+child->nuc*4+AD_PRED_OFS + j)); -// } - copySSE(child->pred, parent->pred, parent->window_start << 2); - - copySSE(child->sequence, parent->sequence, parent->sequence_length); - - if(state_inphase_enabled_){ - if(child->flow > 0){ - int cpSize = (parent->flow+1)*sizeof(float); - copySSE(child->state_inphase, parent->state_inphase, cpSize); - } - //extending from parent->state_inphase[parent->flow] to fill the gap - for(int tempInd = parent->flow+1; tempInd < child->flow; tempInd++){ - child->state_inphase[tempInd] = max(child->state[child->flow],0.01f); - } - child->state_inphase[child->flow] = max(child->state[child->flow],0.01f); - } - child->sequence_length = parent->sequence_length + 1; - child->sequence[parent->sequence_length] = flow_order_[child->flow]; - if (parent->sequence_length and child->sequence[parent->sequence_length] != child->sequence[parent->sequence_length-1]) - child->last_hp = 0; - else - child->last_hp = parent->last_hp; - child->last_hp++; - - // copy whole vector to avoid memory access to fields that have been written to by (longer) previously discarded paths XXX - // --> Reintroducing memory overrun since it seems to yield better performance - if (recalibrate_predictions_) { - if(child->flow > 0){ - // --- Reverting to old code with memory overrun - int cpSize = (parent->flow+1) << 2; - //memcpy(child->calib_A, parent->calib_A, cpSize); - //memcpy(child->calib_B, parent->calib_B, cpSize); - // --- - copySSE(child->calib_A, parent->calib_A, cpSize); - copySSE(child->calib_B, parent->calib_B, cpSize); - } - //explicitly fill zeros between parent->flow and child->flow; - for(int tempInd = parent->flow + 1; tempInd < child->flow; tempInd++){ - child->calib_A[tempInd] = 1.0f; - child->calib_B[tempInd] = 0.0f; + int numChild=0; + for(int nuc = 0; nuc < 4; ++nuc) { + if(flow_Buf[nuc] >= end_flow) + continue; + if(penNegV[nuc]-bestpen >= maxMetrDiff) + continue; + + float newSignal=rd_NormMeasureAdj[flow_Buf[nuc]] / parent->state[flow_Buf[nuc]][nuc]; + if(newSignal < 0.3f && parent->newSignal < 0.3f) + continue; + distV[nuc] += rd_SqNormMeasureSum[winEnd_Buf[nuc]]-rd_SqNormMeasureSum[end_flow]; + + // child path survives at this point + PathRecV RESTRICT_PTR child = sv_PathPtr[pathCnt]; + child->flow = flow_Buf[nuc]; + child->window_start = winStart_Buf[nuc]; + child->window_end = winEnd_Buf[nuc]; + child->res = resV[nuc]; + child->newSignal = newSignal; + child->metr = metrV[nuc]; + child->flowMetr = penParV[nuc]; + child->penalty = penNegV[nuc]; + child->nuc = nuc; + child->dist = distV[nuc]; + numChild++; + if((childPathIdx < 0) && (bestDist < parent->dist || (parent->dist >= child->dist))){ + sv_PathPtr[pathCnt] = sv_PathPtr[MAX_PATHS-1]; + sv_PathPtr[MAX_PATHS-1] = child; + childPathIdx = MAX_PATHS-1; + if(bestDist >= child->dist){ + best=parent; + bestDist=child->dist; } - int hp_length = min(child->last_hp, MAX_HPXLEN); - child->calib_A[child->flow] = (*As_).at(child->flow).at(flow_order_.int_at(child->flow)).at(hp_length); - child->calib_B[child->flow] = (*Bs_).at(child->flow).at(flow_order_.int_at(child->flow)).at(hp_length); + }else{ + CopyPathNew(child,parent,child,saveFlow,numSaved,cached_flow,cached_flow_ws,cached_flow_seq); + ++pathCnt; } - ++pathCnt; } - } - - // In the event, there is no best path, one of the child is copied to the parent - if(childPathIdx >= 0) { - PathRec RESTRICT_PTR child = sv_PathPtr[childPathIdx]; - parent_flow = parent->flow; //MJ - parent->flow = child->flow; - parent->window_end = child->window_end; - parent->res = child->res; - parent->metr = child->metr; - (child->flow == 0) ? (parent->flowMetr == 0) : (parent->flowMetr = (child->metr + 0.5f*child->flowMetr) / child->flow); - parent->dotCnt = child->dotCnt; - //char RESTRICT_PTR p = ad_Buf+child->nuc*4+AD_STATE_OFS; - for(int i = parent->window_start, j = 1, e = child->window_end; i < e; ++i, j ++) { - parent->state[i] = state_Buf[j].A[child->nuc];//*((float*)(ad_Buf+child->nuc*4+AD_STATE_OFS+j)); - parent->pred[i] = pred_Buf[j].A[child->nuc];//*((float*)(ad_Buf+child->nuc*4+AD_PRED_OFS+j)); - } - - parent->sequence[parent->sequence_length] = flow_order_[parent->flow]; - if (parent->sequence_length and parent->sequence[parent->sequence_length] != parent->sequence[parent->sequence_length-1]) - parent->last_hp = 0; - parent->last_hp++; - parent->sequence_length++; - - //update calib_A and calib_B for parent - if (recalibrate_predictions_) { - for(int tempInd = parent_flow + 1; tempInd < child->flow; tempInd++){ - parent->calib_A[tempInd] = 1.0f; - parent->calib_B[tempInd] = 0.0f; - } - parent->calib_A[parent->flow] = (*As_).at(parent->flow).at(flow_order_.int_at(parent->flow)).at(parent->last_hp); - parent->calib_B[parent->flow] = (*Bs_).at(parent->flow).at(flow_order_.int_at(parent->flow)).at(parent->last_hp); - } - - if(state_inphase_enabled_){ - for(int tempInd = parent_flow+1; tempInd < parent->flow; tempInd++){ - parent->state_inphase[tempInd] = parent->state[parent->flow]; - } - parent->state_inphase[parent->flow] = parent->state[parent->flow]; - } - - parent->window_start = child->window_start; - parentPathIdx = -1; - } + } - // updating parent as best path - if(bestPathIdx >= 0) { - bestDist = dist; - sv_PathPtr[bestPathIdx] = sv_PathPtr[--pathCnt]; - sv_PathPtr[pathCnt] = sv_PathPtr[MAX_PATHS]; - sv_PathPtr[MAX_PATHS] = parent; - } else if(parentPathIdx >= 0) { - sv_PathPtr[parentPathIdx] = sv_PathPtr[--pathCnt]; - sv_PathPtr[pathCnt] = parent; + if(childPathIdx >= 0) { + CopyPath(parent,parent,sv_PathPtr[childPathIdx],saveFlow,numSaved,cached_flow,cached_flow_ws,cached_flow_seq); + }else{ + if(bestDist >= parent->dist){ + bestDist = parent->dist; + sv_PathPtr[parentPathIdx] = sv_PathPtr[--pathCnt]; + sv_PathPtr[pathCnt] = sv_PathPtr[BEST_PATH]; + sv_PathPtr[BEST_PATH] = parent; + best=parent; + }else{ + sv_PathPtr[parentPathIdx] = sv_PathPtr[--pathCnt]; + sv_PathPtr[pathCnt] = parent; + } + } + if(pathCnt > 1){ + if(cached_flow==DFLT_CACHE){ + cached_flow=0;//pf; + cached_flow_ws=0;//pws; + cached_flow_seq=0;//pseq; + for(int pthi=0;pthi<=BEST_PATH;pthi++){ + PathRecV RESTRICT_PTR pth = sv_PathPtr[pthi]; + pth->cached_flow=min(pth->cached_flow,cached_flow); + pth->cached_flow_ws=min(pth->cached_flow_ws,cached_flow_ws); + pth->cached_flow_seq=min(pth->cached_flow_seq,cached_flow_seq); + } + } + }else if(cached_flow != DFLT_CACHE){ + cached_flow=DFLT_CACHE; + cached_flow_ws=DFLT_CACHE; + cached_flow_seq=DFLT_CACHE; + } + + if(saveFlow > 0){ + if(best->flow >= saveFlow && (pathCnt == 1 || best->flow >= end_flow)){ + + if(numSaved == 0){ + // save all the current paths + if(sv_PathPtr[BEST_PATH] != best){ + CopyPathDeep(sv_PathPtr[BEST_PATH],best); + best=sv_PathPtr[BEST_PATH]; + } + for(int i=0;iflow >= (saveFlow-8) && pathCnt != 1){ + for(int i=0;i 2) + manyPaths++; + } while(pathCnt > 0 && badPaths < bad_path_limit_ && manyPaths < many_path_limit_); + + for(int i=0;i<4;i++){ + if(best == sv_PathPtr[i]){ + sv_PathPtr[i]=sv_PathPtr[BEST_PATH]; + sv_PathPtr[BEST_PATH]=best; } - - } while(pathCnt > 0); + } + best=sv_PathPtr[BEST_PATH]; + memcpy_4F(&best->pred[best->window_start], + &best->pred_Buf[best->window_start][best->nuc], + best->window_end - best->window_start); // At the end change predictions according to recalibration model and reset data structures if (recalibrate_predictions_) { - RecalibratePredictions(sv_PathPtr[MAX_PATHS]); + RecalibratePredictions(sv_PathPtr[BEST_PATH]); ResetRecalibrationStructures(end_flow); } - - return false; + if(saveFlow > 0 && numSaved==0) + return true; + else + return false; } -void TreephaserSSE::WindowedNormalize(BasecallerRead& read, int num_steps) +void TreephaserVEC::WindowedNormalize(BasecallerRead& read, int num_steps) { // int num_flows = read.raw_measurements.size(); float median_set[windowSize_]; @@ -1216,33 +962,38 @@ void TreephaserSSE::WindowedNormalize(BasecallerRead& read, int num_steps) float next_normalizer = 0; int estim_flow = 0; int apply_flow = 0; + PathRecV *path=sv_PathPtr[BEST_PATH]; + int start_step=max(0,num_steps-1); - for (int step = 0; step <= num_steps; ++step) { + for (int step = start_step; step <= num_steps; ++step) { - int window_end = estim_flow + windowSize_; - int window_middle = estim_flow + windowSize_ / 2; - if (window_middle > num_flows_) - break; + int window_start = (step+0) * windowSize_; + int window_end = (step+1) * windowSize_; + int apply_flow_start = max(0,window_start-(windowSize_/2)); + int apply_flow_end = min(num_flows_,window_start+(windowSize_/2)); float normalizer = next_normalizer; int median_set_size = 0; - for (; estim_flow < window_end and estim_flow < num_flows_ and estim_flow < sv_PathPtr[MAX_PATHS]->window_end; ++estim_flow) - if (sv_PathPtr[MAX_PATHS]->pred[estim_flow] < 0.3) - median_set[median_set_size++] = read.raw_measurements[estim_flow] - sv_PathPtr[MAX_PATHS]->pred[estim_flow]; + float average=0; + for (estim_flow=window_start; estim_flow < window_end ; ++estim_flow){ + if (path->pred[estim_flow] < 0.3){ + average += read.raw_measurements[estim_flow] - path->pred[estim_flow]; + median_set_size++; + } + } if (median_set_size > 5) { - //cout << step << ":" << median_set_size << ":" << windowSize_ << endl; - std::nth_element(median_set, median_set + median_set_size/2, median_set + median_set_size); - next_normalizer = median_set[median_set_size / 2]; + next_normalizer = average/(float)median_set_size; if (step == 0) normalizer = next_normalizer; + else + normalizer = read.additive_correction[apply_flow_start-1]; } - float delta = (next_normalizer - normalizer) / static_cast(windowSize_); + float delta = (next_normalizer - normalizer) / (float)windowSize_; - for (; apply_flow < window_middle and apply_flow < num_flows_; ++apply_flow) { - //cout << apply_flow << ":" << window_middle << ":" << num_flows_ << endl; + for (apply_flow=apply_flow_start; apply_flow < apply_flow_end; ++apply_flow) { rd_NormMeasure[apply_flow] = read.raw_measurements[apply_flow] - normalizer; read.additive_correction[apply_flow] = normalizer; normalizer += delta; @@ -1260,30 +1011,37 @@ void TreephaserSSE::WindowedNormalize(BasecallerRead& read, int num_steps) estim_flow = 0; apply_flow = 0; - for (int step = 0; step <= num_steps; ++step) { + for (int step = start_step; step <= num_steps; ++step) { - int window_end = estim_flow + windowSize_; - int window_middle = estim_flow + windowSize_ / 2; - if (window_middle > num_flows_) - break; + int window_start = (step+0) * windowSize_; + int window_end = (step+1) * windowSize_; + int apply_flow_start = max(0,window_start-(windowSize_/2)); + int apply_flow_end = min(num_flows_,window_start+(windowSize_/2)); float normalizer = next_normalizer; int median_set_size = 0; - for (; estim_flow < window_end and estim_flow < num_flows_ and estim_flow < sv_PathPtr[MAX_PATHS]->window_end; ++estim_flow) - if (sv_PathPtr[MAX_PATHS]->pred[estim_flow] > 0.5 and rd_NormMeasure[estim_flow] > 0) - median_set[median_set_size++] = rd_NormMeasure[estim_flow] / sv_PathPtr[MAX_PATHS]->pred[estim_flow]; + float average=0; + for (estim_flow=window_start; estim_flow < window_end ; ++estim_flow){ + if (path->pred[estim_flow] > 0.5 and rd_NormMeasure[estim_flow] > 0){ + median_set[median_set_size++] = rd_NormMeasure[estim_flow] / path->pred[estim_flow]; + average+=rd_NormMeasure[estim_flow] / path->pred[estim_flow]; + } + } if (median_set_size > 5) { + average /= (float)median_set_size; std::nth_element(median_set, median_set + median_set_size/2, median_set + median_set_size); - next_normalizer = median_set[median_set_size / 2]; + next_normalizer = (median_set[median_set_size / 2] + average)/2; if (step == 0) normalizer = next_normalizer; + else + normalizer = read.multiplicative_correction[apply_flow_start-1]; } float delta = (next_normalizer - normalizer) / static_cast(windowSize_); - for (; apply_flow < window_middle and apply_flow < num_flows_; ++apply_flow) { + for (apply_flow=apply_flow_start; apply_flow < apply_flow_end; ++apply_flow) { rd_NormMeasure[apply_flow] /= normalizer; read.multiplicative_correction[apply_flow] = normalizer; normalizer += delta; @@ -1297,11 +1055,7 @@ void TreephaserSSE::WindowedNormalize(BasecallerRead& read, int num_steps) } -// ------------------------------------------------------------------------ -// Compute quality metrics -// Why does this function completely ignore recalibration? - -void TreephaserSSE::ComputeQVmetrics(BasecallerRead& read) +void TreephaserVEC::ComputeQVmetrics_flow(BasecallerRead& read, vector& flow_to_base, const bool flow_predictors_,const bool flow_quality) { static const char nuc_int_to_char[5] = "ACGT"; int num_flows = flow_order_.num_flows(); @@ -1314,19 +1068,19 @@ void TreephaserSSE::ComputeQVmetrics(BasecallerRead& read) read.penalty_mismatch.assign(num_bases, 0); read.penalty_residual.assign(num_bases, 0); - PathRec RESTRICT_PTR parent = sv_PathPtr[0]; - PathRec RESTRICT_PTR children[4] = {sv_PathPtr[1], sv_PathPtr[2], sv_PathPtr[3], sv_PathPtr[4]}; + PathRecV RESTRICT_PTR parent = sv_PathPtr[0]; parent->flow = 0; parent->window_start = 0; parent->window_end = 1; parent->res = 0.0f; parent->metr = 0.0f; parent->flowMetr = 0.0f; - parent->dotCnt = 0; - parent->state[0] = 1.0f; + parent->newSignal = 1.0f; + parent->state[0] = LD_VEC4F(1.0f); parent->sequence_length = 0; parent->last_hp = 0; parent->pred[0] = 0.0f; + parent->pred_Buf[0]=LD_VEC4F(0); float recent_state_inphase = 1; float recent_state_total = 1; @@ -1340,214 +1094,48 @@ void TreephaserSSE::ComputeQVmetrics(BasecallerRead& read) } // compute child path flow states, predicted signal,negative and positive penalties advanceState4(parent, num_flows); - - float penalty[4] = { 0, 0, 0, 0 }; - int called_nuc = -1; + int called_nuc = -1; for(int nuc = 0; nuc < 4; ++nuc) { - PathRec RESTRICT_PTR child = children[nuc]; if (nuc_int_to_char[nuc] == flow_order_[solution_flow]) called_nuc = nuc; - child->flow = min(ad_Idx.A[nuc], flow_order_.num_flows()); - child->window_end = min(ad_End.A[nuc], flow_order_.num_flows()); - child->window_start = min(ad_Beg.A[nuc], child->window_end); - - // Apply easy termination rules - if (child->flow >= num_flows || parent->last_hp >= MAX_HPXLEN ) { - penalty[nuc] = 25; // Mark for deletion - continue; - } - - // pointer in the ad_Buf buffer pointing at the running sum of positive residuals at start of parent window -// char RESTRICT_PTR pn = ad_Buf+nuc*4+(AD_NRES_OFS-16)-parent->window_start*16; - - // sum of squared residuals for positive residuals for flows < child->flow - float penPar = pres_Buf[child->flow-parent->window_start].A[nuc];// *((float RESTRICT_PTR)(ad_Buf+nuc*4+(AD_PRES_OFS)+(child->flow-parent->window_start-1)*16)); - - // sum of squared residuals for negative residuals for flows < child->window_end - float penNeg = nres_Buf[child->window_end-parent->window_start].A[nuc];// *((float RESTRICT_PTR)(ad_Buf+nuc*4+AD_NRES_OFS+(child->window_end-parent->window_start-1)*16)); - - penalty[nuc] = penPar + penNeg; } - // find current incorporating base - assert(called_nuc > -1); - assert(children[called_nuc]->flow == solution_flow); - - PathRec RESTRICT_PTR childToKeep = children[called_nuc]; - //copy -// char RESTRICT_PTR p = ad_Buf+ called_nuc*4 + AD_STATE_OFS; - - recent_state_total = 0; - for(int i = parent->window_start, j = 1, e = childToKeep->window_end; i < e; ++i, j ++) { - childToKeep->state[i] = state_Buf[j].A[called_nuc];// *((float*)(p+j*16)); - childToKeep->pred[i] = pred_Buf[j].A[called_nuc];// *((float*)(p+j*16+(AD_PRED_OFS-AD_STATE_OFS))); - recent_state_total += childToKeep->state[i]; + for(int i = parent->window_start, e = winStart_Buf[called_nuc]; i < e; ++i) { + parent->pred[i] = parent->pred_Buf[i][called_nuc]; } - //sse implementation with aligned memory; no gain as the number of elements to be summed up is small -// recent_state_total = vecSumSSE(state_Buf, countStates); - copySSE(childToKeep->pred, parent->pred, parent->window_start << 2); - - if (childToKeep->flow == parent->flow) - childToKeep->last_hp = parent->last_hp + 1; + if (flow_Buf[called_nuc] == parent->flow) + parent->last_hp = parent->last_hp + 1; else - childToKeep->last_hp = 1; + parent->last_hp = 1; - recent_state_inphase = childToKeep->state[solution_flow]; + recent_state_inphase = parent->state[solution_flow][called_nuc]; // Get delta penalty to next best solution read.penalty_mismatch[base] = -1; // min delta penalty to earlier base hypothesis read.penalty_residual[base] = 0; if (solution_flow - parent->window_start > 0) - read.penalty_residual[base] = penalty[called_nuc] / (solution_flow - parent->window_start); + read.penalty_residual[base] = penParV[called_nuc] / (solution_flow - parent->window_start); for (int nuc = 0; nuc < 4; ++nuc) { if (nuc == called_nuc) continue; - float penalty_mismatch = penalty[called_nuc] - penalty[nuc]; + float penalty_mismatch = penParV[called_nuc] - penParV[nuc]; read.penalty_mismatch[base] = max(read.penalty_mismatch[base], penalty_mismatch); } - // Called state is the starting point for next base - PathRec RESTRICT_PTR swap = parent; - parent = children[called_nuc]; - children[called_nuc] = swap; + parent->flow = min((int)(flow_Buf[called_nuc]), flow_order_.num_flows()); + parent->window_end = min((int)(winEnd_Buf[called_nuc]), flow_order_.num_flows()); + parent->window_start = min((int)(winStart_Buf[called_nuc]), parent->window_end); + parent->nuc=called_nuc; } read.state_inphase[solution_flow] = max(recent_state_inphase, 0.01f); - read.state_total[solution_flow] = max(recent_state_total, 0.01f); - } - - if(recalibrate_predictions_) { - RecalibratePredictions(parent); - ResetRecalibrationStructures(num_flows_); } - setZeroSSE(&read.prediction[0], num_flows_*sizeof(float)); - copySSE(&read.prediction[0], parent->pred, parent->window_end*sizeof(float)); -} - - -void TreephaserSSE::ComputeQVmetrics_flow(BasecallerRead& read, vector& flow_to_base, const bool flow_predictors_,const bool flow_quality) -{ - static const char nuc_int_to_char[5] = "ACGT"; - int num_flows = flow_order_.num_flows(); - read.state_inphase.assign(num_flows, 1); - read.state_total.assign(num_flows, 1); - - if (read.sequence.empty()) - return; - int num_bases = read.sequence.size(); - read.penalty_mismatch.assign(num_bases, 0); - read.penalty_residual.assign(num_bases, 0); - if (flow_predictors_ || flow_quality) { - read.penalty_mismatch_flow.assign(num_flows, 0); - read.penalty_residual_flow.assign(num_flows, 0); + for(int i = parent->window_start, e = parent->window_end; i < e; ++i) { + parent->pred[i] = parent->pred_Buf[i][parent->nuc]; } - PathRec RESTRICT_PTR parent = sv_PathPtr[0]; - PathRec RESTRICT_PTR children[4] = {sv_PathPtr[1], sv_PathPtr[2], sv_PathPtr[3], sv_PathPtr[4]}; - parent->flow = 0; - parent->window_start = 0; - parent->window_end = 1; - parent->res = 0.0f; - parent->metr = 0.0f; - parent->flowMetr = 0.0f; - parent->dotCnt = 0; - parent->state[0] = 1.0f; - parent->sequence_length = 0; - parent->last_hp = 0; - parent->pred[0] = 0.0f; - - float recent_state_inphase = 1; - float recent_state_total = 1; - - // main loop for base calling - for (int solution_flow = 0, base = 0; solution_flow < num_flows; ++solution_flow) { - for (; basecalib_A[parent->flow] = (*As_).at(parent->flow).at(flow_order_.int_at(parent->flow)).at(parent->last_hp); - parent->calib_B[parent->flow] = (*Bs_).at(parent->flow).at(flow_order_.int_at(parent->flow)).at(parent->last_hp); - } - // compute child path flow states, predicted signal,negative and positive penalties - advanceState4(parent, num_flows); - - float penalty[4] = { 0, 0, 0, 0 }; - int called_nuc = -1; - for(int nuc = 0; nuc < 4; ++nuc) { - PathRec RESTRICT_PTR child = children[nuc]; - if (nuc_int_to_char[nuc] == flow_order_[solution_flow]) - called_nuc = nuc; - child->flow = min(ad_Idx.A[nuc], flow_order_.num_flows()); - child->window_end = min(ad_End.A[nuc], flow_order_.num_flows()); - child->window_start = min(ad_Beg.A[nuc], child->window_end); - - // Apply easy termination rules - if (child->flow >= num_flows || parent->last_hp >= MAX_HPXLEN ) { - penalty[nuc] = 25; // Mark for deletion - continue; - } - - // pointer in the ad_Buf buffer pointing at the running sum of positive residuals at start of parent window -// char RESTRICT_PTR pn = ad_Buf+nuc*4+(AD_NRES_OFS-16)-parent->window_start*16; - - // sum of squared residuals for positive residuals for flows < child->flow - float penPar = pres_Buf[child->flow-parent->window_start].A[nuc];// *((float RESTRICT_PTR)(ad_Buf+nuc*4+(AD_PRES_OFS)+(child->flow-parent->window_start-1)*16)); - - // sum of squared residuals for negative residuals for flows < child->window_end - float penNeg = nres_Buf[child->window_end-parent->window_start].A[nuc];// *((float RESTRICT_PTR)(ad_Buf+nuc*4+AD_NRES_OFS+(child->window_end-parent->window_start-1)*16)); - - penalty[nuc] = penPar + penNeg; - } - - // find current incorporating base - assert(called_nuc > -1); - assert(children[called_nuc]->flow == solution_flow); - - PathRec RESTRICT_PTR childToKeep = children[called_nuc]; - //copy -// char RESTRICT_PTR p = ad_Buf+ called_nuc*4 + AD_STATE_OFS; - - recent_state_total = 0; - for(int i = parent->window_start, j = 1, e = childToKeep->window_end; i < e; ++i, j ++) { - childToKeep->state[i] = state_Buf[j].A[called_nuc];// *((float*)(p+j*16)); - childToKeep->pred[i] = pred_Buf[j].A[called_nuc];// *((float*)(p+j*16+(AD_PRED_OFS-AD_STATE_OFS))); - recent_state_total += childToKeep->state[i]; - } - //sse implementation with aligned memory; no gain as the number of elements to be summed up is small -// recent_state_total = vecSumSSE(state_Buf, countStates); - - copySSE(childToKeep->pred, parent->pred, parent->window_start << 2); - - if (childToKeep->flow == parent->flow) - childToKeep->last_hp = parent->last_hp + 1; - else - childToKeep->last_hp = 1; - - recent_state_inphase = childToKeep->state[solution_flow]; - - // Get delta penalty to next best solution - read.penalty_mismatch[base] = -1; // min delta penalty to earlier base hypothesis - read.penalty_residual[base] = 0; - - if (solution_flow - parent->window_start > 0) - read.penalty_residual[base] = penalty[called_nuc] / (solution_flow - parent->window_start); - - for (int nuc = 0; nuc < 4; ++nuc) { - if (nuc == called_nuc) - continue; - float penalty_mismatch = penalty[called_nuc] - penalty[nuc]; - read.penalty_mismatch[base] = max(read.penalty_mismatch[base], penalty_mismatch); - } - - // Called state is the starting point for next base - PathRec RESTRICT_PTR swap = parent; - parent = children[called_nuc]; - children[called_nuc] = swap; - } - read.state_inphase[solution_flow] = max(recent_state_inphase, 0.01f); - read.state_total[solution_flow] = max(recent_state_total, 0.01f); - } - if (flow_predictors_ || flow_quality) { //if (flow_predictors_) //vector flows_to_proc; for (int solution_flow = 0; solution_flow < num_flows; ++solution_flow) { @@ -1556,30 +1144,15 @@ void TreephaserSSE::ComputeQVmetrics_flow(BasecallerRead& read, vector& fl // copy from what's stored in read.penalty_mismatch[base] read.penalty_mismatch_flow[solution_flow] = read.penalty_mismatch[curr_base]; read.penalty_residual_flow[solution_flow] = read.penalty_residual[curr_base]; - /* - int nFlows = flows_to_proc.size(); - if (nFlows>0) { - for (int i=0; ipred, parent->window_end*sizeof(float)); + memset_F(&read.prediction[parent->window_end], 0, num_flows_-parent->window_end); + memcpy_F(&read.prediction[0], &parent->pred[0], parent->window_end); } diff --git a/Analysis/BaseCaller/TreephaserVEC.h b/Analysis/BaseCaller/TreephaserVEC.h index 8e64119f..ddf83e72 100644 --- a/Analysis/BaseCaller/TreephaserVEC.h +++ b/Analysis/BaseCaller/TreephaserVEC.h @@ -1,7 +1,7 @@ /* Copyright (C) 2012 Ion Torrent Systems, Inc. All Rights Reserved */ -#ifndef TREEPHASERSSE_H -#define TREEPHASERSSE_H +#ifndef TREEPHASERVEC_H +#define TREEPHASERVEC_H #include "DPTreephaser.h" @@ -46,47 +46,72 @@ // MAX_STEPS set large enough to handle minimum window size #define MAX_STEPS (1+(MAX_VALS/DPTreephaser::kMinWindowSize_)) #define MAX_PATHS 8 +#define NUM_SAVED_PATHS 4 +#define NUM_BEST_PATH 1 +#define MAX_ACT_PATHS (MAX_PATHS+NUM_BEST_PATH+NUM_SAVED_PATHS) +#define BEST_PATH MAX_PATHS +#define SAVED_PATHS (MAX_PATHS+NUM_BEST_PATH) #define MAX_PATH_DELAY 40 //#pragma pack(push, 1) -struct __attribute__((packed)) ALIGN(64) PathRec { +struct __attribute__((packed)) ALIGN(64) PathRecV { int flow; int window_start; int window_end; float res; float metr; float flowMetr; - int dotCnt; + float newSignal; float penalty; - float state[MAX_VALS] ALIGN(64); - float pred[MAX_VALS] ALIGN(64); - char sequence[2*MAX_VALS + 12]; // +12 makes the enitre struct align well - int sequence_length; int last_hp; int nuc; + float dist; + + // cache entries + int saved; + int cached_flow; + int cached_flow_ws; + int cached_flow_seq; + + // per-flow metrics + v4f state[MAX_VALS] ALIGN(64); + float pred[MAX_VALS] ALIGN(64); + v4f pred_Buf[MAX_VALS] ALIGN(64); float calib_A[MAX_VALS] ALIGN(64); float calib_B[MAX_VALS] ALIGN(64); float state_inphase[MAX_VALS] ALIGN(64); + + // per-basse metrics + int sequence_length; + char sequence[2*MAX_VALS + 12]; // +12 makes the entire struct align well }; //#pragma pack(pop) -class TreephaserSSE { +class TreephaserVEC { public: //! @brief Default constructor - TreephaserSSE(); + TreephaserVEC(); //! @brief Constructor //! @param[in] flow_order Flow order object //! @param[in] windowSize Size of the normalization window to use. - TreephaserSSE(const ion::FlowOrder& flow_order, const int windowSize); + TreephaserVEC(const ion::FlowOrder& flow_order, const int windowSize); //! @brief Set flow order and initialize internal variables //! @param[in] flow_order Flow order object void SetFlowOrder(const ion::FlowOrder& flow_order); + void SetBadPathLimit(int bad_path_limit){bad_path_limit_=bad_path_limit;} + + void SetManyPathLimit(int many_path_limit){many_path_limit_=many_path_limit;} + + void SetInitalPaths(int initial_paths){initial_paths_=initial_paths;} + + void SetMaxMetrDiff(float max_metr_diff){max_metr_diff_=max_metr_diff;} + //! @brief Set the normalization window size //! @param[in] windowSize Size of the normalization window to use. inline void SetNormalizationWindowSize(const int windowSize) { windowSize_ = max(DPTreephaser::kMinWindowSize_, min(windowSize, DPTreephaser::kMaxWindowSize_));} @@ -102,8 +127,8 @@ class TreephaserSSE { //! @brief Iterative solving and normalization routine void NormalizeAndSolve(BasecallerRead& read); - PathRec* parent; - int best; +// PathRecV* parent; +// int best; //! @brief Set pointers to recalibration model bool SetAsBs(const vector > > *As, const vector > > *Bs){ @@ -132,55 +157,76 @@ class TreephaserSSE { //! @brief Perform a more advanced simulation to generate QV predictors void ComputeQVmetrics(BasecallerRead& read); - void ComputeQVmetrics_flow(BasecallerRead& read, vector& flow_to_base, const bool flow_predictors_=false); + void ComputeQVmetrics_flow(BasecallerRead& read, vector& flow_to_base, const bool flow_predictors_=false, const bool flow_quality = false); int nuc_char_to_int(char nuc) {if (nuc=='A') return 0; if (nuc=='C') return 1; if (nuc=='G') return 2; if (nuc=='T') return 3; return -1;} protected: - inline void CalcResidualI(PathRec RESTRICT_PTR parent, + inline void CalcResidualI(PathRecV RESTRICT_PTR parent, int flow, int j, v4f &rS, v4f rTemp1s_, v4f &rPenNeg, v4f &rPenPos); + inline v4i CheckWindowStartBase(v4i rBeg, v4i rParNuc, int flow, v4f rS); + inline void CheckWindowStart1(v4i & rBeg, v4i rParNuc, int flow, v4f rS); + inline void CheckWindowStart2(v4i & rBeg, v4i rParNuc, int flow, v4f rS, v4i rEnd); + inline void CheckWindowEnd(v4i rBeg, v4i rParNuc, int flow, v4f & rS, v4i & rEnd, v4f rAlive, v4i rFlowEnd); + inline void advanceI( float parentState, int j, v4i rParNuc, v4f ts_tr, v4f & rAlive, v4f & rS); + inline void advanceE(int j, v4i rParNuc, v4f ts_tr, v4f & rAlive, v4f & rS); + void catchup (PathRecV RESTRICT_PTR parent,PathRecV RESTRICT_PTR best, int begin_flow, int end_flow); + //! @brief Solving a read - bool Solve(int begin_flow, int end_flow); + bool Solve(int begin_flow, int end_flow, int save_flow, int numActivePaths, float maxMetrDiff); //! @brief Normalizing a read + PathRecV *sortPaths(int & pathCnt, int &parentPathIdx, int & badPaths, int numAcitvePaths); + float computeParentDist(PathRecV RESTRICT_PTR parent, int end_flow); + void CopyPath(PathRecV RESTRICT_PTR dest, PathRecV RESTRICT_PTR parent, + PathRecV RESTRICT_PTR child, int saveFlow, int &numSaved, + int cached_flow, int cached_flow_ws, int cached_flow_seq); + void CopyPathNew(PathRecV RESTRICT_PTR dest, PathRecV RESTRICT_PTR parent, + PathRecV RESTRICT_PTR child, int saveFlow, int &numSaved, + int cached_flow, int cached_flow_ws, int cached_flow_seq); + void CopyPathDeep(PathRecV RESTRICT_PTR dest, PathRecV RESTRICT_PTR src); void WindowedNormalize(BasecallerRead& read, int step); //! @brief Make recalibration changes to predictions explicitly visible - void RecalibratePredictions(PathRec *maxPathPtr); + void RecalibratePredictions(PathRecV *maxPathPtr); //! @brief Resetting recalibration data structure void ResetRecalibrationStructures(int num_flows); //! @brief Initialize floating point array variables with a value - void InitializeVariables(float init_val); + void InitializeVariables(); void sumNormMeasures(); - void advanceState4(PathRec RESTRICT_PTR parent, int end); - void advanceStateInPlace(PathRec RESTRICT_PTR path, int nuc, int end); + void advanceState4(PathRecV RESTRICT_PTR parent, int end); + void advanceStateInPlace(PathRecV RESTRICT_PTR path, int nuc, int end, int end_flow); + inline float CalcNewSignal(int nuc, PathRecV RESTRICT_PTR parent); // There was a small penalty in making these arrays class members, as opposed to static variables - ALIGN(64) short ts_NextNuc[4][MAX_VALS]; - ALIGN(64) float ts_Transition[4][MAX_VALS]; - ALIGN(64) v4i_u ts_NextNuc4[MAX_VALS]; - ALIGN(64) v4f_u ts_Transition4[MAX_VALS]; + ALIGN(64) v4i ts_NextNuc[MAX_VALS]; + ALIGN(64) v4f ts_Transition[MAX_VALS]; ALIGN(64) float rd_NormMeasure[MAX_VALS]; + ALIGN(64) float rd_NormMeasureAdj[MAX_VALS]; + ALIGN(64) float rd_SqNormMeasureSum[MAX_VALS]; - ALIGN(64) PathRec sv_pathBuf[MAX_PATHS+1]; + ALIGN(64) PathRecV sv_pathBuf[MAX_ACT_PATHS]; ALIGN(64) float ft_stepNorms[MAX_STEPS]; - ALIGN(64) v4f_u ad_MinFrac; - ALIGN(16) v4i_u ad_FlowEnd; - ALIGN(16) v4i_u ad_Idx; - ALIGN(16) v4i_u ad_End; - ALIGN(16) v4i_u ad_Beg; - ALIGN(64)v4f_u state_Buf[MAX_VALS+1]; - ALIGN(64)v4f_u pred_Buf[MAX_VALS+1]; - ALIGN(64)v4f_u nres_Buf[MAX_VALS+1]; - ALIGN(64)v4f_u pres_Buf[MAX_VALS+1]; + ALIGN(16) v4i ad_FlowEnd; + ALIGN(16) v4i flow_Buf; + ALIGN(16) v4i winEnd_Buf; + ALIGN(16) v4i winStart_Buf; + ALIGN(64)v4f nres_WE; + ALIGN(64)v4f pres_WE; + ALIGN(64)v4f metrV={0,0,0,0}; + ALIGN(64)v4f penParV={0,0,0,0}; + ALIGN(64)v4f penNegV={0,0,0,0}; + ALIGN(64)v4f resV={0,0,0,0}; + ALIGN(64)v4f distV={0,0,0,0}; + ion::FlowOrder flow_order_; //!< Sequence of nucleotide flows - PathRec *sv_PathPtr[MAX_PATHS+1]; + PathRecV *sv_PathPtr[MAX_ACT_PATHS]; int ad_Adv; int num_flows_; int ts_StepCnt; @@ -197,7 +243,11 @@ class TreephaserSSE { bool recalibrate_predictions_; //!< Switch to use recalibration model during metric generation bool skip_recal_during_normalization_; //!< Switch to skip recalibration during the normalization phase bool state_inphase_enabled_; //!< Switch to save inphase population of molecules + int bad_path_limit_; //!< number of dead end paths before aborting + int many_path_limit_; //!< number of >3 path decisions before aborting + int initial_paths_; //!< number of initial max paths to use in solve + float max_metr_diff_; //!< maximum metric difference to create a branch }; -#endif // TREEPHASERSSE_H +#endif // TREEPHASERVEC_H diff --git a/Analysis/BkgModel/Fitters/Complex/MultiLevMar.cpp b/Analysis/BkgModel/Fitters/Complex/MultiLevMar.cpp index c4419b1f..a3ed717b 100644 --- a/Analysis/BkgModel/Fitters/Complex/MultiLevMar.cpp +++ b/Analysis/BkgModel/Fitters/Complex/MultiLevMar.cpp @@ -196,9 +196,9 @@ int MultiFlowLevMar::MultiFlowSpecializedLevMarFitParametersOnlyRegion ( total_iter++; } } - if (lm_state.region_success_step<1){ - printf("No successes: MultiFlowSpecializedLevMarFitParametersOnlyRegion in region(col=%d,row=%d)\n", bkg.region_data->region->col, bkg.region_data->region->row); - } +// if (lm_state.region_success_step<1){ +// printf("No successes: MultiFlowSpecializedLevMarFitParametersOnlyRegion in region(col=%d,row=%d)\n", bkg.region_data->region->col, bkg.region_data->region->row); +// } CleanTerminateOptimization(); return ( total_iter ); } @@ -510,8 +510,8 @@ void MultiFlowLevMar::LevMarFitRegion ( else { cont_proc = lm_state.IncreaseRegionStep(); - if (cont_proc) - printf ( "LevMarFitRegion: Reached max lambda %f in region(col=%d,row=%d):\n", lm_state.reg_lambda,bkg.region_data->region->col, bkg.region_data->region->row); +//if (cont_proc) +// printf ( "LevMarFitRegion: Reached max lambda %f in region(col=%d,row=%d):\n", lm_state.reg_lambda,bkg.region_data->region->col, bkg.region_data->region->row); } } else diff --git a/Analysis/BkgModel/Fitters/FitExpDecay.h b/Analysis/BkgModel/Fitters/FitExpDecay.h index 0d0ab8b5..7ebee399 100755 --- a/Analysis/BkgModel/Fitters/FitExpDecay.h +++ b/Analysis/BkgModel/Fitters/FitExpDecay.h @@ -70,10 +70,22 @@ class FitExpDecay : public LevMarFitterV2 protected: virtual void Evaluate(float *y, float *params) { - memset(y,0,sizeof(float[npts])); - - for (int i=i_start;i < i_end;i++) - y[i] = params[0]*ExpApprox(-(xvals[i]-xvals[i_start])/params[1]) + params[2]; + float param0=params[0]; + float param1=params[1] * 256.0f; + float param2=params[2]; + float startVal=1.0f + xvals[i_start]/param1; + int i=0; + for(;i #include "MathUtil.h" +#include "Vecs.h" // shielding layer to insulate from choice @@ -119,19 +120,19 @@ void MathModel::UnsignedParallelSimpleComputeCumulativeIncorporationHydrogens ( int i; int common_start; - float totocc[FLOW_STEP], totgen[FLOW_STEP]; - float pact[FLOW_STEP],pact_new[FLOW_STEP]; - float c_dntp_top[FLOW_STEP], c_dntp_bot[FLOW_STEP]; - float hplus_events_sum[FLOW_STEP], hplus_events_current[FLOW_STEP]; // mean events per molecule, cumulative and current - float enzyme_dt[FLOW_STEP]; - float Aint[FLOW_STEP]; + v4f totocc, totgen; + v4f pact,pact_new=LD_VEC4F(0); + v4f c_dntp_top, c_dntp_bot; + v4f hplus_events_sum, hplus_events_current; // mean events per molecule, cumulative and current + v4f enzyme_dt; + v4f Aint; // A a pointer, so isolate by copying for (int q=0;q 0.0f) - { - // cannot accelerate here because half_kr is distinct per - for (int q=0; q 0.0f);st++) // someone needs computation - { - // update top of well concentration in the bulk for FLOW_STEP flows - for (int q=0; q 0.0f) + { + // cannot accelerate here because half_kr is distinct per + enzyme_dt = deltaFrameSeconds[i]*half_kr; + +// for (int st=1; (st <= SUB_STEPS) && (sum_totgen > 0.0f);st++) // someone needs computation + { + // update top of well concentration in the bulk for 4 flows + for (int q=0; q<4; q++) + c_dntp_top[q] = nuc_rise_ptr[q][c_dntp_top_ndx]; + c_dntp_top_ndx += 1; + + // assume instantaneous equilibrium within the well + c_dntp_bot = c_dntp_top/ (1.0f+ scaled_kr*pact*c_dntp_bot_plus_kmax); // the level at which new nucs are used up as fast as they diffuse in + c_dntp_bot_plus_kmax = 1.0f/ (c_dntp_bot + kmaxV); // scale for michaelis-menten kinetics, assuming nucs are limiting factor + + // Now compute effect of concentration on enzyme rate + c_dntp_old_effect = c_dntp_new_effect; + c_dntp_new_effect = c_dntp_bot*c_dntp_bot_plus_kmax; // current effect of concentration on enzyme rate + + // update events per molecule + hplus_events_current = enzyme_dt* (c_dntp_new_effect+c_dntp_old_effect); // events per molecule is average rate * time of rate + hplus_events_sum += hplus_events_current; + + // how many active molecules left at end of time period given poisson process with total intensity of events + for (int q=0; q<4; q++) + pact_new[q] = mix_memo[q].GetStep ((float)hplus_events_sum[q]); + + + // how many hplus were generated + totgen -= ( (pact+pact_new) * 0.5f) * hplus_events_current; // active molecules * events per molecule + pact = pact_new; + totgen = __builtin_ia32_maxps (totgen,(v4f){0,0,0,0}); + // or is there a "max" within command? + sum_totgen = 0.0f; + for (int q=0; q<4; q++) + sum_totgen += totgen[q]; + } + + } + v4f tmptot=totocc-totgen; + for (int q=0; q<4; q++) + ival_offset[q][i] = tmptot[q]; } } - // try to simplify void MathModel::SimplifyComputeCumulativeIncorporationHydrogens ( float *ival_offset, int npts, const float *deltaFrameSeconds, diff --git a/Analysis/BkgModel/MathModel/MathOptim.h b/Analysis/BkgModel/MathModel/MathOptim.h index 35d5986d..378f7668 100644 --- a/Analysis/BkgModel/MathModel/MathOptim.h +++ b/Analysis/BkgModel/MathModel/MathOptim.h @@ -138,7 +138,7 @@ float ErfApprox ( float x ); float Expm2Approx ( float x ); inline float ExpApprox ( float x ) { - x = 1.0 + x / 256.0; + x = 1.0f + x / 256.0f; x *= x; x *= x; x *= x; x *= x; x *= x; x *= x; x *= x; x *= x; return x; diff --git a/Analysis/BkgModel/RegionalizedData.cpp b/Analysis/BkgModel/RegionalizedData.cpp index dd2497fa..d81a1fd3 100644 --- a/Analysis/BkgModel/RegionalizedData.cpp +++ b/Analysis/BkgModel/RegionalizedData.cpp @@ -372,9 +372,9 @@ void RegionalizedData::PickRepresentativeHighQualityWells (float copy_stringency my_beads.LowCopyBeadsAreLowQuality (final_filter, top_filter); int test_sampled = my_beads.NumberSampled(); - printf("DEBUGFILTER: %d %d %d %d %f %f %f %f %f %f %f %f\n", region->index, test_sampled, num_sampled, my_beads.numLBeads, - min_percentage, max_percentage, robust_filter, stringent_filter, final_filter, top_filter, - low_filter, high_filter); +// printf("DEBUGFILTER: %d %d %d %d %f %f %f %f %f %f %f %f\n", region->index, test_sampled, num_sampled, my_beads.numLBeads, +// min_percentage, max_percentage, robust_filter, stringent_filter, final_filter, top_filter, +// low_filter, high_filter); // should check if not enough beads and rebuild filter if we fail diff --git a/Analysis/BkgModel/Sampling/FitDensity.cpp b/Analysis/BkgModel/Sampling/FitDensity.cpp index 57bebc7e..bcb932b3 100644 --- a/Analysis/BkgModel/Sampling/FitDensity.cpp +++ b/Analysis/BkgModel/Sampling/FitDensity.cpp @@ -96,13 +96,9 @@ void FitDensity::kdensity(vector const& dat, vector &density, ve k++; } } - vector rowIndex(n,0); - for (int i=0; iRefinePerFlowTimeEstimate ( region_data->my_regions.rp.nuc_shape.t_mid_nuc_shift_per_flow, flow_block_size, flow_block_start ); // adjust buffering for every bead using specialized fitter - refine_buffering->AdjustBufferingEveryBead(flow_block_size, flow_block_start); +//MARK + if (inception_state->bkg_control.gpuControl.gpuWorkLoad == 0) + refine_buffering->AdjustBufferingEveryBead(flow_block_size, flow_block_start); // Set things up for double exponential smoothing. region_data->my_regions.tmidnuc_smoother.Initialize( & region_data->my_regions.rp ); @@ -1005,7 +1007,7 @@ void SignalProcessingMasterFitter::RegionalFittingForLaterFlowBlock( int flow_ke region_data->my_regions.tmidnuc_smoother.Smooth( & region_data->my_regions.rp ); region_data->my_regions.copy_drift_smoother.Smooth( & region_data->my_regions.rp ); region_data->my_regions.ratio_drift_smoother.Smooth( & region_data->my_regions.rp ); - +// MARK refine_time_fit->RefinePerFlowTimeEstimate ( region_data->my_regions.rp.nuc_shape.t_mid_nuc_shift_per_flow, flow_block_size, flow_block_start ); } @@ -1014,7 +1016,12 @@ void SignalProcessingMasterFitter::RefineAmplitudeEstimates ( double &elapsed_ti // in either case, finish by fitting amplitude to finalized regional parameters region_data->SetFineEmphasisVectors(); fit_timer.restart(); - refine_fit->FitAmplitudePerFlow ( flow_block_size, flow_block_start ); + + //MARK + //my_search.ParasitePointers ( math_poiss, ®ion_data->my_trace,region_data->emptytrace,®ion_data->my_scratch,region_data_extras.cur_bead_block, region_data_extras.cur_buffer_block, & ( region_data->my_regions ),®ion_data->time_c, + // region_data_extras.my_flow,®ion_data->emphasis_data ); + + refine_fit->FitAmplitudePerFlow ( flow_block_size, flow_block_start/*(, my_search*/); double fit_ampl_time = fit_timer.elapsed(); elapsed_time += fit_ampl_time; if ( ( my_debug.region_trace_file != NULL ) && ( my_debug.region_only_trace_file != NULL ) ) diff --git a/Analysis/CMakeLists.txt b/Analysis/CMakeLists.txt index ccca6e6f..fb1c86a7 100644 --- a/Analysis/CMakeLists.txt +++ b/Analysis/CMakeLists.txt @@ -1,5 +1,5 @@ # Copyright (C) 2010 Ion Torrent Systems, Inc. All Rights Reserved -cmake_minimum_required (VERSION 2.6) +cmake_minimum_required (VERSION 2.8.12) file(STRINGS "project_name.txt" PROJECT_NAME_TXT) list(GET PROJECT_NAME_TXT 0 PROJECT_NAME) project (${PROJECT_NAME}) @@ -338,6 +338,11 @@ add_dependencies(Crop IONVERSION) target_link_libraries(Crop ion-analysis pthread dl) install(TARGETS Crop DESTINATION bin) +#add_executable(lbTest crop/lbTest.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp) +#add_dependencies(lbTest IONVERSION) +#target_link_libraries(lbTest ion-analysis pthread dl) +#install(TARGETS lbTest DESTINATION bin) + add_executable(ChkDat crop/ChkDat.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp) add_dependencies(ChkDat IONVERSION) target_link_libraries(ChkDat ion-analysis pthread dl) @@ -482,6 +487,8 @@ set(BaseCallerSRCS if("${CMAKE_SYSTEM_PROCESSOR}" STREQUAL "x86_64") list(APPEND BaseCallerSRCS BaseCaller/TreephaserSSE.cpp) + list(APPEND BaseCallerSRCS + BaseCaller/TreephaserVEC.cpp) endif() add_executable(BaseCaller ${BaseCallerSRCS}) @@ -1110,6 +1117,8 @@ install(FILES "${PROJECT_SOURCE_DIR}/config/phredTable.GX5v2.h5" DESTINATION ${I install(FILES "${PROJECT_SOURCE_DIR}/config/phredTable.GX5v2.Recal.h5" DESTINATION ${ION_INSTALL_PREFIX}/config) install(FILES "${PROJECT_SOURCE_DIR}/config/phredTable.GX7v1.h5" DESTINATION ${ION_INSTALL_PREFIX}/config) install(FILES "${PROJECT_SOURCE_DIR}/config/phredTable.GX7v1.Recal.h5" DESTINATION ${ION_INSTALL_PREFIX}/config) +install(FILES "${PROJECT_SOURCE_DIR}/config/phredTable.GX9v1.h5" DESTINATION ${ION_INSTALL_PREFIX}/config) +install(FILES "${PROJECT_SOURCE_DIR}/config/phredTable.GX9v1.Recal.h5" DESTINATION ${ION_INSTALL_PREFIX}/config) install(FILES "${PROJECT_SOURCE_DIR}/config/nnmodel.530.h5" DESTINATION ${ION_INSTALL_PREFIX}/config) install(FILES "${PROJECT_SOURCE_DIR}/config/nnmodel.540.h5" DESTINATION ${ION_INSTALL_PREFIX}/config) install(FILES "${PROJECT_SOURCE_DIR}/config/nnmodel.550.h5" DESTINATION ${ION_INSTALL_PREFIX}/config) @@ -1148,6 +1157,8 @@ install(FILES "${PROJECT_SOURCE_DIR}/config/args_GX5v2_analysis.json" DESTINATIO install(FILES "${PROJECT_SOURCE_DIR}/config/args_GX5v2_beadfind.json" DESTINATION ${ION_INSTALL_PREFIX}/config) install(FILES "${PROJECT_SOURCE_DIR}/config/args_GX7v1_analysis.json" DESTINATION ${ION_INSTALL_PREFIX}/config) install(FILES "${PROJECT_SOURCE_DIR}/config/args_GX7v1_beadfind.json" DESTINATION ${ION_INSTALL_PREFIX}/config) +install(FILES "${PROJECT_SOURCE_DIR}/config/args_GX9v1_analysis.json" DESTINATION ${ION_INSTALL_PREFIX}/config) +install(FILES "${PROJECT_SOURCE_DIR}/config/args_GX9v1_beadfind.json" DESTINATION ${ION_INSTALL_PREFIX}/config) install(FILES "${PROJECT_SOURCE_DIR}/config/args_900_analysis.json" DESTINATION ${ION_INSTALL_PREFIX}/config) install(FILES "${PROJECT_SOURCE_DIR}/config/args_900_beadfind.json" DESTINATION ${ION_INSTALL_PREFIX}/config) install(FILES "${PROJECT_SOURCE_DIR}/config/args_P1.0.19_analysis.json" DESTINATION ${ION_INSTALL_PREFIX}/config) @@ -1209,6 +1220,7 @@ install(FILES "${PROJECT_SOURCE_DIR}/config/gopt_560.param.json" DESTINATION ${I install(FILES "${PROJECT_SOURCE_DIR}/config/gopt_541v2.param.json" DESTINATION ${ION_INSTALL_PREFIX}/config) install(FILES "${PROJECT_SOURCE_DIR}/config/gopt_GX5v2.param.json" DESTINATION ${ION_INSTALL_PREFIX}/config) install(FILES "${PROJECT_SOURCE_DIR}/config/gopt_GX7v1.param.json" DESTINATION ${ION_INSTALL_PREFIX}/config) +install(FILES "${PROJECT_SOURCE_DIR}/config/gopt_GX9v1.param.json" DESTINATION ${ION_INSTALL_PREFIX}/config) # # # @@ -1242,13 +1254,13 @@ install(FILES "${PROJECT_SOURCE_DIR}/config/datasets_calibration.json" DESTINATI install(FILES "${PROJECT_SOURCE_DIR}/config/StructureMetaInfo.json" DESTINATION ${ION_INSTALL_PREFIX}/config) #if(NOT ION_USE_SYSTEM_ARMADILLO) -# install(FILES "${PROJECT_BINARY_DIR}/../armadillo-6.100.0+ion0-install/lib/libarmadillo.so.6" DESTINATION lib) -# install(FILES "${PROJECT_BINARY_DIR}/../armadillo-6.100.0+ion0-install/lib/libarmadillo.so.6.100.0" DESTINATION lib) +# install(FILES "${PROJECT_BINARY_DIR}/../armadillo-6.100.0+ion1-install/lib/libarmadillo.so.6" DESTINATION lib) +# install(FILES "${PROJECT_BINARY_DIR}/../armadillo-6.100.0+ion1-install/lib/libarmadillo.so.6.100.0" DESTINATION lib) #endif() -install(PROGRAMS "${PROJECT_BINARY_DIR}/../htslib-1.2.1+ion0/tabix" DESTINATION bin) -install(PROGRAMS "${PROJECT_BINARY_DIR}/../htslib-1.2.1+ion0/bgzip" DESTINATION bin) -install(PROGRAMS "${PROJECT_BINARY_DIR}/../samtools-1.2+ion2/samtools" DESTINATION bin) +install(PROGRAMS "${PROJECT_BINARY_DIR}/../htslib-1.2.1+ion2/tabix" DESTINATION bin) +install(PROGRAMS "${PROJECT_BINARY_DIR}/../htslib-1.2.1+ion2/bgzip" DESTINATION bin) +install(PROGRAMS "${PROJECT_BINARY_DIR}/../samtools-1.2+ion4/samtools" DESTINATION bin) add_test("trimfastq.pl" "perl" "-cw" "${PROJECT_SOURCE_DIR}/trimfastq.pl") install(PROGRAMS "${PROJECT_SOURCE_DIR}/trimfastq.pl" DESTINATION bin) diff --git a/Analysis/DataViewer/AlignmentSpatial.cpp b/Analysis/DataViewer/AlignmentSpatial.cpp index 2f2ee35a..3474e305 100644 --- a/Analysis/DataViewer/AlignmentSpatial.cpp +++ b/Analysis/DataViewer/AlignmentSpatial.cpp @@ -257,6 +257,7 @@ float AlignmentSpatial::Get_Data(int frame, int y, int x) void AlignmentSpatial::CustomTracePlotAdder(double &xmin, double &xmax, double &ymin, double &ymax) { static QCPItemText *seqText[MAX_NUM_TRACES]={NULL}; + static QCPItemText *seqText2[MAX_NUM_TRACES]={NULL}; if(ymin > -0.5) ymin=-0.5; if(ymax < 5) @@ -267,7 +268,7 @@ void AlignmentSpatial::CustomTracePlotAdder(double &xmin, double &xmax, double & for(int trc=0;trcsetFont(myfont); seqText[trc]->setPositionAlignment(Qt::AlignLeft|Qt::AlignVCenter); } + if(seqText2[trc] == NULL){ + //QPen qp; + + uint xcolorIdx= trc*ColormapSize/MAX_NUM_TRACES; + uint xcolor=colormap[xcolorIdx % ColormapSize]; + + //qp.setColor(QColor(qRed(xcolor),qGreen(xcolor),qBlue(xcolor))); + QFont myfont("QFont::Courier", 7); + myfont.setStyleHint(QFont::TypeWriter); + + seqText2[trc] = new QCPItemText(_mTracePlot); + _mTracePlot->addItem(seqText2[trc]); + seqText2[trc]->setColor(QColor(qRed(xcolor),qGreen(xcolor),qBlue(xcolor))); + seqText2[trc]->setFont(myfont); + seqText2[trc]->setPositionAlignment(Qt::AlignLeft|Qt::AlignVCenter); + } seqText[trc]->position->setCoords(x_coord, y_coord); + seqText2[trc]->position->setCoords(x_coord, y_coord+30); + //printf("%s: setting text to %s",__FUNCTION__,SequenceAlignedBasesOut[idx]); char localStr[250]; - sprintf(localStr,"%s%s:%.200s",(showQueryBases?"QB":"AB"),(SequenceAlignedBasesOut[idx]?"(A)":""),seq); - + sprintf(localStr,"QB:%d:%.200s",strlen(SequenceQueryBasesOut[idx]),SequenceQueryBasesOut[idx]); seqText[trc]->setText(localStr); + sprintf(localStr,"AB:%d:%.200s",strlen(SequenceAlignedBasesOut[idx]),SequenceAlignedBasesOut[idx]); + seqText2[trc]->setText(localStr); + }else{ if(seqText[trc]) seqText[trc]->setText(""); + if(seqText2[trc]) + seqText2[trc]->setText(""); } } } diff --git a/Analysis/DataViewer/DataViewer.pro b/Analysis/DataViewer/DataViewer.pro index d5af7504..ef78a749 100644 --- a/Analysis/DataViewer/DataViewer.pro +++ b/Analysis/DataViewer/DataViewer.pro @@ -1,7 +1,7 @@ QT += widgets core gui printsupport CONFIG += c++11 -INCLUDEPATH += /usr/include/hdf5/serial/ ../ ../file-io/ ../Util/ ../Mask/ ../AnalysisOrg ../TsInputUtil/ ../Wells/ ../Image/ ../../build/bamtools-2.4.0.20150702+git15eadb925f-install/include/bamtools/ ../VariantCaller/Bookkeeping/ ../../external/jsoncpp-src-amalgated0.6.0-rc1/ ../../build/armadillo-6.100.0+ion0/include/ +INCLUDEPATH += /usr/include/hdf5/serial/ ../ ../file-io/ ../Util/ ../Mask/ ../AnalysisOrg ../TsInputUtil/ ../Wells/ ../Image/ ../BaseCaller/ ../../build/bamtools-2.4.0.20150702+git15eadb925f-install/include/bamtools/ ../VariantCaller/Bookkeeping/ ../../external/jsoncpp-src-amalgated0.6.0-rc1/ ../../build/armadillo-6.100.0+ion1/include/ # for 18.04 INCLUDEPATH += /usr/include/bamtools/ @@ -66,9 +66,10 @@ SOURCES = main.cpp \ GainTab.cpp \ AlignmentSpatial.cpp \ modeltab.cpp \ - ../BaseCaller/WellsNormalization.cpp \ + ../Wells/WellsNormalization.cpp \ ../Mask/Mask.cpp \ ../BaseCaller/BaseCallerParameters.cpp \ + ../BaseCaller/ReadClassMap.cpp \ # ../BaseCaller/OrderedDatasetWriter.cpp \ # ../Calibration/FlowAlignment.cpp \ # ../BaseCaller/PhaseEstimator.cpp \ diff --git a/Analysis/DataViewer/RawSpatial.cpp b/Analysis/DataViewer/RawSpatial.cpp index a20b3a4e..85fb009c 100644 --- a/Analysis/DataViewer/RawSpatial.cpp +++ b/Analysis/DataViewer/RawSpatial.cpp @@ -46,6 +46,10 @@ void RawSpatial::SetOption(QString txt, int state) display_blocks = state; else if(txt == "Histogram") display_histogram = state; + else if(txt == "AverageSub") + AverageSubState = state; + else if(txt == "BitsNeeded") + display_bitsNeeded = state; render(); } @@ -165,7 +169,8 @@ void RawSpatial::doConvert(int &loading) (AdvcApplied && !AdvcState) || (stdApplied && !stdState) || (noPCAApplied != noPCAState) || - (lastcurDisplayFlow != curDisplayFlow)){ + (lastcurDisplayFlow != curDisplayFlow) || + (AverageSubApplied != AverageSubState)){ // re-load the image.0...+1 last_fname.clear(); } @@ -242,6 +247,7 @@ void RawSpatial::doConvert(int &loading) ColFlApplied=0; AdvcApplied=0; stdApplied=0; + AverageSubApplied=0; if(endX==0){ startX=0; startY=0; @@ -319,12 +325,42 @@ void RawSpatial::doConvert(int &loading) TakeStdDev(); stdApplied=1; } + if(!AverageSubApplied && AverageSubState){ + // subtract the average signa + SubAverage(); + AverageSubApplied=1; + } + CalculateBitsNeededData(); fflush(stdout); UpdateTraceData(); } } +void RawSpatial::CalculateBitsNeededData() +{ + int frameStride=rows*cols; + + memset(bitsNeededData,0,sizeof(bitsNeededData)); + + for(int frm=1;frm=0;bit--){ + if((1< x(0); + QVector y(0); + for(int bin=0;bingraph(0)->setData(x, y); + } + for(int trc=1;trcgraph(trc)->setName(name); + _mTracePlotSet[trc]=0; + QVector x(0); + QVector y(0); + _mTracePlot->graph(trc)->setData(x, y); + } + } + float ymax=0; + float ymin=1000; + float xmax = maxVal; + float xmin = minVal; + + for(int bin=0;bin ymax) + ymax = hist[bin]; + if(hist[bin] < ymin) + ymin = hist[bin]; + } + + qDebug() << __PRETTY_FUNCTION__ << ": xmin=" << xmin << " xmax=" << xmax << " ymin=" << ymin << " ymax=" << ymax; + _mTraceRange=ymax-ymin; + _mTracePlot->xAxis->setRange(xmin, xmax); + _mTracePlot->yAxis->setRange(ymin, ymax); + _mTracePlot->yAxis->setScaleType(useLog?QCPAxis::stLogarithmic:QCPAxis::stLinear); + + _mTracePlot->replot(); +} void SpatialPlot::UpdateTracePlot() { // plot the data in traces qDebug() << __PRETTY_FUNCTION__ << ": hist=" << display_histogram; - if(display_histogram){ - // just use trace 0 for the histogram - { - QVector x(0); - QVector y(0); - for(int bin=0;bingraph(0)->setData(x, y); - } - for(int trc=1;trcgraph(trc)->setName(name); - _mTracePlotSet[trc]=0; - QVector x(0); - QVector y(0); - _mTracePlot->graph(trc)->setData(x, y); - } - } - float ymax=0; - float ymin=1000; - float xmax = maxPixVal; - float xmin = minPixVal; - - for(int bin=0;bin ymax) - ymax = histData[bin]; - if(histData[bin] < ymin) - ymin = histData[bin]; - } + if(display_bitsNeeded){ + DisplayHistogram(bitsNeededData,sizeof(bitsNeededData)/sizeof(bitsNeededData[0]),0,16,0); - qDebug() << __PRETTY_FUNCTION__ << ": xmin=" << xmin << " xmax=" << xmax << " ymin=" << ymin << " ymax=" << ymax; - _mTraceRange=ymax-ymin; - _mTracePlot->xAxis->setRange(xmin, xmax); - _mTracePlot->yAxis->setRange(ymin, ymax); - _mTracePlot->yAxis->setScaleType(QCPAxis::stLogarithmic); - _mTracePlot->replot(); + }else if(display_histogram){ + DisplayHistogram(histData,sizeof(histData)/sizeof(histData[0]),minPixVal,maxPixVal,1); }else if (traces_len) { diff --git a/Analysis/DataViewer/SpatialPlot.h b/Analysis/DataViewer/SpatialPlot.h index 9f735991..e3215134 100644 --- a/Analysis/DataViewer/SpatialPlot.h +++ b/Analysis/DataViewer/SpatialPlot.h @@ -177,8 +177,19 @@ class SpatialPlot : public QWidget int histMax=0; #define NUM_HIST_BINS 256 int histData[NUM_HIST_BINS]={}; + + int bitsNeededData[16]={}; + int bitsNeededMax=0; + int bitsNeededMin=0; + int display_histogram=0; + int AverageSubState=0; + int lastAverageSub=0; + int AverageSubApplied=0; + + int display_bitsNeeded=0; + protected slots: virtual void updatePixmap(const QImage &image); void zoom(double zoomFactor, double XWeight=0.5, double YWeight=0.5); @@ -189,7 +200,7 @@ protected slots: void axisDoubleClick_traces(QCPAxis *axis, QCPAxis::SelectablePart part, QMouseEvent *event); private: - + void DisplayHistogram(int *hist, int len, int minVal, int maxVal, int useLog); void mousePressEvent(QMouseEvent *); void mouseReleaseEvent(QMouseEvent *); void scroll(int deltaX, int deltaY); diff --git a/Analysis/DataViewer/WellsSpatial.cpp b/Analysis/DataViewer/WellsSpatial.cpp index e4d508e2..93ccc714 100644 --- a/Analysis/DataViewer/WellsSpatial.cpp +++ b/Analysis/DataViewer/WellsSpatial.cpp @@ -1,8 +1,8 @@ /* Copyright (C) 2016 Ion Torrent Systems, Inc. All Rights Reserved */ #include "WellsSpatial.h" #include "RawWells.h" -#include "../BaseCaller/WellsNormalization.h" -#include "../BaseCaller/BaseCallerParameters.h" +#include "WellsNormalization.h" +#include "BaseCallerParameters.h" #include #include @@ -222,7 +222,13 @@ void WellsRdrThread::run() WellsNormalization wells_norm(&bc.flow_order, "default"); - wells_norm.SetWells(&wells, &mMask); + ReadClassMap read_class_map; + std::vector maskNames; + maskNames.push_back(mask_fn); + read_class_map.LoadMaskFiles(maskNames, true); + + + wells_norm.SetWells(&wells, &read_class_map,0); wells.ReadWells(); wells_norm.CorrectSignalBias(bc.keys); wells_norm.DoKeyNormalization(bc.keys); diff --git a/Analysis/Image/Image.cpp b/Analysis/Image/Image.cpp index bf04badc..56dc8cf6 100644 --- a/Analysis/Image/Image.cpp +++ b/Analysis/Image/Image.cpp @@ -320,28 +320,35 @@ double TinyTimer() return ( curT ); } +char FileCacherDummy=0; // to keep the access from being optimized away void Image::JustCacheOneImage(const char *name) { - int totalLen = 0; double startT = TinyTimer(); - char buf[1024 * 1024]; - int len; - - // just read the file in... It will be stored in cache - int fd = open(name, O_RDONLY); - if (fd >= 0) - { - while ((len = read(fd, &buf[0], sizeof(buf))) > 0) - totalLen += len; - close(fd); - } - else - { - printf("failed to open %s\n", name); - } - - CacheAccessTime = TinyTimer()-startT; -// fprintf ( stdout, "File %s cache access = %0.2lf sec. with %d bytes\n", name,stopT - startT,totalLen ); + struct stat statbuf; + stat(name,&statbuf); + int fd = open(name,O_RDONLY,0); + char cntr=0; + if(fd >= 0){ + char *dst; + if ((dst = (char *)mmap (0, statbuf.st_size, PROT_READ, + MAP_SHARED, fd, 0)) == (caddr_t) -1) + assert ("mmap error for output"); + + __off_t addr=0; + while(addr < statbuf.st_size){ + cntr+=dst[addr]; + addr += 4096; + } + FileCacherDummy=cntr; + munmap((void *)dst,statbuf.st_size); + //printf("Done caching %s\n",fname); + close(fd); + }else{ + printf("failed to open %s\n", name); + } + + CacheAccessTime = TinyTimer()-startT; +// fprintf ( stdout, "File %s cache access = %0.2lf sec. with %d bytes\n", name,stopT - startT,statbuf.st_size ); // fflush ( stdout ); } diff --git a/Analysis/Image/Vecs.h b/Analysis/Image/Vecs.h index f9198c4e..675765f7 100644 --- a/Analysis/Image/Vecs.h +++ b/Analysis/Image/Vecs.h @@ -83,6 +83,7 @@ typedef union{ typedef union{ v8i V; + v4i v4[2]; int A[VEC8_SIZE]; }v8i_u; typedef union{ @@ -94,6 +95,7 @@ typedef union{ v8f V; v8f V8[1]; float A[VEC8_SIZE]; + v4f v4[2]; }v8f_u; typedef union{ v8su V; diff --git a/Analysis/MapLab/CMakeLists.txt b/Analysis/MapLab/CMakeLists.txt index 2813662d..68724da5 100644 --- a/Analysis/MapLab/CMakeLists.txt +++ b/Analysis/MapLab/CMakeLists.txt @@ -1,5 +1,5 @@ # Copyright (C) 2015 Thermo Fisher Scientific. All Rights Reserved. -cmake_minimum_required (VERSION 2.6) +cmake_minimum_required (VERSION 2.8.12) project (MapLab) @@ -17,6 +17,7 @@ add_subdirectory (context_align) add_subdirectory (tmap_samtools_lib) add_subdirectory (tmap_lib) add_subdirectory (tmap_lib_test) +add_subdirectory (tmap_lib_unit_tests) add_subdirectory (cigar_man_lib) add_subdirectory (cigar_man_lib_test) diff --git a/Analysis/MapLab/cigar_man_lib/CMakeLists.txt b/Analysis/MapLab/cigar_man_lib/CMakeLists.txt index ce03d180..bd538c32 100644 --- a/Analysis/MapLab/cigar_man_lib/CMakeLists.txt +++ b/Analysis/MapLab/cigar_man_lib/CMakeLists.txt @@ -1,5 +1,5 @@ # Copyright (C) 2015 Thermo Fisher Scientific. All Rights Reserved. -cmake_minimum_required (VERSION 2.6) +cmake_minimum_required (VERSION 2.8.12) project (cigar_man_lib) diff --git a/Analysis/MapLab/cigar_man_lib_test/CMakeLists.txt b/Analysis/MapLab/cigar_man_lib_test/CMakeLists.txt index 57b5befc..83879739 100644 --- a/Analysis/MapLab/cigar_man_lib_test/CMakeLists.txt +++ b/Analysis/MapLab/cigar_man_lib_test/CMakeLists.txt @@ -1,5 +1,5 @@ # Copyright (C) 2020 Thermo Fisher Scientific. All Rights Reserved. -cmake_minimum_required (VERSION 2.6) +cmake_minimum_required (VERSION 2.8.12) project (cigar_man_lib_test) diff --git a/Analysis/MapLab/cigar_man_lib_test/test_align_util.h b/Analysis/MapLab/cigar_man_lib_test/test_align_util.h index 5186235e..a3e34188 100644 --- a/Analysis/MapLab/cigar_man_lib_test/test_align_util.h +++ b/Analysis/MapLab/cigar_man_lib_test/test_align_util.h @@ -4,12 +4,6 @@ #include #include "test_alignment_generator.h" -// Below is a template for a derivative from Test -// To add a case, -// - copy class below and substitute name/constructor name/ heading with proper values -// - instantiate an instance of this class wiin CommonLibTest object -// - register the instance in the init method of the CommonLibTest class -// - fill in "process" and add "init", "report" and "cleanup" if needed class TestValidateAlignment : public Test { diff --git a/Analysis/MapLab/context_align/CMakeLists.txt b/Analysis/MapLab/context_align/CMakeLists.txt index 97140290..055cea49 100644 --- a/Analysis/MapLab/context_align/CMakeLists.txt +++ b/Analysis/MapLab/context_align/CMakeLists.txt @@ -1,5 +1,5 @@ # Copyright (C) 2015 Thermo Fisher Scientific. All Rights Reserved. -cmake_minimum_required (VERSION 2.6) +cmake_minimum_required (VERSION 2.8.12) project (context_align) diff --git a/Analysis/MapLab/min_common_lib/CMakeLists.txt b/Analysis/MapLab/min_common_lib/CMakeLists.txt index 4fb8dba3..267384d3 100644 --- a/Analysis/MapLab/min_common_lib/CMakeLists.txt +++ b/Analysis/MapLab/min_common_lib/CMakeLists.txt @@ -1,5 +1,5 @@ # Copyright (C) 2015 Thermo Fisher Scientific. All Rights Reserved. -cmake_minimum_required (VERSION 2.6) +cmake_minimum_required (VERSION 2.8.12) project (min_common_lib) diff --git a/Analysis/MapLab/min_common_lib_test/CMakeLists.txt b/Analysis/MapLab/min_common_lib_test/CMakeLists.txt index 390dec28..bf4b08a2 100644 --- a/Analysis/MapLab/min_common_lib_test/CMakeLists.txt +++ b/Analysis/MapLab/min_common_lib_test/CMakeLists.txt @@ -1,5 +1,5 @@ # Copyright (C) 2015 Thermo Fisher Scientific. All Rights Reserved. -cmake_minimum_required (VERSION 2.6) +cmake_minimum_required (VERSION 2.8.12) project (min_common_lib_test) diff --git a/Analysis/MapLab/seqdata_lib/CMakeLists.txt b/Analysis/MapLab/seqdata_lib/CMakeLists.txt index 7bc68e88..3606b081 100644 --- a/Analysis/MapLab/seqdata_lib/CMakeLists.txt +++ b/Analysis/MapLab/seqdata_lib/CMakeLists.txt @@ -1,5 +1,5 @@ # Copyright (C) 2015 Thermo Fisher Scientific. All Rights Reserved. -cmake_minimum_required (VERSION 2.6) +cmake_minimum_required (VERSION 2.8.12) project (seqdata_lib) diff --git a/Analysis/MapLab/seqdata_lib_test/CMakeLists.txt b/Analysis/MapLab/seqdata_lib_test/CMakeLists.txt index db7aa5a4..f6a2c61c 100644 --- a/Analysis/MapLab/seqdata_lib_test/CMakeLists.txt +++ b/Analysis/MapLab/seqdata_lib_test/CMakeLists.txt @@ -1,5 +1,5 @@ # Copyright (C) 2015 Thermo Fisher Scientific. All Rights Reserved. -cmake_minimum_required (VERSION 2.6) +cmake_minimum_required (VERSION 2.8.12) project (seqdata_lib_test) @@ -33,4 +33,4 @@ include_directories (../min_common_lib ../seqdata_lib ${ION_STATGEN_INCLUDES} ) find_package(Threads REQUIRED) -target_link_libraries ( seqdata_lib_test min_common seqdata ${ION_STATGEN_LIBS} ${CMAKE_THREAD_LIBS_INIT} rt ) \ No newline at end of file +target_link_libraries ( seqdata_lib_test min_common seqdata ${ION_STATGEN_LIBS} ${CMAKE_THREAD_LIBS_INIT} rt ) diff --git a/Analysis/MapLab/tmap_lib/CMakeLists.txt b/Analysis/MapLab/tmap_lib/CMakeLists.txt index 7fe85dbc..9c3739e2 100644 --- a/Analysis/MapLab/tmap_lib/CMakeLists.txt +++ b/Analysis/MapLab/tmap_lib/CMakeLists.txt @@ -1,5 +1,5 @@ # Copyright (C) 2015 Thermo Fisher Scientific. All Rights Reserved. -cmake_minimum_required (VERSION 2.6) +cmake_minimum_required (VERSION 2.8.12) project (tmap_lib) diff --git a/Analysis/MapLab/tmap_lib_test/CMakeLists.txt b/Analysis/MapLab/tmap_lib_test/CMakeLists.txt index f51aa78e..72e1f030 100644 --- a/Analysis/MapLab/tmap_lib_test/CMakeLists.txt +++ b/Analysis/MapLab/tmap_lib_test/CMakeLists.txt @@ -1,11 +1,12 @@ # Copyright (C) 2020 Thermo Fisher Scientific. All Rights Reserved. -cmake_minimum_required (VERSION 2.6) +cmake_minimum_required (VERSION 2.8.12) project (tmap_lib_test) include (../tmap_lib/tmapCommonBuild.txt) -set (PROJECT_DESCRIPTION "Test suite for tmap_lib") +set (PROJECT_DESCRIPTION "Tmap executable built using tmap_lib") + set (SOURCES ${TMAP_SRC_DIR}/tmap_main.c @@ -21,9 +22,10 @@ configure_file ( add_executable (tmap_lib_test ${SOURCES}) set_target_properties(tmap_lib_test PROPERTIES COMPILE_FLAGS ${TMAP_COMPILE_FLAGS}) +set_target_properties(tmap_lib_test PROPERTIES LINKER_LANGUAGE CXX) find_package(Threads REQUIRED) # TODO: need to check if CMAKE_USE_PTHREADS_INIT is true - pthreads is the only threading mechanism supported -target_link_libraries (tmap_lib_test tmapl tmap_samtools m z pthread bz2 rt) +target_link_libraries (tmap_lib_test tmapl tmap_samtools m z pthread bz2) diff --git a/Analysis/MapLab/tmap_lib_unit_tests/CMakeLists.txt b/Analysis/MapLab/tmap_lib_unit_tests/CMakeLists.txt new file mode 100644 index 00000000..78e2decb --- /dev/null +++ b/Analysis/MapLab/tmap_lib_unit_tests/CMakeLists.txt @@ -0,0 +1,27 @@ +# Copyright (C) 2020 Thermo Fisher Scientific. All Rights Reserved. +cmake_minimum_required (VERSION 2.8.12) + +project (tmap_lib_test) + +include (../tmap_lib/tmapCommonBuild.txt) + +set (PROJECT_DESCRIPTION "Test suite for tmap_lib") + +include_directories ( ../min_common_lib ) +include_directories ( BEFORE ${PROJECT_BINARY_DIR} ) + +set (SOURCES + tmap_lib_unit_tests_main.cpp + test_tmap_binary_search.cpp + ) + +add_executable (tmap_lib_unit_tests ${SOURCES}) +set_target_properties(tmap_lib_unit_tests PROPERTIES COMPILE_FLAGS ${TMAP_COMPILE_FLAGS}) +set_target_properties(tmap_lib_unit_tests PROPERTIES LINKER_LANGUAGE CXX) + +find_package(Threads REQUIRED) + +# TODO: need to check if CMAKE_USE_PTHREADS_INIT is true - pthreads is the only threading mechanism supported + +target_link_libraries (tmap_lib_unit_tests min_common tmapl tmap_samtools m z pthread bz2) + diff --git a/Analysis/MapLab/tmap_lib_unit_tests/test_tmap_binary_search.cpp b/Analysis/MapLab/tmap_lib_unit_tests/test_tmap_binary_search.cpp new file mode 100644 index 00000000..4563c87b --- /dev/null +++ b/Analysis/MapLab/tmap_lib_unit_tests/test_tmap_binary_search.cpp @@ -0,0 +1,59 @@ +#include "test_tmap_binary_search.h" +#include +#include +#include + + +TestTmapBinarySearch::TestTmapBinarySearch () +: +Test ("TmapBinarySearch") +{ +} + +int lt_char (const void* k, const void* e) +{ + return (*(char *) k) < (*(char *) e); +} + + +bool TestTmapBinarySearch::process () +{ + unsigned char test_data [] = "ACEFGIKLMPSTXZ"; + unsigned char buf [sizeof test_data]; + size_t test_data_size = sizeof (test_data)/sizeof (*test_data) - 1; // for char array only, exclude terminating zero + + TEST_ASSERT (test_data [test_data_size - 1] == 'Z'); + TEST_ASSERT (test_data [0] > 2); + TEST_ASSERT (test_data [test_data_size - 1] < (unsigned char) 252); + + size_t tot_tests = 0; + for (size_t upper_bound = 0; upper_bound <= test_data_size; ++upper_bound) + { + for (unsigned char key = test_data [0] - 2; key != test_data [test_data_size -1] + 2; ++key) + { + const unsigned char* expected_location = test_data; + while ( + expected_location != test_data + upper_bound + && lt_char (expected_location, &key) + ) + ++expected_location; + + unsigned const char* computed_location = (const unsigned char*) tmap_binary_search (&key, test_data, upper_bound, sizeof (*test_data), lt_char); + + int expected_off = expected_location - test_data; + int computed_off = computed_location - test_data; + + memcpy (buf, test_data, upper_bound * sizeof (*test_data)); + buf [upper_bound] = 0; + TEST_ASSERTX (computed_location == expected_location, "Data is %s (%d el), key is '%c' (%d), expected: '%c' (%d) at position %d, found '%c' (%d) at position %d", + buf, upper_bound, + isprint (key)?key:'*', int (key), + isprint (*expected_location)?*expected_location:'*', int (*expected_location), expected_off, + isprint (*computed_location)?*computed_location:'*', int (*computed_location), computed_off); + ++ tot_tests; + } + } + o_ << name () << ":" << tot_tests << " invocations checked" << std::endl; + + return 1; +} diff --git a/Analysis/MapLab/tmap_lib_unit_tests/test_tmap_binary_search.h b/Analysis/MapLab/tmap_lib_unit_tests/test_tmap_binary_search.h new file mode 100644 index 00000000..edf1120a --- /dev/null +++ b/Analysis/MapLab/tmap_lib_unit_tests/test_tmap_binary_search.h @@ -0,0 +1,13 @@ +#ifndef __TEST_TMAP_BINARY_SEARCH_H__ +#define __TEST_TMAP_BINARY_SEARCH_H__ + +#include + +class TestTmapBinarySearch : public Test +{ +public: + TestTmapBinarySearch (); + bool process (); +}; + +#endif // __TEST_TMAP_BINARY_SEARCH_H__ diff --git a/Analysis/MapLab/tmap_lib_unit_tests/tmap_lib_unit_tests_main.cpp b/Analysis/MapLab/tmap_lib_unit_tests/tmap_lib_unit_tests_main.cpp new file mode 100644 index 00000000..fce61b73 --- /dev/null +++ b/Analysis/MapLab/tmap_lib_unit_tests/tmap_lib_unit_tests_main.cpp @@ -0,0 +1,39 @@ +/* Copyright (C) 2015 Ion Torrent Systems, Inc. All Rights Reserved. */ + +////////////////////////////////////////////////////////////////////////////// +////////////////////////////////////////////////////////////////////////////// + +#include +#include +#include + +#include "test_tmap_binary_search.h" + +class TmapLibUnitTests : public TestSuite +{ + TestTmapBinarySearch testTmapBinarySearch; +public: + TmapLibUnitTests (int argc, char* argv [], char* envp [] = NULL) + : + TestSuite (argc, argv, envp) + { + } + void init () + { + reg (testTmapBinarySearch); + } +}; + +int main (int argc, char** argv) +{ + std::cerr.imbue (deccomma_locale); + std::cout.imbue (deccomma_locale); + ers.imbue (deccomma_locale); + + TmapLibUnitTests test (argc, argv); + bool retcode = !test.run (); + return retcode; +} + + + diff --git a/Analysis/MapLab/tmap_samtools_lib/CMakeLists.txt b/Analysis/MapLab/tmap_samtools_lib/CMakeLists.txt index d6430f49..eea0a7b1 100644 --- a/Analysis/MapLab/tmap_samtools_lib/CMakeLists.txt +++ b/Analysis/MapLab/tmap_samtools_lib/CMakeLists.txt @@ -1,4 +1,4 @@ -cmake_minimum_required (VERSION 2.6) +cmake_minimum_required (VERSION 2.8.12) project (tmap_samtools) diff --git a/Analysis/SamUtils/tempa.fa b/Analysis/SamUtils/tempa.fa new file mode 100644 index 00000000..3b8c86af --- /dev/null +++ b/Analysis/SamUtils/tempa.fa @@ -0,0 +1,2 @@ +>chr3:41266064-41266115 +GCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTG diff --git a/Analysis/Separator/DifferentialSeparator.cpp b/Analysis/Separator/DifferentialSeparator.cpp index 77aec87a..b48120e6 100644 --- a/Analysis/Separator/DifferentialSeparator.cpp +++ b/Analysis/Separator/DifferentialSeparator.cpp @@ -1541,26 +1541,88 @@ void DifferentialSeparator::PrintWell(TraceStore &store, int well, int flow) { PrintVec(vec); } +typedef struct{ + int thread_id; + int bin_start; + int bin_end; + + TraceStoreCol *store; + int rowStep; + int colStep; + char *filter; + int filter_len; + float *mad; + GridMesh *mesh; + + DifferentialSeparator *obj; +}WellDeviationContext_t; + + +void DifferentialSeparator::WellDeviationThread(TraceStoreCol *store, + GridMesh *mesh, int rowStep, int colStep, char *filter, + int filter_len, float *mad, int bin_start, int bin_end) +{ + vector mean(filter_len); + vector m2(filter_len); + vector summary(filter_len); + vector normalize(filter_len * store->GetNumFrames()); + int rowStart = -1, rowEnd = -1, colStart = -1, colEnd = -1; + for (int binIx = bin_start; binIx < bin_end; binIx++) { + mesh->GetBinCoords (binIx, rowStart, rowEnd, colStart, colEnd); + WellDeviationRegion(*store, rowStart, rowEnd, colStart, colEnd, + 0, store->GetNumFrames(), 0, store->GetNumFlows(), + &mean[0], &m2[0], + &normalize[0], + &summary[0], filter, mad); + } + +} + +void *WellDeviationThreadEntry(void *arg) +{ + WellDeviationContext_t *args=(WellDeviationContext_t *)arg; + args->obj->WellDeviationThread(args->store,args->mesh, + args->rowStep,args->colStep,args->filter, + args->filter_len,args->mad, + args->bin_start,args->bin_end); + return NULL; +} + void DifferentialSeparator::WellDeviation(TraceStoreCol &store, int rowStep, int colStep, vector &filter, - vector &mad) { + vector &mad, + int ncores ) { GridMesh mesh; mesh.Init(mMask.H(), mMask.W(), rowStep, colStep); - vector mean(filter.size()); - vector m2(filter.size()); - vector summary(filter.size()); - vector normalize(filter.size() * store.GetNumFrames()); - int rowStart = -1, rowEnd = -1, colStart = -1, colEnd = -1; - for (size_t binIx = 0; binIx < mesh.GetNumBin(); binIx++) { - mesh.GetBinCoords (binIx, rowStart, rowEnd, colStart, colEnd); - WellDeviationRegion(store, rowStart, rowEnd, colStart, colEnd, - 0, store.GetNumFrames(), 0, store.GetNumFlows(), - &mean[0], &m2[0], - &normalize[0], - &summary[0], filter, mad); - } + int numBin=mesh.GetNumBin(); + + WellDeviationContext_t pac[ncores]; + + pthread_t worker_id[ncores]; + int lastEnd=0; + for (int worker = 0; worker < ncores; worker++) { + WellDeviationContext_t *pacp=&pac[worker]; + pacp->thread_id=worker; + pacp->bin_start=lastEnd; + pacp->bin_end=lastEnd=numBin*(worker+1)/ncores; + pacp->colStep=colStep; + pacp->rowStep=rowStep; + pacp->filter=&filter[0]; + pacp->filter_len=filter.size(); + pacp->mad=&mad[0]; + pacp->mesh=&mesh; + pacp->obj=this; + pacp->store=&store; + if (pthread_create(&worker_id[worker], NULL, WellDeviationThreadEntry, pacp)) { + cerr << "ERROR: problem starting thread" << endl; + exit (EXIT_FAILURE); + } + } + + for (int worker = 0; worker < ncores; worker++) + pthread_join(worker_id[worker], NULL); } @@ -1572,8 +1634,8 @@ void DifferentialSeparator::WellDeviationRegion(TraceStoreCol &store, float *mean, float *m2, float *normalize, float *summary, - vector &filters, - vector &mad) { + char *filters, + float *mad) { int loc_num_frames = frame_end - frame_start; // calculate the average trace float region_sum[loc_num_frames]; @@ -1589,20 +1651,18 @@ void DifferentialSeparator::WellDeviationRegion(TraceStoreCol &store, for (int flow_ix = flow_start; flow_ix < flow_end; flow_ix++) { for (int frame_ix = frame_start; frame_ix < frame_end; frame_ix++) { size_t offset = row_ix * store_num_cols + col_start; - char *__restrict filter_start = &filters[0] + offset; - int16_t *__restrict store_start = &store.mData[0] + (frame_ix * store.mFlowFrameStride) + (flow_ix * store_num_wells) + offset; - int16_t *__restrict store_end = store_start + loc_num_cols; + char *__restrict filterp = &filters[0] + offset; + int16_t *__restrict storep = &store.mData[0] + (frame_ix * store.mFlowFrameStride) + (flow_ix * store_num_wells) + offset; // assert(store_end - &store.mData[0] <= store.mData.size()); - // assert(filter_start - &filters[0] <= filters.size()); - float &frame_sum = region_sum[frame_ix-frame_start]; - while (store_start != store_end) { - if ((*filter_start) == 0) { - frame_sum += *store_start; + // assert(filterp - &filters[0] <= filters.size()); + float frame_sum = region_sum[frame_ix-frame_start]; + for(size_t trc=0;trc &filter, - vector &refWells) { + vector &refWells, + int ncores) { int count = 0; if (useKeySignal == 1) { @@ -2070,7 +2123,7 @@ void DifferentialSeparator::RankReference(TraceStoreCol &store, std::fill(mEmptyMetrics[0].begin(), mEmptyMetrics[0].end(), 0.0f); std::fill(mEmptyMetrics[1].begin(), mEmptyMetrics[1].end(), 0.0f); store.WellProj(store, mKeys, filter, mEmptyMetrics[0]); - WellDeviation(store, rowStep, colStep, filter, mEmptyMetrics[1]); + WellDeviation(store, rowStep, colStep, filter, mEmptyMetrics[1],ncores); for (size_t well_ix = 0; well_ix < mWells.size(); well_ix++) { mWells[well_ix].bfMetric2 = mEmptyMetrics[0][well_ix]; mWells[well_ix].bfMetric3 = mEmptyMetrics[1][well_ix]; @@ -2654,6 +2707,8 @@ void DifferentialSeparator::FitKeys(PJobQueue &jQueue, DifSepOpt &opts, GridMesh std::min (128,mask.W()), std::min (128,mask.H()), keys); AvgKeyReporter avgReport(keys, opts.outData, opts.flowOrder, opts.analysisDir, usable_flows, traceStore.GetNumFrames()); + mTotalTimer.PrintMicroSecondsUpdate(stdout, "Total Timer: FitKeys before JobQ."); + std::vector evalJobs(emptyEstimates.GetNumBin()); for (size_t binIx = 0; binIx < emptyEstimates.GetNumBin(); binIx++) { int rowStart = -1, rowEnd = -1, colStart = -1, colEnd = -1; @@ -2665,29 +2720,112 @@ void DifferentialSeparator::FitKeys(PJobQueue &jQueue, DifSepOpt &opts, GridMesh jQueue.AddJob(evalJobs[binIx]); } jQueue.WaitUntilDone(); + mTotalTimer.PrintMicroSecondsUpdate(stdout, "Total Timer: FitKeys after JobQ."); avgReport.Finish(); keySumReport.Finish(); } +typedef struct { + int thread_id; + int bin_start; + int bin_end; + + DifSepOpt *opts; + TraceStoreCol *traceStore; + GridMesh *emptyEstimates; + char *filteredWells; + float *ftime; + int *allZeroFlows; + int allZeroFlows_size; + float *taub_est; + int *converged; + int *no_wells; + + DifferentialSeparator *obj; +}FitTauEContext_t; + +void *FitTauEThreadEntry(void *arg) +{ + FitTauEContext_t *args=(FitTauEContext_t *)arg; + + args->obj->FitTauEThread( + args->bin_start, args->bin_end, + *args->opts, *args->traceStore, + *args->emptyEstimates, + args->filteredWells, args->ftime, args->allZeroFlows, + args->allZeroFlows_size, args->taub_est, + *args->converged, *args->no_wells); + + return NULL; +} + void DifferentialSeparator::FitTauE(DifSepOpt &opts, TraceStoreCol &traceStore, GridMesh &emptyEstimates, std::vector &filteredWells, std::vector &ftime, std::vector &allZeroFlows, float *taub_est) { - mTotalTimer.PrintMicroSecondsUpdate(stdout, "Total Timer: Before Zeromers."); + mTotalTimer.PrintMicroSecondsUpdate(stdout, "Total Timer: Before FitTauE."); emptyEstimates.Init (mMask.H(), mMask.W(), opts.tauEEstimateStepY, opts.tauEEstimateStepX); - ZeromerMatDiff z_diff; - ZeromerMatDiff z_diff_big; int converged = 0; int no_wells = 0; - int zero_flows[1] = {0}; + int ncores=opts.nCores; + if (taub_est != NULL) { memset(taub_est, 0, sizeof(float) * filteredWells.size()); } - for (size_t binIx = 0; binIx < emptyEstimates.GetNumBin(); binIx++) { + + int numBin=emptyEstimates.GetNumBin(); + + FitTauEContext_t pac[ncores]; + + pthread_t worker_id[ncores]; + int lastEnd=0; + for (int worker = 0; worker < ncores; worker++) { + FitTauEContext_t *pacp=&pac[worker]; + pacp->thread_id=worker; + pacp->bin_start=lastEnd; + pacp->bin_end=lastEnd=numBin*(worker+1)/ncores; + pacp->allZeroFlows=&allZeroFlows[0]; + pacp->allZeroFlows_size=allZeroFlows.size(); + pacp->emptyEstimates=&emptyEstimates; + pacp->filteredWells=&filteredWells[0]; + pacp->opts=&opts; + pacp->taub_est=taub_est; + pacp->traceStore=&traceStore; + pacp->converged=&converged; + pacp->no_wells=&no_wells; + pacp->ftime=&ftime[0]; + pacp->obj=this; + if (pthread_create(&worker_id[worker], NULL, FitTauEThreadEntry, pacp)) { + cerr << "ERROR: problem starting thread" << endl; + exit (EXIT_FAILURE); + } + } + + for (int worker = 0; worker < ncores; worker++) + pthread_join(worker_id[worker], NULL); + + fprintf(stdout, "FitTauE() - %d %d %d\n", converged, no_wells, (int)emptyEstimates.GetNumBin()); + mTotalTimer.PrintMicroSecondsUpdate(stdout, "Total Timer: After well Zeromers."); + +} + +void DifferentialSeparator::FitTauEThread( + int bin_start, int bin_end, + DifSepOpt &opts, TraceStoreCol &traceStore, + GridMesh &emptyEstimates, + char *filteredWells, float *ftime, int *allZeroFlows, + int allZeroFlows_size, float *taub_est, + int &converged, int &no_wells) +{ + ZeromerMatDiff z_diff; + ZeromerMatDiff z_diff_big; + int zero_flows[1] = {0}; + + for (int binIx = bin_start; binIx < bin_end; binIx++) { int rowStart = -1, rowEnd = -1, colStart = -1, colEnd = -1; emptyEstimates.GetBinCoords (binIx, rowStart, rowEnd, colStart, colEnd); z_diff.SetUpMatricesClean(traceStore, &filteredWells[0], &ftime[0], 2, 3, mMask.W(), mMask.W() * mMask.H(), rowStart, rowEnd, colStart, colEnd, - &allZeroFlows[0], allZeroFlows.size(), + &allZeroFlows[0], allZeroFlows_size, 0, traceStore.GetNumFrames()); struct FitTauEParams ¶m = emptyEstimates.GetItem(binIx); if (z_diff.m_num_wells < MIN_SAMPLE_TAUE_STATS) { @@ -2726,6 +2864,7 @@ void DifferentialSeparator::FitTauE(DifSepOpt &opts, TraceStoreCol &traceStore, converged++; } } + if (taub_est != NULL) { z_diff_big.SetUpMatrices(traceStore, &filteredWells[0], &ftime[0], 1, 1, mMask.W(), mMask.W() * mMask.H(), @@ -2753,13 +2892,37 @@ void DifferentialSeparator::FitTauE(DifSepOpt &opts, TraceStoreCol &traceStore, } } } - fprintf(stdout, "FitTauE() - %d %d %d\n", converged, no_wells, (int)emptyEstimates.GetNumBin()); - mTotalTimer.PrintMicroSecondsUpdate(stdout, "Total Timer: After well Zeromers."); } +typedef struct{ + int thread_id; + int bin_start; + int bin_end; + + DifSepOpt *opts; + Mask *mask; + vector *bfMetric; + float madThreshold; + std::vector *wells; + GridMesh *modelMesh; + std::stringstream *modelOutput; + + DifferentialSeparator *obj; +}RegionalClusteringContext_t; + + +void *RegionalClusteringThreadEntry(void *arg) +{ + RegionalClusteringContext_t *args=(RegionalClusteringContext_t *)arg; + args->obj->RegionalClusteringThread(args->bin_start,args->bin_end, + *args->opts,*args->mask,*args->bfMetric,args->madThreshold, + *args->wells,*args->modelMesh,args->modelOutput); + return NULL; +} void DifferentialSeparator::DoRegionClustering(DifSepOpt &opts, Mask &mask, vector &bfMetric, float madThreshold, std::vector &wells, GridMesh &modelMesh) { int numWells = mask.H() * mask.W(); + int ncores=opts.nCores; ofstream modelOut; if (opts.outputDebug > 1) { string modelFile = opts.outData + ".mix-model.txt"; @@ -2768,10 +2931,10 @@ void DifferentialSeparator::DoRegionClustering(DifSepOpt &opts, Mask &mask, vect } modelMesh.Init (mask.H(), mask.W(), opts.clusterMeshStepY, opts.clusterMeshStepX); - SampleStats bfSnr; +// SampleStats bfSnr; - // double bfMinThreshold = bfQuantiles.GetQuantile (.02); - // cout << "Bf min threshold is: " << bfMinThreshold << " for: " << bfQuantiles.GetMedian() << " +/- " << ( (bfQuantiles.GetQuantile (.75) - bfQuantiles.GetQuantile (.25)) /2) << endl; +// double bfMinThreshold = bfQuantiles.GetQuantile (.02); +// cout << "Bf min threshold is: " << bfMinThreshold << " for: " << bfQuantiles.GetMedian() << " +/- " << ( (bfQuantiles.GetQuantile (.75) - bfQuantiles.GetQuantile (.25)) /2) << endl; // Should we use standard deviation of signal as the beadfind metric // (eg cluster signal vs no signal instead of buffering vs no @@ -2785,7 +2948,49 @@ void DifferentialSeparator::DoRegionClustering(DifSepOpt &opts, Mask &mask, vect } } - for (size_t binIx = 0; binIx < modelMesh.GetNumBin(); binIx++) + int numBin=modelMesh.GetNumBin(); + + RegionalClusteringContext_t pac[ncores]; + std::stringstream modelOutStrStr[numBin]; + pthread_t worker_id[ncores]; + int lastEnd=0; + for (int worker = 0; worker < ncores; worker++) { + RegionalClusteringContext_t *pacp=&pac[worker]; + pacp->thread_id=worker; + pacp->bin_start=lastEnd; + pacp->bin_end=lastEnd=numBin*(worker+1)/ncores; + pacp->bfMetric=&bfMetric; + pacp->madThreshold=madThreshold; + pacp->mask=&mask; + pacp->modelMesh=&modelMesh; + pacp->opts=&opts; + pacp->wells=&wells; + pacp->obj=this; + pacp->modelOutput=&modelOutStrStr[0]; + if (pthread_create(&worker_id[worker], NULL, RegionalClusteringThreadEntry, pacp)) { + cerr << "ERROR: problem starting thread" << endl; + exit (EXIT_FAILURE); + } + } + + for (int worker = 0; worker < ncores; worker++) + pthread_join(worker_id[worker], NULL); + +// cout << "BF SNR: " << bfSnr.GetMean() << " +/- " << (bfSnr.GetSD()) << endl; + if (modelOut.is_open()) { + for (int binIx = 0; binIx < numBin; binIx++){ + modelOut << modelOutStrStr[binIx].str(); + } + + modelOut.close(); + } +} +void DifferentialSeparator::RegionalClusteringThread(int start_bin, int end_bin, + DifSepOpt &opts, Mask &mask, vector &bfMetric, float madThreshold, + std::vector &wells, GridMesh &modelMesh, stringstream *modelOut) +{ + + for (int binIx = start_bin; binIx < end_bin; binIx++) { int rowStart = -1, rowEnd = -1, colStart = -1, colEnd = -1; modelMesh.GetBinCoords (binIx, rowStart, rowEnd, colStart, colEnd); @@ -2818,30 +3023,26 @@ void DifferentialSeparator::DoRegionClustering(DifSepOpt &opts, Mask &mask, vect int minBfGoodWells = max (200, (int) (goodCount * .5)); ClusterRegion (rowStart, rowEnd, colStart, colEnd, madThreshold, opts.minTauESnr, minBfGoodWells, bfMetric, wells, opts.clusterTrim, false, model); - if ( model.count > minBfGoodWells) { - double bf = ( (model.mu2 - model.mu1) / ( (sqrt (model.var2) + sqrt (model.var1)) /2)); - if (isfinite (bf) && bf > 0) { - bfSnr.AddValue (bf); - } - else { - cout << "Region: " << binIx << " has snr of: " << bf << " " << model.mu1 << " " << model.var1 << " " << model.mu2 << " " << model. var2 << endl; - } - } +// if ( model.count > minBfGoodWells) { +// double bf = ( (model.mu2 - model.mu1) / ( (sqrt (model.var2) + sqrt (model.var1)) /2)); +// if (isfinite (bf) && bf > 0) { +// bfSnr.AddValue (bf); +// } +// else { +// cout << "Region: " << binIx << " has snr of: " << bf << " " << model.mu1 << " " << model.var1 << " " << model.mu2 << " " << model. var2 << endl; +// } +// } int binRow, binCol; modelMesh.IndexToXY (binIx, binRow, binCol); if (opts.outputDebug > 1) { - modelOut << binIx << "\t" << binRow << "\t" << binCol << "\t" - << rowStart << "\t" << rowEnd << "\t" << colStart << "\t" << colEnd << "\t" - << model.count << "\t" << model.mix << "\t" - << model.mu1 << "\t" << model.var1 << "\t" - << model.mu2 << "\t" << model.var2 << "\t" - << model.threshold << "\t" << model.refMean << endl; + modelOut[binIx] << binIx << "\t" << binRow << "\t" << binCol << "\t" + << rowStart << "\t" << rowEnd << "\t" << colStart << "\t" << colEnd << "\t" + << model.count << "\t" << model.mix << "\t" + << model.mu1 << "\t" << model.var1 << "\t" + << model.mu2 << "\t" << model.var2 << "\t" + << model.threshold << "\t" << model.refMean << endl; } } - cout << "BF SNR: " << bfSnr.GetMean() << " +/- " << (bfSnr.GetSD()) << endl; - if (modelOut.is_open()) { - modelOut.close(); - } } @@ -3294,6 +3495,7 @@ void DifferentialSeparator::HandleDebug(std::vector &wells, OutputOutliers (opts, traceStore, bg, wells, sdHigh, sdLow, madHigh, bfHigh, bfLow, peakLow); + mTotalTimer.PrintMicroSecondsUpdate(stdout, "Total Timer: After OutputOutliers."); // Write out debugging matrix int n_cols = 25; @@ -3342,6 +3544,7 @@ void DifferentialSeparator::HandleDebug(std::vector &wells, wellMatrix.at (i, currentCol++) = mEmptyMetrics.back().at(i); // 24 } } + mTotalTimer.PrintMicroSecondsUpdate(stdout, "Total Timer: After wellMatrix pop."); string h5Summary = "/separator/summary"; vector flows(2); @@ -3351,9 +3554,15 @@ void DifferentialSeparator::HandleDebug(std::vector &wells, h5file.Open(false); if (opts.outputDebug > 3) saver.WriteResults(h5file); + mTotalTimer.PrintMicroSecondsUpdate(stdout, "Total Timer: After writeResults."); H5Arma::WriteMatrix (h5file, h5Summary, wellMatrix); + mTotalTimer.PrintMicroSecondsUpdate(stdout, "Total Timer: After writeMatrix."); + CalcRegionEmptyStat(h5file, modelMesh, traceStore, h5SummaryRoot, flows, mask); + mTotalTimer.PrintMicroSecondsUpdate(stdout, "Total Timer: After CalcRegionEmptyStat."); + h5file.Close(); + mTotalTimer.PrintMicroSecondsUpdate(stdout, "Total Timer: After close."); } } @@ -3678,7 +3887,7 @@ void DifferentialSeparator::SetUp(DifSepOpt &opts, std::string &bfFile, arma::Co for (size_t kIx = 0; kIx < mKeys.size(); kIx++) { opts.maxKeyFlowLength = max ( (unsigned int) opts.maxKeyFlowLength, mKeys[kIx].usableKeyFlows); } // Setup our job queue int qSize = (mMask.W() / opts.t0MeshStepX + 1) * (mMask.H() / opts.t0MeshStepY + 1); - if (opts.nCores <= 0) { opts.nCores = numCores(); } + if (opts.nCores <= 0) { opts.nCores = min(28,max(numCores(),6)); } mQueue.Init (opts.nCores, qSize); // Figure out which flows can be used for fitting taue @@ -3757,6 +3966,8 @@ void DifferentialSeparator::ClusterToSelectReference(DifSepOpt &opts, const std: if (mBfMask[i] & MaskReference) {maskRefStats.AddWell(mWells[i]);} if (mBfMask[i] & MaskEmpty) {maskEmptyStats.AddWell(mWells[i]);} } + mTotalTimer.PrintMicroSecondsUpdate(stdout, "Total Timer: After AddWell."); + // CountReference("Filtered wells", mFilteredWells); if (libStats.NumSeen() > 10) { libStats.ReportStats(stdout);} if (tfStats.NumSeen() > 50) { tfStats.ReportStats(stdout);} @@ -3765,6 +3976,8 @@ void DifferentialSeparator::ClusterToSelectReference(DifSepOpt &opts, const std: refStats.ReportStats(stdout); filtStats.ReportStats(stdout); OutputStats(opts, mBfMask); + mTotalTimer.PrintMicroSecondsUpdate(stdout, "Total Timer: After OutputStats."); + HandleDebug(mWells, opts, h5SummaryRoot, saver, mMask, traceStore, modelMesh, maskRefStats.m_quantiles[KEY_SD_STAT].GetQuantile(.9), maskRefStats.m_quantiles[KEY_SD_STAT].GetQuantile(.9), @@ -3816,14 +4029,18 @@ int DifferentialSeparator::Run(DifSepOpt opts) { if (opts.isThumbnail) { row_step = col_step = BF_THUMBNAIL_SIZE; } if (opts.filterNoisyCols != "none") { + mTotalTimer.PrintMicroSecondsUpdate(stdout, "Total Timer: Before FilterNoisyColumns."); FilterNoisyColumns(row_step, col_step, mMask, opts, mFilteredWells); + mTotalTimer.PrintMicroSecondsUpdate(stdout, "Total Timer: After FilterNoisyColumns."); } // Pick which wells to use for initial reference for backgound int minWells = ceil(opts.referenceStep*opts.referenceStep * opts.percentReference); + mTotalTimer.PrintMicroSecondsUpdate(stdout, "Total Timer: Before RankReference. " + std::to_string(opts.useSignalReference)); RankReference(traceStore, mBfMetric, opts.referenceStep, opts.referenceStep, opts.useSignalReference, opts.iqrMult, 7, opts.percentReference, mMask, minWells, - mFilteredWells, mRefWells); + mFilteredWells, mRefWells,opts.nCores); + mTotalTimer.PrintMicroSecondsUpdate(stdout, "Total Timer: After RankReference."); if (!opts.skipBuffer) { mEmptyMetrics.push_back(mBfMetric); } @@ -3863,7 +4080,9 @@ int DifferentialSeparator::Run(DifSepOpt opts) { ftime, flowsAllZero, NULL); // See which keys are the best match for wells. + mTotalTimer.PrintMicroSecondsUpdate(stdout, "Total Timer: Before FitKeys."); FitKeys(mQueue, opts, emptyEstimates, traceStore, mKeys, ftime, saver, mMask, mWells); + mTotalTimer.PrintMicroSecondsUpdate(stdout, "Total Timer: After FitKeys."); // Use our dual gaussian mixture clustering to split wells into empty/live ClusterToSelectReference(opts, h5SummaryRoot, saver, traceStore, modelMesh, emptyEstimates); diff --git a/Analysis/Separator/DifferentialSeparator.h b/Analysis/Separator/DifferentialSeparator.h index 272b3988..301ad80c 100644 --- a/Analysis/Separator/DifferentialSeparator.h +++ b/Analysis/Separator/DifferentialSeparator.h @@ -307,6 +307,12 @@ class DifferentialSeparator : public AvgKeyIncorporation /** Do a beadfind/bead classification based on options passed in. */ void FitTauE(DifSepOpt &opts, TraceStoreCol &traceStore, GridMesh &emptyEstimates, std::vector &filteredWells, std::vector &ftime, std::vector &allZeroFlows, float *taub_est); + void FitTauEThread(int bin_start, int bin_end, + DifSepOpt &opts, TraceStoreCol &traceStore, + GridMesh &emptyEstimates, + char *filteredWells, float *ftime, int *allZeroFlows, + int allZeroFlows_size, float *taub_est, + int &converged, int &no_wells); void FitKeys(DifSepOpt &opts, GridMesh &emptyEstimates, TraceStoreCol &traceStore, std::vector &keys, std::vector &ftime, TraceSaver &saver, @@ -319,6 +325,10 @@ class DifferentialSeparator : public AvgKeyIncorporation vector &bfMetric, DifSepOpt &opts, std::vector &traceSd); void DoRegionClustering(DifSepOpt &opts, Mask &mask, vector &bfMetric, float madThreshold, std::vector &wells, GridMesh &modelMesh); + void RegionalClusteringThread(int start_bin, int end_bin, + DifSepOpt &opts, Mask &mask, vector &bfMetric, float madThreshold, + std::vector &wells, GridMesh &modelMesh, stringstream *modelOutput); + void ClusterIndividualWells(DifSepOpt &opts, Mask &bfMask, Mask &mask, TraceStoreCol &traceStore, GridMesh &modelMesh, std::vector &wells, std::vector &confidence, std::vector &clusters); @@ -370,7 +380,17 @@ class DifferentialSeparator : public AvgKeyIncorporation void WellDeviation(TraceStoreCol &store, int rowStep, int colStep, vector &filter, - vector &mad); + vector &mad, + int ncores); + void WellDeviationThread(TraceStoreCol *store, + GridMesh *mesh, + int rowStep, + int colStep, + char *filter, + int filter_len, + float *mad, + int bin_start, + int bin_end); void WellDeviationRegion(TraceStoreCol &store, int row_start, int row_end, @@ -380,8 +400,8 @@ class DifferentialSeparator : public AvgKeyIncorporation float *mean, float *m2, float *normalize, float *summary, - vector &filters, - vector &mad); + char *filters, + float *mad); void RankWellsBySignal(int flow0, int flow1, TraceStore &store, float iqrMult, @@ -446,7 +466,8 @@ class DifferentialSeparator : public AvgKeyIncorporation Mask &mask, int minWells, vector &filter, - vector &refWells); + vector &refWells, + int ncores); static float IQR (SampleQuantiles &s); diff --git a/Analysis/Separator/ZeromerMatDiff.cpp b/Analysis/Separator/ZeromerMatDiff.cpp index c7519446..51e3bc65 100644 --- a/Analysis/Separator/ZeromerMatDiff.cpp +++ b/Analysis/Separator/ZeromerMatDiff.cpp @@ -21,8 +21,8 @@ void ZeromerMatDiff::ShiftReference(int n_frames, size_t n_flow_wells, float shi if (start_frame >= 0 && end_frame < n_frames) { //interpolate... float mult = shift - floor(shift); - shifted.col(frame_ix).array() = (orig.col(end_frame).array() - orig.col(start_frame).array()) * mult; - shifted.col(frame_ix).array() += orig.col(start_frame).array(); + shifted.col(frame_ix).array() = (orig.col(end_frame).array() - orig.col(start_frame).array()) * mult + + orig.col(start_frame).array(); } else { // extrapolate backwards @@ -110,30 +110,29 @@ void ZeromerMatDiff::ZeromerSumSqErrorTrim(const int *zero_flows, size_t n_zero_ double ssq_sum = 0; size_t bad_count = 0; float max_value = 1000.0f; + float max_value_sq = max_value*max_value; for (size_t z_ix = 0; z_ix < n_zero_flows; z_ix++) { size_t flow_ix = zero_flows[z_ix]; for (size_t col_ix = 0; col_ix < n_frames; col_ix++) { float *__restrict signal_start = signal_data + n_wells * flow_ix + n_flow_wells * col_ix; - float *__restrict signal_end = signal_start + n_wells; float *__restrict predict_start = predict_data + n_wells * flow_ix + n_flow_wells * col_ix; const char *__restrict bad_start = bad_wells; - while (signal_start != signal_end) { - double value = *signal_start - *predict_start; //*signal_start * *signal_start; - if (*bad_start == 0 && isfinite(value) && fabs(value) <= max_value) { - ssq_sum += value * value; - } - else if (*bad_start == 0) { - *predict_start = *signal_start + max_value; - ssq_sum += max_value; - bad_count++; + for(size_t trc=0;trc max_value) { - *predict_start = *signal_start + max_value; + else{ + predict_start[trc] = signal_start[trc] + max_value; + if(bad_start[trc] == 0){ + ssq_sum += max_value_sq; + bad_count++; + } } - bad_start++; - signal_start++; - predict_start++; } } } @@ -144,57 +143,42 @@ void ZeromerMatDiff::FitTauB(const int *zero_flows, size_t n_zero_flows, const float *trace_data, const float *ref_data, size_t n_wells, size_t n_flows, size_t n_flow_wells, size_t n_frames, float taue_est, float *__restrict taub) { - Eigen::Map taub_v(taub, n_flow_wells); - Eigen::VectorXf vec_sum_x2(n_wells), vec_sum_xy(n_wells), - vec_previous(n_wells), taub_sum(n_wells); - taub_sum.setZero(); - taub_v.setZero(); + float vec_sum_xx [n_wells] __attribute__ ((aligned (64))); + float vec_sum_xy [n_wells] __attribute__ ((aligned (64))); + float vec_previous [n_wells] __attribute__ ((aligned (64))); + float taub_sum [n_wells] __attribute__ ((aligned (64))); + + memset(taub_sum,0,sizeof(taub_sum)); for (size_t flow_ix = 0; flow_ix < n_zero_flows; flow_ix++) { int z_ix = zero_flows[flow_ix]; - vec_sum_x2.setZero(); - vec_sum_xy.setZero(); - vec_previous.setZero(); + memset(vec_sum_xx,0,sizeof(vec_sum_xx)); + memset(vec_sum_xy,0,sizeof(vec_sum_xy)); + memset(vec_previous,0,sizeof(vec_previous)); for (size_t frame_ix = 0; frame_ix < n_frames; frame_ix++) { size_t offset = frame_ix * n_flow_wells + n_wells * z_ix; - const float * __restrict trace_ptr_start = trace_data + offset; - const float * __restrict trace_ptr_end = trace_ptr_start + n_wells; + const float * __restrict trace_ptr = trace_data + offset; const float * __restrict ref_ptr = ref_data + offset; - float * __restrict previous_ptr = vec_previous.data(); - float * __restrict xx_ptr = vec_sum_x2.data(); - float * __restrict xy_ptr = vec_sum_xy.data(); - while (trace_ptr_start != trace_ptr_end) { - float diff = *ref_ptr - *trace_ptr_start; - float taues = *ref_ptr * taue_est; - float y = *previous_ptr + diff + taues; - *previous_ptr += diff; - float x = *trace_ptr_start; - *xx_ptr += x * x; - *xy_ptr += x * y; - - trace_ptr_start++; - ref_ptr++; - previous_ptr++; - xx_ptr++; - xy_ptr++; + for(size_t trc=0;trc taub_v(taub, n_flow_wells); - Eigen::VectorXf vec_sum_x2(n_wells), vec_sum_xy(n_wells), - vec_previous(n_wells), taub_sum(n_wells); - Eigen::MatrixXf taub_nuc(n_wells, 4); + float vec_sum_xx[n_wells] __attribute__ ((aligned (64))); + float vec_sum_xy[n_wells] __attribute__ ((aligned (64))); + float vec_previous[n_wells] __attribute__ ((aligned (64))); + float taub_sum[n_wells] __attribute__ ((aligned (64))); + float taub_nuc[4][n_wells] __attribute__ ((aligned (64))); int nuc_counts[4] = {0,0,0,0}; - taub_nuc.setZero(); - taub_v.setZero(); - taub_sum.setZero(); + + memset(taub_nuc,0,sizeof(taub_nuc)); + memset(taub_sum,0,sizeof(taub_sum)); for (size_t flow_ix = 0; flow_ix < n_zero_flows; flow_ix++) { int z_ix = zero_flows[flow_ix]; - vec_sum_x2.setZero(); - vec_sum_xy.setZero(); - vec_previous.setZero(); + memset(vec_sum_xx,0,sizeof(vec_sum_xx)); + memset(vec_sum_xy,0,sizeof(vec_sum_xy)); + memset(vec_previous,0,sizeof(vec_previous)); for (size_t frame_ix = 0; frame_ix < n_frames; frame_ix++) { size_t offset = frame_ix * n_flow_wells + n_wells * z_ix; - const float * __restrict trace_ptr_start = trace_data + offset; - const float * __restrict trace_ptr_end = trace_ptr_start + n_wells; - const float * __restrict ref_ptr = ref_data + offset; - float * __restrict previous_ptr = vec_previous.data(); - float * __restrict xx_ptr = vec_sum_x2.data(); - float * __restrict xy_ptr = vec_sum_xy.data(); - while (trace_ptr_start != trace_ptr_end) { - float diff = *ref_ptr - *trace_ptr_start; - float taues = *ref_ptr * taue_est; - float y = *previous_ptr + diff + taues; - *previous_ptr += diff; - float x = *trace_ptr_start; - *xx_ptr += x * x; - *xy_ptr += x * y; - - trace_ptr_start++; - ref_ptr++; - previous_ptr++; - xx_ptr++; - xy_ptr++; + const float * trace_ptr = trace_data + offset; + const float * ref_ptr = ref_data + offset; + for(size_t trc=0;trc 0.0f ? nuc_weight / nuc_div : 0.0f; float total_weight = nuc_weight + combo_weight_mult; float combo_mult = combo_weight_mult/n_zero_flows; - while (tau_b_start != tau_b_end) { + for(size_t trc=0;trc" + "|".join ("(" + var_name + ")" for var_name in var_names) + ")\s*(?P.*)$" + var_names_matcher = re.compile (var_names_re) + var_end_re = r"((?P.*)\s*\))|$" + var_end_matcher = re.compile (var_end_re) + + # read the needed variable definition sections + value_lists = {} # var_name->[value lines] + cur_section = None + with file (source_fname) as source: + for line in source: + line = line.strip () + if cur_section is None: + m = var_names_matcher.match (line) + if m is None: + continue + cur_section = m.group ("varname") + var_values = m.group ("tail") + if len (var_values): + value_lists.setdefault (cur_section, []).append (var_values) + else: + m = var_end_matcher.match (line) + if m is not None: + var_values = m.group ("head") + if len (var_values): + value_lists.setdefault (cur_section, []).append (var_values) + cur_section = None + else: + if len (line) and not line.startswith ("#"): + value_lists.setdefault (cur_section, []).append (line) + + if cur_section is not None: + raise Exception ("Source CMakeLlists file ({}) parsing error: unterminated assignment section for '{}'".format (source_fname, cur_section)) + seen_vars = set (value_lists) + expected_vars = set (var_names) + if seen_vars != expected_vars: + dd = expected_vars - seen_vars + raise Exception ("Source CMakeLlists file ({}) parsing error: missing assignment{} for: {}".format (source_fname, ("" if len (dd) == 1 else "s"), ", ".join (dd))) + + # now read the template and output to destination + cur_section = None + written_sections = set () + with file (template_fname) as template: + with file (dest_fname, "w") as dest: + for line in template: + sline = line.strip () + if cur_section is None: + m = var_names_matcher.match (sline) + if m is None: + dest.write (line) + else: + cur_section = m.group ("varname") + if cur_section in written_sections: + error_logger.error ("Warning: duplicate section '{}' found in template '{}'".format (cur_section, template_fname)) + written_sections.add (cur_section) + dest.write ("set ( {}\n".format (cur_section)) + for content_line in value_lists [cur_section]: + dest.write (" {}\n".format (content_line)) + dest.write (")\n") + else: + m = var_end_matcher.match (sline) + if m is not None: + cur_section = None + + if cur_section is not None: + raise Exception ("Template CMakeLlists file ({}) parsing error: unterminated assignment section for '{}'".format (template_fname, cur_section)) + if written_sections != expected_vars: + dd = expected_vars - written_sections + raise Exception ("Template CMakeLlists file ({}) parsing error: missing assignment section{} for '{}'".format (template_fname, ("" if len (dd) == 1 else "s"), ", ".join (dd))) + return 1 + +def parse_cmdline (args): + epilog = "Destination directory should be pre-populated with the following directories/files:\n {}".format ("\n ".join (fsobj for fsobj in checklist)) + parser = argparse.ArgumentParser (description = __doc__, epilog = epilog, formatter_class = argparse.RawTextHelpFormatter) + parser.add_argument ( + "--verbose", + dest = "verbose", + action = "store_true", + default = False, + help="Print out the actions performed" + ) + parser.add_argument ( + "-D", + dest = "debug", + action = "store_true", + default = False, + help="Enable debug output" + ) + parser.add_argument ( + "--dest", + dest = "dest", + default = "./", + help="Destination directory, defaults to current" + ) + parser.add_argument ( + "source", + help="TorrentSuite source code directory" + ) + params = parser.parse_args (args [1:]) + return params + +def check_ts_dir (dirname): + if not os.path.isdir (dirname): + raise Exception ("TorrentSuite source directory ({}) not found".format (dirname)) + +def check_presence (path, fname): + tt = os.path.join (path, fname) + if not os.path.exists (tt): + raise Exception ("File or directory {} not found".format (tt)) + +def process (par): + + status_logger.info ("Checking pre-requisites for TMAP standalone preparation from TorrentSuite in {} ".format (par.source)) + + check_ts_dir (par.source) + for fname in checklist: + check_presence (par.dest, fname) + check_presence (os.path.join (par.source, CMAKELISTS_RPATH), CMAKELISTS_FNAME) + + status_logger.info ("Preparing TMAP standalone from torrent-suite in %s".format (par.source)) + + cp = Copier (par.source, par.dest) + for spec in copylist: + cp (spec) + + status_logger.info ("Preparing TMAP standalone CMakeLists.txt in %s".format (par.dest)) + + cmake_templ_fname = os.path.join (par.dest, CMAKELISTS_TEMPLATE_FNAME) + cmake_src_fname = os.path.join (par.source, CMAKELISTS_RPATH, CMAKELISTS_FNAME) + cmake_dest_fname = os.path.join (par.dest, CMAKELISTS_FNAME) + prepare_cmakelists (cmake_templ_fname, cmake_src_fname, cmake_dest_fname) + + status_logger.info ("Done: all files are successfully prepared in %s\n" % par.dest) + + return 0 + +def main (args): + par = parse_cmdline (args) + if not par.verbose: + status_logger.setLevel (logging.ERROR) + if not par.debug: + debug_logger.setLevel (logging.ERROR) + return process (par) + #except Exception as e: + # error_logger.error ("Error: {}".format (e)) + # return 1 + +if __name__ == "__main__": + sys.exit (main (sys.argv)) diff --git a/Analysis/TMAP/src/index/tmap_refseq.c b/Analysis/TMAP/src/index/tmap_refseq.c index 5b06c546..25006b57 100644 --- a/Analysis/TMAP/src/index/tmap_refseq.c +++ b/Analysis/TMAP/src/index/tmap_refseq.c @@ -1252,6 +1252,8 @@ enum ovr_opt_code // --c-bw OO_c_bw, + // --score-thr + OO_score_thr, // --end-repair OO_end_repair, // --max-one-large-indel-rescue @@ -1396,10 +1398,12 @@ static const sysopt_t overridable_opts [] = { "c-gep", required_argument, NULL, OO_c_gep }, // --c-bw { "c-bw", required_argument, NULL, OO_c_bw }, + // --score-thr + { "score_thr", required_argument, NULL, OO_score_thr }, // Following options are recognised per se as well as with -le and -he suffixes: // --end-repair - { "end-repair", required_argument, NULL, OO_end_repair }, + { "end-repair", required_argument, NULL, OO_end_repair }, // --max-one-large-indel-rescue { "max-one-large-indel-rescue", required_argument, NULL, OO_max_one_large_indel_rescue }, // --min-anchor-large-indel-rescue @@ -1528,8 +1532,8 @@ int string_to_args (char* argstring, char*** argv_p) // this would return 0 or 2 static uint8_t str2int (const char* str, int* value) { char* endptr; - int errono_save = errno; - errno = 0; + // int errno_save = errno; + // errno = 0; long val = strtol (str, &endptr, 10); if (*endptr) // there was some garbage down a string return 0; @@ -1554,8 +1558,8 @@ static uint8_t str2int (const char* str, int* value) static uint8_t str2double (const char* str, double* value) { char* endptr; - int errono_save = errno; - errno = 0; + // int errno_save = errno; + // errno = 0; double val = strtod (str, &endptr); if (*endptr) // there was some garbage down a string return 0; @@ -1891,6 +1895,14 @@ uint32_t parse_overrides (tmap_map_locopt_t* local_params, char* param_spec_str, else tmap_user_fileproc_msg (bed_fname, lineno, "Error parsing parameters override: --c-bw"); break; + case OO_score_thr: + if (str2int (optarg, &value)) + local_params->score_thr.value = value, + local_params->score_thr.over = 1, + ++ovr_count; + else + tmap_user_fileproc_msg (bed_fname, lineno, "Error parsing parameters override: --end-repair"); + break; case OO_end_repair: if (str2int (optarg, &value)) local_params->end_repair.value = value, @@ -2669,6 +2681,24 @@ tmap_refseq_read_bed_core (tmap_refseq_t *refseq, char *bedfile, int flag, int32 } else { + if (b [num-1] > beg) + { + tmap_error ("Bed file is not sorted by begin", Warn, OutOfRange); + fclose (fp); + return 0; + } + else if (e [num-1] >= end) + { + // ZZ:current ampl is contained in the previous one + continue; + // DK: overrides for containing one preceed + } + else if (b [num-1] == beg) + { + // ZZ:current one has same beg, but larger end, replace previous one + num--; + // DK: overrides for longer one preceed + } if (num >= memsize) { uint32_t prevsize = memsize; @@ -2689,24 +2719,6 @@ tmap_refseq_read_bed_core (tmap_refseq_t *refseq, char *bedfile, int flag, int32 last_parovr_mem_size = memsize; } } - if (b [num-1] > beg) - { - tmap_error ("Bed file is not sorted by begin", Warn, OutOfRange); - fclose (fp); - return 0; - } - else if (e [num-1] >= end) - { - // ZZ:current ampl is contained in the previous one - continue; - // DK: overrides for containing one preceed - } - else if (b [num-1] == beg) - { - // ZZ:current one has same beg, but larger end, replace previous one - num--; - // DK: overrides for longer one preceed - } } b [num] = beg; e [num] = end; diff --git a/Analysis/TMAP/src/io/tmap_file.c b/Analysis/TMAP/src/io/tmap_file.c index 183198f9..dd7bbcb5 100644 --- a/Analysis/TMAP/src/io/tmap_file.c +++ b/Analysis/TMAP/src/io/tmap_file.c @@ -408,6 +408,7 @@ tmap_file_vfprintf(tmap_file_t *fp, const char *format, va_list ap) if(n < 0) { tmap_error("vfprintf failed", Exit, WriteFileError); } + fflush (fp->fp); return n; } @@ -423,6 +424,7 @@ tmap_file_fprintf(tmap_file_t *fp, const char *format, ...) va_start(ap, format); n = vfprintf(fp->fp, format, ap); va_end(ap); + fflush (fp->fp); return n; } @@ -438,6 +440,7 @@ tmap_file_printf(const char *format, ...) va_start(ap, format); n = vfprintf(tmap_file_stdout->fp, format, ap); va_end(ap); + fflush (tmap_file_stdout->fp); return n; } diff --git a/Analysis/TMAP/src/map/pairing/tmap_map_pairing.c b/Analysis/TMAP/src/map/pairing/tmap_map_pairing.c index d5119788..43ea892a 100644 --- a/Analysis/TMAP/src/map/pairing/tmap_map_pairing.c +++ b/Analysis/TMAP/src/map/pairing/tmap_map_pairing.c @@ -335,7 +335,7 @@ tmap_map_pairing_read_rescue_helper(tmap_refseq_t *refseq, double ins_size_mean, double ins_size_std, int32_t strandedness, int32_t positioning, // positioning should be relateive to one/two int32_t read_rescue_std_num, - tmap_rand_t *rand, tmap_map_opt_t *opt) + tmap_rand_t *rand, tmap_map_opt_t *opt, tmap_map_stats_t* stats) { int32_t i, j; int32_t best, n_best, best_mapq=-1; @@ -452,7 +452,7 @@ tmap_map_pairing_read_rescue_helper(tmap_refseq_t *refseq, opt_local.max_seed_band = 0; opt_local.stage_seed_freqc = 0.0; opt_local.bw += ins_size_std * read_rescue_std_num; - sams = tmap_map_util_sw_gen_score(refseq, two_orig, sams, two_seq, rand, &opt_local, NULL); + sams = tmap_map_util_sw_gen_score(refseq, two_orig, sams, two_seq, rand, &opt_local, NULL, stats); return sams; } @@ -462,7 +462,7 @@ tmap_map_pairing_read_rescue(tmap_refseq_t *refseq, tmap_seq_t *one_seq_orig, tmap_seq_t *two_seq_orig, tmap_map_sams_t *one, tmap_map_sams_t *two, tmap_seq_t *one_seq[2], tmap_seq_t *two_seq[2], - tmap_rand_t *rand, tmap_map_opt_t *opt) + tmap_rand_t *rand, tmap_map_opt_t *opt, tmap_map_stats_t* stat) { tmap_map_sams_t *one_rr = NULL, *two_rr = NULL; int32_t i, flag = 0; @@ -472,7 +472,7 @@ tmap_map_pairing_read_rescue(tmap_refseq_t *refseq, opt->ins_size_mean, opt->ins_size_std, opt->strandedness, 1-opt->positioning, // NB: update positioning opt->read_rescue_std_num, - rand, opt); + rand, opt, stat); //fprintf(stderr, "RR #1: %d\n", one_rr->n); if(0 < one_rr->n) { /* @@ -494,7 +494,7 @@ tmap_map_pairing_read_rescue(tmap_refseq_t *refseq, opt->ins_size_mean, opt->ins_size_std, opt->strandedness, opt->positioning, opt->read_rescue_std_num, - rand, opt); + rand, opt, stat); //fprintf(stderr, "RR #2: %d\n", one_rr->n); if(0 < two_rr->n) { /* diff --git a/Analysis/TMAP/src/map/pairing/tmap_map_pairing.h b/Analysis/TMAP/src/map/pairing/tmap_map_pairing.h index 89a7160c..7f7664d2 100644 --- a/Analysis/TMAP/src/map/pairing/tmap_map_pairing.h +++ b/Analysis/TMAP/src/map/pairing/tmap_map_pairing.h @@ -60,7 +60,7 @@ tmap_map_pairing_read_rescue(tmap_refseq_t *refseq, tmap_seq_t *one_orig, tmap_seq_t *two_orig, tmap_map_sams_t *one, tmap_map_sams_t *two, tmap_seq_t *one_seq[2], tmap_seq_t *two_seq[2], - tmap_rand_t *rand, tmap_map_opt_t *opt); + tmap_rand_t *rand, tmap_map_opt_t *opt, tmap_map_stats_t* stat); /*! given sets of seeds for two ends of pair, scores all possible pairs of seeds and diff --git a/Analysis/TMAP/src/map/tmap_map_driver.c b/Analysis/TMAP/src/map/tmap_map_driver.c index 2f2c8d78..c4bb862c 100644 --- a/Analysis/TMAP/src/map/tmap_map_driver.c +++ b/Analysis/TMAP/src/map/tmap_map_driver.c @@ -5,6 +5,7 @@ #include #include #include +#include #ifdef HAVE_LIBPTHREAD #include #endif @@ -38,6 +39,56 @@ #define PARANOID_TESTS 0 +// DK: declare fileno here to avoid using __USE_POSIX (which may have unknown effect on build) + +extern int fileno (FILE *__stream); + +/*! + Driver data to be passed to a thread + */ +typedef struct { + sam_header_t *sam_header; /*!< the SAM Header */ + tmap_seqs_t **seqs_buffer; /*!< the buffers of sequences */ + int32_t seqs_buffer_length; /*!< the buffers length */ + tmap_map_record_t **records; /*!< the alignments for each sequence */ + tmap_map_bams_t **bams; /*!< the BAM alignments for each sequence */ + tmap_index_t *index; /*!< pointer to the reference index */ + tmap_map_driver_t *driver; /*!< the main driver object */ + tmap_map_stats_t *stat; /*!< the driver statistics */ + tmap_rand_t *rand; /*!< the random number generator */ + // DVK - realigner + struct RealignProxy *realigner; /*!< post-processing realigner engine */ + struct RealignProxy *context; /*!< post-processing context-dependent realignment engine */ + int32_t do_pairing; /*!< 1 if we are performing pairing paramter calculation, 0 otherwise */ + int32_t tid; /*!< the zero-based thread id */ + int32_t *seqCntr; + sem_t processor_trigger_sem; + sem_t processor_done_sem; + int32_t dismantle; +} tmap_map_driver_thread_data_t; + +typedef struct { + tmap_seqs_io_t *io_in; + tmap_sam_io_t *io_out; + tmap_seqs_t **seqs_buffer; + int32_t seqs_buffer_length; + int32_t reads_queue_size; + sem_t reader_trigger_sem; + sem_t reader_done_sem; + int32_t dismantle; +} tmap_map_driver_thread_io_data_t; + +typedef struct{ + //struct to hold data for writer thread + int32_t seqs_buffer_length; + tmap_map_bams_t **bams; + tmap_map_record_t **records; + tmap_sam_io_t *io_out; + sem_t writer_trigger_sem; + sem_t writer_done_sem; + int32_t dismantle; +} tmap_map_driver_thread_writer_data_t; + // NB: do not turn these on, as they do not currently improve run time. They // could be useful if many duplicate lookups are performed and the hash @@ -943,7 +994,7 @@ void tail_repeats_clip_read tmap_seq_t* qryseq, tmap_refseq_t* refseq, tmap_map_sams_t* sams, - struct RealignProxy* realigner, + // struct RealignProxy* realigner, tmap_map_stats_t *stat, int32_t repclip_continuation, int32_t repclip_flag, @@ -1010,7 +1061,8 @@ void tail_repeats_clip_read filtered ++; continue; } - uint8_t* ref = (uint8_t*) ref_mem (realigner, ref_tail_len); + // uint8_t* ref = (uint8_t*) ref_mem (realigner, ref_tail_len); + uint8_t* ref = alloca ( sizeof (uint8_t) * ref_tail_len); int32_t converted_cnt; tmap_refseq_subseq2 (refseq, ref_id+1, ref_tail_beg+1, ref_tail_end, ref, 0, &converted_cnt); // convert reference to ascii format @@ -1129,21 +1181,7 @@ void tail_repeat_clip_reads (tmap_seqs_t *seqs_buffer, tmap_refseq_t* refseq, tm #endif void -tmap_map_driver_core_worker(sam_header_t *sam_header, - tmap_seqs_t **seqs_buffer, - tmap_map_record_t **records, - tmap_map_bams_t **bams, - int32_t seqs_buffer_length, - int32_t *buffer_idx, - tmap_index_t *index, - tmap_map_driver_t *driver, - tmap_map_stats_t *stat, - tmap_rand_t *rand, - // DVK - realigner - struct RealignProxy* realigner, - struct RealignProxy* context, - int32_t do_pairing, - int32_t tid) +tmap_map_driver_core_worker(tmap_map_driver_thread_data_t *params) { int32_t i, j, k, low = 0; int32_t found; @@ -1155,6 +1193,16 @@ tmap_map_driver_core_worker(sam_header_t *sam_header, // common memory resource for WS traceback paths tmap_sw_path_t *path_buf = NULL; // buffer for traceback path int32_t path_buf_sz = 0; // used portion and allocated size of traceback path. + sam_header_t *sam_header=params->sam_header; + tmap_index_t *index=params->index; + tmap_map_driver_t *driver=params->driver; + tmap_map_stats_t *stat=params->stat; + tmap_rand_t *rand=params->rand; + // DVK - realigner + struct RealignProxy* realigner=params->realigner; + struct RealignProxy* context=params->context; + int32_t tid=params->tid; + int32_t *seqCntr=params->seqCntr; #ifdef TMAP_DRIVER_USE_HASH // init the occurence hash @@ -1175,450 +1223,472 @@ tmap_map_driver_core_worker(sam_header_t *sam_header, tmap_map_driver_do_threads_init (driver, tid); // Go through the buffer - while (low < seqs_buffer_length) + while(1) { - if (tid == (low % driver->opt->num_threads)) + sem_wait (¶ms->processor_trigger_sem); + if (params->dismantle) + break; + while (1) { - tmap_map_stats_t *stage_stat = NULL; - tmap_map_record_t *record_prev = NULL; - int32_t num_ends; - - #ifdef TMAP_DRIVER_USE_HASH - #ifdef TMAP_DRIVER_CLEAR_HASH_PER_READ - // TODO: should we hash each read, or across the thread? - tmap_bwt_match_hash_clear (hash); - #endif - #endif - - num_ends = seqs_buffer [low]->n; - if(max_num_ends < num_ends) + int32_t lowStart = __atomic_fetch_add(seqCntr,10,__ATOMIC_SEQ_CST); + int32_t lowEnd = lowStart+10; + if(lowEnd >params->seqs_buffer_length) + lowEnd=params->seqs_buffer_length; + if(lowStart >= params->seqs_buffer_length) + break; + for(low=lowStart;lowseqs_buffer_length;low++) { - seqs = tmap_realloc (seqs, sizeof (tmap_seq_t**) * num_ends, "seqs"); - while(max_num_ends < num_ends) + // if (!(tid == (low % driver->opt->num_threads))) + // continue; + tmap_map_stats_t *stage_stat = NULL; + tmap_map_record_t *record_prev = NULL; + int32_t num_ends; + + #ifdef TMAP_DRIVER_USE_HASH + #ifdef TMAP_DRIVER_CLEAR_HASH_PER_READ + // TODO: should we hash each read, or across the thread? + tmap_bwt_match_hash_clear (hash); + #endif + #endif + + num_ends = params->seqs_buffer [low]->n; + if(max_num_ends < num_ends) { - seqs [max_num_ends] = tmap_calloc(4, sizeof(tmap_seq_t*), "seqs[max_num_ends]"); - max_num_ends++; + seqs = tmap_realloc (seqs, sizeof (tmap_seq_t**) * num_ends, "seqs"); + while(max_num_ends < num_ends) + { + seqs [max_num_ends] = tmap_calloc(4, sizeof(tmap_seq_t*), "seqs[max_num_ends]"); + max_num_ends++; + } + max_num_ends = num_ends; } - max_num_ends = num_ends; - } - // re-initialize the random seed - if(driver->opt->rand_read_name) - tmap_rand_reinit(rand, tmap_hash_str_hash_func_exc(tmap_seq_get_name(seqs_buffer[low]->seqs[0])->s, driver->opt->prefix_exclude, driver->opt->suffix_exclude)); + // re-initialize the random seed + if(driver->opt->rand_read_name) + tmap_rand_reinit(rand, tmap_hash_str_hash_func_exc(tmap_seq_get_name(params->seqs_buffer[low]->seqs[0])->s, driver->opt->prefix_exclude, driver->opt->suffix_exclude)); - // init - for(i = 0; i < num_ends; i++) - { - tmap_map_driver_init_seqs (seqs [i], seqs_buffer [low]->seqs [i], -1); - if (NULL != stat) stat->num_reads++; - } + // init + for(i = 0; i < num_ends; i++) + { + tmap_map_driver_init_seqs (seqs [i], params->seqs_buffer [low]->seqs [i], -1); + if (NULL != stat) stat->num_reads++; + } - // init records - records [low] = tmap_map_record_init (num_ends); - - // go through each stage - int32_t stage_ord; - for (stage_ord = 0; stage_ord < driver->num_stages; ++stage_ord) - { // for each stage - - tmap_map_driver_stage_t *stage = driver->stages [stage_ord]; - //// tmap_sw_param_t sw_par; - // stage may have special sw parameters - // DK here handling of global arrays matrix and iupac_matrix is completely messed up. - // The threads would randomly and concurrently override the matix as each of them go through stages. - // Safe fix would be to allocate matrix locally here and populate it. - // That would be unnecessary extra work per each read (which is performed here anyway) - // Better option is to allocate per-stage parameters storage and compute them once per stage. - // Implementing the latter - // To avoid race when filling in the stage params, init them when thread data gets initialized. - - // tmap_map_util_populate_sw_par_iupac (&(stage->sw_param), stage->opt); - - // stage stats - stage_stat = tmap_map_stats_init (); - - // seed - for (j = 0; j < num_ends; j++) - { // for each end - tmap_seq_t** stage_seqs = NULL; - // should we seed using the whole read? - if(0 < stage->opt->stage_seed_max_length && stage->opt->stage_seed_max_length < tmap_seq_get_bases_length (seqs [j][0])) - { - stage_seqs = tmap_calloc (4, sizeof (tmap_seq_t*), "seqs[]"); - tmap_map_driver_init_seqs (stage_seqs, seqs_buffer [low]->seqs [stage_ord], stage->opt->stage_seed_max_length); - } - else - stage_seqs = seqs [j]; - for (k = 0; k < stage->num_algorithms; k++) - { // for each algorithm - tmap_map_driver_algorithm_t *algorithm = stage->algorithms [k]; - tmap_map_sams_t *sams = NULL; - if (stage_ord + 1 != algorithm->opt->algo_stage) - tmap_bug(); - // map - sams = algorithm->func_thread_map (&algorithm->thread_data [tid], stage_seqs, index, hash, rand, algorithm->opt); - if (NULL == sams) - tmap_error ("the thread function did not return a mapping", Exit, OutOfRange); - // append - tmap_map_sams_merge (records [low]->sams [j], sams); - // destroy - tmap_map_sams_destroy (sams); - } - stage_stat->num_after_seeding += records [low]->sams [j]->n; - if (0 < stage->opt->stage_seed_max_length && stage->opt->stage_seed_max_length < tmap_seq_get_bases_length (seqs [j][0])) - { - // free - for (j = 0; j < 4; j++) + // init records + params->records [low] = tmap_map_record_init (num_ends); + + // go through each stage + int32_t stage_ord; + for (stage_ord = 0; stage_ord < driver->num_stages; ++stage_ord) + { // for each stage + + tmap_map_driver_stage_t *stage = driver->stages [stage_ord]; + //// tmap_sw_param_t sw_par; + // stage may have special sw parameters + // DK here handling of global arrays matrix and iupac_matrix is completely messed up. + // The threads would randomly and concurrently override the matix as each of them go through stages. + // Safe fix would be to allocate matrix locally here and populate it. + // That would be unnecessary extra work per each read (which is performed here anyway) + // Better option is to allocate per-stage parameters storage and compute them once per stage. + // Implementing the latter + // To avoid race when filling in the stage params, init them when thread data gets initialized. + + // tmap_map_util_populate_sw_par_iupac (&(stage->sw_param), stage->opt); + + // stage stats + stage_stat = tmap_map_stats_init (); + + // seed + for (j = 0; j < num_ends; j++) + { // for each end + tmap_seq_t** stage_seqs = NULL; + // should we seed using the whole read? + if(0 < stage->opt->stage_seed_max_length && stage->opt->stage_seed_max_length < tmap_seq_get_bases_length (seqs [j][0])) + { + stage_seqs = tmap_calloc (4, sizeof (tmap_seq_t*), "seqs[]"); + tmap_map_driver_init_seqs (stage_seqs, params->seqs_buffer [low]->seqs [stage_ord], stage->opt->stage_seed_max_length); + } + else + stage_seqs = seqs [j]; + for (k = 0; k < stage->num_algorithms; k++) + { // for each algorithm + tmap_map_driver_algorithm_t *algorithm = stage->algorithms [k]; + tmap_map_sams_t *sams = NULL; + if (stage_ord + 1 != algorithm->opt->algo_stage) + tmap_bug(); + // map + sams = algorithm->func_thread_map (&algorithm->thread_data [tid], stage_seqs, index, hash, rand, algorithm->opt); + if (NULL == sams) + tmap_error ("the thread function did not return a mapping", Exit, OutOfRange); + // append + tmap_map_sams_merge (params->records [low]->sams [j], sams); + // destroy + tmap_map_sams_destroy (sams); + } + stage_stat->num_after_seeding += params->records [low]->sams [j]->n; + if (0 < stage->opt->stage_seed_max_length && stage->opt->stage_seed_max_length < tmap_seq_get_bases_length (seqs [j][0])) { - tmap_seq_destroy (stage_seqs [j]); - stage_seqs [j] = NULL; + // free + for (j = 0; j < 4; j++) + { + tmap_seq_destroy (stage_seqs [j]); + stage_seqs [j] = NULL; + } } + stage_seqs = NULL; // do not use } - stage_seqs = NULL; // do not use - } - // keep mappings for subsequent stages or restore mappings from - // previous stages - if (1 == stage->opt->stage_keep_all) - { - // merge from the previous stage - if (0 < i) + // keep mappings for subsequent stages or restore mappings from + // previous stages + if (1 == stage->opt->stage_keep_all) { - tmap_map_record_merge (records [low], record_prev); - // destroy the record - tmap_map_record_destroy (record_prev); - record_prev = NULL; - } + // merge from the previous stage + if (0 < i) + { + tmap_map_record_merge (params->records [low], record_prev); + // destroy the record + tmap_map_record_destroy (record_prev); + record_prev = NULL; + } - // keep for the next stage - if (i < driver->num_stages - 1) // more stages left - record_prev = tmap_map_record_clone (records [low]); - } + // keep for the next stage + if (i < driver->num_stages - 1) // more stages left + record_prev = tmap_map_record_clone (params->records [low]); + } - // generate scores with smith waterman - for (j = 0; j < num_ends; j++) - { // for each end - records [low]->sams [j] = tmap_map_util_sw_gen_score (index->refseq, seqs_buffer [low]->seqs [j], records [low]->sams [j], seqs [j], rand, stage->opt, &k); - stage_stat->num_after_scoring += records [low]->sams [j]->n; - stage_stat->num_after_grouping += k; - } + // generate scores with smith waterman + for (j = 0; j < num_ends; j++) + { // for each end + params->records [low]->sams [j] = tmap_map_util_sw_gen_score (index->refseq, params->seqs_buffer [low]->seqs [j], params->records [low]->sams [j], seqs [j], rand, stage->opt, &k, stat); + stage_stat->num_after_scoring += params->records [low]->sams [j]->n; + stage_stat->num_after_grouping += k; + } - // remove duplicates - for (j = 0; j < num_ends; j++) - { // for each end - tmap_map_util_remove_duplicates (records [low]->sams [j], stage->opt->dup_window, rand); - stage_stat->num_after_rmdup += records [low]->sams [j]->n; - } + // remove duplicates + for (j = 0; j < num_ends; j++) + { // for each end + tmap_map_util_remove_duplicates (params->records [low]->sams [j], stage->opt->dup_window, rand); + stage_stat->num_after_rmdup += params->records [low]->sams [j]->n; + } - // (single-end) mapping quality - for (j = 0;j < num_ends; j++) // for each end - driver->func_mapq (records [low]->sams [j], tmap_seq_get_bases_length (seqs [j][0]), stage->opt, index->refseq); + // (single-end) mapping quality + for (j = 0;j < num_ends; j++) // for each end + driver->func_mapq (params->records [low]->sams [j], tmap_seq_get_bases_length (seqs [j][0]), stage->opt, index->refseq); - // filter if we have more stages - if (stage_ord < driver->num_stages-1) - { - for (j = 0; j < num_ends; j++) // for each end - tmap_map_sams_filter2 (records [low]->sams [j], stage->opt->stage_score_thr, stage->opt->stage_mapq_thr); - } - - if (0 == do_pairing && 0 <= driver->opt->strandedness && 0 <= driver->opt->positioning - && 2 == num_ends && 0 < records [low]->sams [0]->n && 0 < records [low]->sams [1]->n) - { // pairs of reads! - // read rescue - if (1 == stage->opt->read_rescue) + // filter if we have more stages + if (stage_ord < driver->num_stages-1) { - int32_t flag = tmap_map_pairing_read_rescue (index->refseq, - seqs_buffer [low]->seqs[0], seqs_buffer [low]->seqs [1], - records [low]->sams [0], records [low]->sams [1], - seqs [0], seqs [1], - rand, stage->opt); - // recalculate mapping qualities if necessary - if (0 < (flag & 0x1)) // first end was rescued - driver->func_mapq (records [low]->sams [0], tmap_seq_get_bases_length (seqs [0][0]), stage->opt, index->refseq); - if(0 < (flag & 0x2)) // second end was rescued - driver->func_mapq (records [low]->sams [1], tmap_seq_get_bases_length (seqs [1][0]), stage->opt, index->refseq); + for (j = 0; j < num_ends; j++) // for each end + tmap_map_sams_filter2 (params->records [low]->sams [j], stage->opt->stage_score_thr, stage->opt->stage_mapq_thr); } - // pick pairs - tmap_map_pairing_pick_pairs (records [low]->sams [0], records [low]->sams [1], - seqs [0][0], seqs [1][0], - rand, stage->opt); - } - else - { - // choose alignments - for (j = 0; j < num_ends; ++j) - { // for each end - tmap_map_sams_filter1 (records [low]->sams [j], stage->opt->aln_output_mode, TMAP_MAP_ALGO_NONE, rand); - stage_stat->num_after_filter += records [low]->sams [j]->n; + + if (0 == params->do_pairing && 0 <= driver->opt->strandedness && 0 <= driver->opt->positioning + && 2 == num_ends && 0 < params->records [low]->sams [0]->n && 0 < params->records [low]->sams [1]->n) + { // pairs of reads! + // read rescue + if (1 == stage->opt->read_rescue) + { + int32_t flag = tmap_map_pairing_read_rescue (index->refseq, + params->seqs_buffer [low]->seqs[0], params->seqs_buffer [low]->seqs [1], + params->records [low]->sams [0], params->records [low]->sams [1], + seqs [0], seqs [1], + rand, stage->opt, stat); + // recalculate mapping qualities if necessary + if (0 < (flag & 0x1)) // first end was rescued + driver->func_mapq (params->records [low]->sams [0], tmap_seq_get_bases_length (seqs [0][0]), stage->opt, index->refseq); + if(0 < (flag & 0x2)) // second end was rescued + driver->func_mapq (params->records [low]->sams [1], tmap_seq_get_bases_length (seqs [1][0]), stage->opt, index->refseq); + } + // pick pairs + tmap_map_pairing_pick_pairs (params->records [low]->sams [0], params->records [low]->sams [1], + seqs [0][0], seqs [1][0], + rand, stage->opt); } - } - - // generate and post-process alignments - found = 0; - for (j = 0; j < num_ends; ++j) // for each end - { - tmap_map_sams_t* sams = records [low]->sams [j]; - tmap_seq_t* seq = seqs_buffer [low]->seqs [j]; - tmap_seq_t** seq_variants = seqs [j]; - // if there are no mappings, continue - if (!sams->n) - continue; - // find alignment starts - sams = records [low]->sams [j] = tmap_map_util_find_align_starts - ( - index->refseq, // reference server - sams, // initial rough mapping - seq, // read - seq_variants, // array of size 4 that contains pre-computed inverse / complement combinations - stage->opt, // stage parameters - &target, // target cache control structure - stat // statistics accumulator - ); - if (!sams->n) - continue; - - // map to amplicons (if BED is given and parameters override enabled) - if (index->refseq->bed_exist && (stage->opt->use_param_ovr || stage->opt->use_bed_in_end_repair || stage->opt->use_bed_read_ends_stat)) - tmap_map_find_amplicons ( - stage_ord, // stage index - stage->opt, // stage options - &(stage->sw_param), // stage sw parameters - index->refseq, // reference server - sams // mappings - ); - - // reference alignment - tmap_map_util_align - ( - index->refseq, // reference server - sams, // mappings to compute alignments for - seq_variants, // array of size 4 that contains pre-computed inverse / complement combinations - &target, // target cache control structure - stage_ord, // processing stage index - &(stage->sw_param), // Smith-Waterman scoring parameters - &path_buf, // buffer for traceback path - &path_buf_sz, // used portion and allocated size of traceback path. - stat // statistics accumulator - ); - // realign in flowspace or with context, if requested - if (stage->opt->aln_flowspace || stage->opt->use_param_ovr) - // NB: seqs_buffer should have its key sequence if 0 < key_seq_len - tmap_map_util_fsw - ( - seq, - sams, - index->refseq, - stage->opt->bw, - stage->opt->softclip_type, - stage->opt->score_thr, - stage->opt->score_match, - stage->opt->pen_mm, - stage->opt->pen_gapo, - stage->opt->pen_gape, - stage->opt->fscore, - 1 - stage->opt->ignore_flowgram, - stage->opt->aln_flowspace, - stage->opt->use_param_ovr, - stat - ); - // context-sensitive (hp-indel-liberal) realignment - if (stage->opt->do_hp_weight || stage->opt->use_param_ovr) - context_align_read - ( - seq, - index->refseq, - sams, - context, - stat, - stage->opt - ); - // perform anti-dyslexic realignment if enabled - if (stage->opt->do_realign || stage->opt->use_param_ovr) + else { - realign_read - ( - seq, - index->refseq, - sams, - realigner, - stat, - stage->opt - ); + // choose alignments + for (j = 0; j < num_ends; ++j) + { // for each end + tmap_map_sams_filter1 (params->records [low]->sams [j], stage->opt->aln_output_mode, TMAP_MAP_ALGO_NONE, rand); + stage_stat->num_after_filter += params->records [low]->sams [j]->n; + } } - // salvage ends - if (stage->opt->pen_gapl >= 0 || stage->opt->use_param_ovr) - tmap_map_util_salvage_edge_indels + + // generate and post-process alignments + found = 0; + for (j = 0; j < num_ends; ++j) // for each end + { + tmap_map_sams_t* sams = params->records [low]->sams [j]; + tmap_seq_t* seq = params->seqs_buffer [low]->seqs [j]; + tmap_seq_t** seq_variants = seqs [j]; + // if there are no mappings, continue + if (!sams->n) + continue; + // find alignment starts + sams = params->records [low]->sams [j] = tmap_map_util_find_align_starts ( index->refseq, // reference server - sams, // mappings to compute alignments for - seq_variants, // array of size 4 that contains pre-computed inverse / complement combinations - &target, // target cache control structure - stage->opt, // tmap parameters - stage_ord, // processing stage index - &stage->sw_param, // Smith-Waterman scoring parameters - &path_buf, // buffer for traceback path - &path_buf_sz, // used portion and allocated size of traceback path. - stat - ); - // trim key (no local overriding for this option) - if (1 == stage->opt->softclip_key) - tmap_map_util_trim_key - ( - sams, // mappings to compute alignments for + sams, // initial rough mapping seq, // read seq_variants, // array of size 4 that contains pre-computed inverse / complement combinations - index->refseq, // reference server + stage->opt, // stage parameters &target, // target cache control structure - stat + stat // statistics accumulator ); - // end repair - if (stage->opt->end_repair != 0 || stage->opt->use_param_ovr) - tmap_map_util_end_repair_bulk + if (!sams->n) + continue; + + // map to amplicons (if BED is given and parameters override enabled) + if (index->refseq->bed_exist && (stage->opt->use_param_ovr || stage->opt->use_bed_in_end_repair || stage->opt->use_bed_read_ends_stat)) + tmap_map_find_amplicons ( + stage_ord, // stage index + stage->opt, // stage options + &(stage->sw_param), // stage sw parameters + index->refseq, // reference server + sams // mappings + ); + + // reference alignment + tmap_map_util_align ( index->refseq, // reference server sams, // mappings to compute alignments for - seq, // read seq_variants, // array of size 4 that contains pre-computed inverse / complement combinations - stage->opt, // tmap parameters &target, // target cache control structure - &path_buf, // buffer for traceback path - &path_buf_sz, // used portion and allocated size of traceback path. - stat - ); - // REPAiR - if (stage->opt->use_bed_read_ends_stat != 0 || stage->opt->use_param_ovr) - tmap_map_util_REPAiR_bulk - ( - index->refseq, // reference server - sams, // mappings to compute alignments for - seq, // read - seq_variants, // array of size 4 that contains pre-computed inverse / complement combinations - stage->opt, // tmap parameters stage_ord, // processing stage index - &stage->sw_param, // swage SW parameters - &target, // target cache control structure + &(stage->sw_param), // Smith-Waterman scoring parameters &path_buf, // buffer for traceback path &path_buf_sz, // used portion and allocated size of traceback path. - stat + stat // statistics accumulator ); - // explicitly fix 5' softclip is required - if ((!stage->opt->end_repair_5_prime_softclip && (stage->opt->softclip_type == 2 || stage->opt->softclip_type == 3)) - || stage->opt->use_param_ovr) - { - int i; - for (i = 0; i != sams->n; ++i) - { - tmap_map_sam_t* s = sams->sams + i; - tmap_map_util_remove_5_prime_softclip + // realign in flowspace or with context, if requested + if (stage->opt->aln_flowspace || stage->opt->use_param_ovr) + // NB: seqs_buffer should have its key sequence if 0 < key_seq_len + tmap_map_util_fsw ( - index->refseq, - s, - seq, - seq_variants, - &target, - &path_buf, - &path_buf_sz, - stage_ord, - &(stage->sw_param), - stage->opt, + seq, + sams, + index->refseq, + stage->opt->bw, + stage->opt->softclip_type, + stage->opt->score_thr, + stage->opt->score_match, + stage->opt->pen_mm, + stage->opt->pen_gapo, + stage->opt->pen_gape, + stage->opt->fscore, + 1 - stage->opt->ignore_flowgram, + stage->opt->aln_flowspace, + stage->opt->use_param_ovr, stat ); - } - } - if (stage->opt->cigar_sanity_check || stage->opt->use_param_ovr) // do this before tail repeat clipping as the latter does not update alignment box. TODO: update box in tail clip and move this to the very end of alignment post processing - { - int i; - for (i = 0; i != sams->n; ++i) + // context-sensitive (hp-indel-liberal) realignment + // if (stage->opt->do_hp_weight || stage->opt->use_param_ovr) + if (context) // the logic that determines if context realignment is to be tried is used to define context ptr; it is NULL if context realignment is not required + context_align_read + ( + seq, + index->refseq, + sams, + context, + stat, + stage->opt + ); + // perform anti-dyslexic realignment if enabled + // if (stage->opt->do_realign || stage->opt->use_param_ovr) + if (realigner) // the logic that determines if context realignment is to be tried is used to define context ptr; it is NULL if context realignment is not required { - cigar_sanity_check + realign_read ( - index->refseq, - sams->sams + i, - seq, - seq_variants, - &target, + seq, + index->refseq, + sams, + realigner, + stat, stage->opt ); } - } - // clip repeats - if (driver->opt->do_repeat_clip || stage->opt->use_param_ovr) - tail_repeats_clip_read - ( - seq, - index->refseq, - sams, - realigner, - stat, - stage->opt->repclip_continuation, - stage->opt->do_repeat_clip, - stage->opt->use_param_ovr - ); + // salvage ends + if (stage->opt->pen_gapl >= 0 || stage->opt->use_param_ovr) + tmap_map_util_salvage_edge_indels + ( + index->refseq, // reference server + sams, // mappings to compute alignments for + seq_variants, // array of size 4 that contains pre-computed inverse / complement combinations + &target, // target cache control structure + stage->opt, // tmap parameters + stage_ord, // processing stage index + &stage->sw_param, // Smith-Waterman scoring parameters + &path_buf, // buffer for traceback path + &path_buf_sz, // used portion and allocated size of traceback path. + stat + ); + // trim key (no local overriding for this option) + if (1 == stage->opt->softclip_key) + tmap_map_util_trim_key + ( + sams, // mappings to compute alignments for + seq, // read + seq_variants, // array of size 4 that contains pre-computed inverse / complement combinations + index->refseq, // reference server + &target, // target cache control structure + stat + ); + // end repair + if (stage->opt->end_repair != 0 || stage->opt->use_param_ovr) + tmap_map_util_end_repair_bulk + ( + index->refseq, // reference server + sams, // mappings to compute alignments for + seq, // read + seq_variants, // array of size 4 that contains pre-computed inverse / complement combinations + stage->opt, // tmap parameters + &target, // target cache control structure + &path_buf, // buffer for traceback path + &path_buf_sz, // used portion and allocated size of traceback path. + stat + ); + // REPAiR + if (stage->opt->use_bed_read_ends_stat != 0 || stage->opt->use_param_ovr) + tmap_map_util_REPAiR_bulk + ( + index->refseq, // reference server + sams, // mappings to compute alignments for + seq, // read + seq_variants, // array of size 4 that contains pre-computed inverse / complement combinations + stage->opt, // tmap parameters + stage_ord, // processing stage index + &stage->sw_param, // swage SW parameters + &target, // target cache control structure + &path_buf, // buffer for traceback path + &path_buf_sz, // used portion and allocated size of traceback path. + stat + ); + // explicitly fix 5' softclip is required + if ((!stage->opt->end_repair_5_prime_softclip && (stage->opt->softclip_type == 2 || stage->opt->softclip_type == 3)) + || stage->opt->use_param_ovr) + { + int i; + for (i = 0; i != sams->n; ++i) + { + tmap_map_sam_t* s = sams->sams + i; + tmap_map_util_remove_5_prime_softclip + ( + index->refseq, + s, + seq, + seq_variants, + &target, + &path_buf, + &path_buf_sz, + stage_ord, + &(stage->sw_param), + stage->opt, + stat + ); + } + } + if (stage->opt->cigar_sanity_check || stage->opt->use_param_ovr) // do this before tail repeat clipping as the latter does not update alignment box. TODO: update box in tail clip and move this to the very end of alignment post processing + { + int i; + for (i = 0; i != sams->n; ++i) + { + cigar_sanity_check + ( + index->refseq, + sams->sams + i, + seq, + seq_variants, + &target, + stage->opt + ); + } + } + // clip repeats + if (driver->opt->do_repeat_clip || stage->opt->use_param_ovr) + tail_repeats_clip_read + ( + seq, + index->refseq, + sams, + // realigner, // DK: dependency of repeat clipper on realignment is removed to allow easier conditional realigner memory management for massively parallel setups + stat, + stage->opt->repclip_continuation, + stage->opt->do_repeat_clip, + stage->opt->use_param_ovr + ); - stage_stat->num_with_mapping++; - found = 1; - } + stage_stat->num_with_mapping++; + found = 1; + } - // TODO - // if paired, update pairing score based on target start? + // TODO + // if paired, update pairing score based on target start? - // did we find any mappings? - if (found) - { // yes - if (stat) - tmap_map_stats_add (stat, stage_stat); + // did we find any mappings? + if (found) + { // yes + if (stat) + tmap_map_stats_add (stat, stage_stat); + tmap_map_stats_destroy (stage_stat); + break; + } + else + { // no + tmap_map_record_destroy (params->records [low]); + // re-init + params->records [low] = tmap_map_record_init (num_ends); + } tmap_map_stats_destroy (stage_stat); - break; - } - else - { // no - tmap_map_record_destroy (records [low]); - // re-init - records [low] = tmap_map_record_init (num_ends); } - tmap_map_stats_destroy (stage_stat); - } - // only convert to BAM and destroy the records if we are not trying to - // estimate the pairing parameters - if (0 == do_pairing) - { - // convert the record to bam - if (1 == seqs_buffer [low]->n) - { - bams [low] = tmap_map_bams_init (1); - bams [low]->bams [0] = tmap_map_sams_print (seqs_buffer [low]->seqs [0], index->refseq, records [low]->sams [0], - 0, NULL, driver->opt->sam_flowspace_tags, driver->opt->bidirectional, driver->opt->seq_eq, driver->opt->min_al_len, driver->opt->min_al_cov, driver->opt->min_identity, driver->opt->score_match, &(stat->num_filtered_als)); - } - else + // only convert to BAM and destroy the records if we are not trying to + // estimate the pairing parameters + if (0 == params->do_pairing) { - bams [low] = tmap_map_bams_init (seqs_buffer [low]->n); - for (j = 0; j < seqs_buffer [low]->n; j++) - bams [low]->bams [j] = tmap_map_sams_print (seqs_buffer [low]->seqs [j], index->refseq, records [low]->sams [j], - (0 == j) ? 1 : ((seqs_buffer [low]->n-1 == j) ? 2 : 0), - records [low]->sams[(j+1) % seqs_buffer [low]->n], - driver->opt->sam_flowspace_tags, driver->opt->bidirectional, driver->opt->seq_eq, driver->opt->min_al_len, driver->opt->min_al_cov, driver->opt->min_identity, driver->opt->score_match, &(stat->num_filtered_als)); + + if(params->bams[low]){ + tmap_map_bams_destroy(params->bams[low]); + params->bams[low] = NULL; + } + + // convert the record to bam + if (1 == params->seqs_buffer [low]->n) + { + params->bams [low] = tmap_map_bams_init (1); + params->bams [low]->bams [0] = tmap_map_sams_print (params->seqs_buffer [low]->seqs [0], index->refseq, params->records [low]->sams [0], + 0, NULL, driver->opt->sam_flowspace_tags, driver->opt->bidirectional, driver->opt->seq_eq, driver->opt->min_al_len, driver->opt->min_al_cov, driver->opt->min_identity, driver->opt->score_match, &(stat->num_filtered_als)); + } + else + { + params->bams [low] = tmap_map_bams_init (params->seqs_buffer [low]->n); + for (j = 0; j < params->seqs_buffer [low]->n; j++) + params->bams [low]->bams [j] = tmap_map_sams_print (params->seqs_buffer [low]->seqs [j], index->refseq, params->records [low]->sams [j], + (0 == j) ? 1 : ((params->seqs_buffer [low]->n-1 == j) ? 2 : 0), + params->records [low]->sams[(j+1) % params->seqs_buffer [low]->n], + driver->opt->sam_flowspace_tags, driver->opt->bidirectional, driver->opt->seq_eq, driver->opt->min_al_len, driver->opt->min_al_cov, driver->opt->min_identity, driver->opt->score_match, &(stat->num_filtered_als)); + } + // free alignments, for space + tmap_map_record_destroy (params->records [low]); + params->records [low] = NULL; } - // free alignments, for space - tmap_map_record_destroy (records [low]); - records [low] = NULL; - } - // free seqs - for (i = 0; i < num_ends; i++) - { - for (j = 0; j < 4; j++) + // free seqs + for (i = 0; i < num_ends; i++) { - tmap_seq_destroy (seqs [i][j]); - seqs [i][j] = NULL; + for (j = 0; j < 4; j++) + { + tmap_seq_destroy (seqs [i][j]); + seqs [i][j] = NULL; + } } + tmap_map_record_destroy (record_prev); } - tmap_map_record_destroy (record_prev); + // next + low++; } - // next - (*buffer_idx) = low; - low++; + sem_post(¶ms->processor_done_sem); } - (*buffer_idx) = seqs_buffer_length; // free thread variables for (i = 0; i < max_num_ends; i++) @@ -1640,136 +1710,18 @@ tmap_map_driver_core_thread_worker(void *arg) { tmap_map_driver_thread_data_t *thread_data = (tmap_map_driver_thread_data_t*)arg; - tmap_map_driver_core_worker(thread_data->sam_header, thread_data->seqs_buffer, thread_data->records, thread_data->bams, - thread_data->seqs_buffer_length, thread_data->buffer_idx, thread_data->index, thread_data->driver, - thread_data->stat, thread_data->rand, /* DVK - realigner */ thread_data->realigner, thread_data->context, thread_data->do_pairing, thread_data->tid); + tmap_map_driver_core_worker(thread_data); return arg; } -//static inline void -static int32_t -tmap_map_driver_create_threads(sam_header_t *header, - tmap_seqs_t **seqs_buffer, - tmap_map_record_t **records, - tmap_map_bams_t **bams, - int32_t seqs_buffer_length, - tmap_index_t *index, - tmap_map_driver_t *driver, - tmap_map_stats_t *stat, -#ifdef ENABLE_TMAP_DEBUG_FUNCTIONS - tmap_rand_t *rand_core, -#endif -#ifdef HAVE_LIBPTHREAD - pthread_attr_t **attr, - pthread_t **threads, - tmap_map_driver_thread_data_t **thread_data, - tmap_rand_t **rand, - tmap_map_stats_t **stats, - struct RealignProxy** realigner, - struct RealignProxy** context, -#endif - int32_t do_pairing) -{ -#ifdef ENABLE_TMAP_DEBUG_FUNCTIONS - int32_t j; -#endif - int32_t buffer_idx; // buffer index for processing data with a single thread - -#ifdef ENABLE_TMAP_DEBUG_FUNCTIONS - // sample reads - { - int32_t i; - if(driver->opt->sample_reads < 1) { - for(i=j=0;iopt->sample_reads < tmap_rand_get(rand_core)) continue; // skip - if(j < i) { - tmap_seqs_t *seqs; - seqs = seqs_buffer[j]; - seqs_buffer[j] = seqs_buffer[i]; - seqs_buffer[i] = seqs; - } - j++; - } - tmap_progress_print2("sampling %d out of %d [%.2lf%%]", j, seqs_buffer_length, 100.0*j/(double)seqs_buffer_length); - seqs_buffer_length = j; - if(0 == seqs_buffer_length) return 0; - } - } -#endif - - // do alignment -#ifdef HAVE_LIBPTHREAD - if(1 == driver->opt->num_threads) { - buffer_idx = 0; - tmap_map_driver_core_worker(header, seqs_buffer, records, bams, - seqs_buffer_length, &buffer_idx, index, driver, stat, rand[0], realigner [0], context [0], do_pairing, 0); - } - else { - int32_t i; - (*attr) = tmap_calloc(1, sizeof(pthread_attr_t), "(*attr)"); - pthread_attr_init((*attr)); - pthread_attr_setdetachstate((*attr), PTHREAD_CREATE_JOINABLE); - - (*threads) = tmap_calloc(driver->opt->num_threads, sizeof(pthread_t), "(*threads)"); - (*thread_data) = tmap_calloc(driver->opt->num_threads, sizeof(tmap_map_driver_thread_data_t), "(*thread_data)"); - - // create threads - for(i=0;iopt->num_threads;i++) { - (*thread_data)[i].sam_header = header; - (*thread_data)[i].seqs_buffer = seqs_buffer; - (*thread_data)[i].seqs_buffer_length = seqs_buffer_length; - (*thread_data)[i].buffer_idx = tmap_calloc(1, sizeof(int32_t), "(*thread_data)[i].buffer_id"); - (*thread_data)[i].records = records; - (*thread_data)[i].bams = bams; - (*thread_data)[i].index = index; - (*thread_data)[i].driver = driver; - if(NULL != stats) (*thread_data)[i].stat = stats[i]; - else (*thread_data)[i].stat = NULL; - (*thread_data)[i].rand = rand[i]; - // DVK - realigner - (*thread_data)[i].realigner = realigner [i]; - (*thread_data)[i].context = context [i]; - (*thread_data)[i].do_pairing = do_pairing; - (*thread_data)[i].tid = i; - if(0 != pthread_create(&(*threads)[i], (*attr), tmap_map_driver_core_thread_worker, &(*thread_data)[i])) { - tmap_error("error creating threads", Exit, ThreadError); - } - } - } -#else - buffer_idx = 0; - tmap_map_driver_core_worker(header, seqs_buffer, records, bams, - seqs_buffer_length, &buffer_idx, index, driver, stat, rand, do_pairing, 0); -#endif - return 1; -} - static int32_t -tmap_map_driver_infer_pairing(tmap_seqs_io_t *io_in, - sam_header_t *header, - tmap_seqs_t **seqs_buffer, +tmap_map_driver_infer_pairing(tmap_seqs_t **seqs_buffer, tmap_map_record_t **records, - tmap_map_bams_t **bams, int32_t seqs_buffer_length, - int32_t reads_queue_size, - tmap_index_t *index, tmap_map_driver_t *driver, - tmap_map_stats_t *stat, -#ifdef ENABLE_TMAP_DEBUG_FUNCTIONS - tmap_rand_t *rand_core, -#endif -#ifdef HAVE_LIBPTHREAD - pthread_attr_t **attr, - pthread_t **threads, - tmap_map_driver_thread_data_t **thread_data, - tmap_rand_t **rand, - tmap_map_stats_t **stats, - // DVK - realigner - struct RealignProxy** realigner, - struct RealignProxy** context -#endif - ) // NB: just so that the function definition is clean + tmap_map_driver_thread_data_t *thread_data + ) { int32_t i, isize_num = 0, tmp; int32_t *isize = NULL; @@ -1777,46 +1729,34 @@ tmap_map_driver_infer_pairing(tmap_seqs_io_t *io_in, int32_t max_len = 0; // check if we should do pairing - if(driver->opt->strandedness < 0 || driver->opt->positioning < 0 || !(driver->opt->ins_size_std < 0)) return 0; + if(driver->opt->strandedness < 0 || + driver->opt->positioning < 0 || + !(driver->opt->ins_size_std < 0) || + (0 == seqs_buffer_length)) return 0; // NB: infers from the first chunk of reads tmap_progress_print("inferring pairing parameters"); - tmap_progress_print("loading reads"); - seqs_buffer_length = tmap_seqs_io_read_buffer(io_in, seqs_buffer, reads_queue_size, header); - tmap_progress_print2("loaded %d reads", seqs_buffer_length); - if(0 == seqs_buffer_length) return 0; // holds the insert sizes isize = tmap_malloc(sizeof(int32_t) * seqs_buffer_length, "isize"); - // TODO: check that he data is paired... // TODO: check that we choose only the best scoring alignment - // create the threads - if(0 == tmap_map_driver_create_threads(header, seqs_buffer, records, - bams, seqs_buffer_length, index, driver, NULL, -#ifdef ENABLE_TMAP_DEBUG_FUNCTIONS - rand_core, -#endif -#ifdef HAVE_LIBPTHREAD - attr, threads, thread_data, rand, NULL, realigner, context, -#endif - 1)) { - return 0; + + for(int32_t i=0;iopt->num_threads;i++) { + thread_data[i].seqs_buffer = seqs_buffer; + thread_data[i].seqs_buffer_length = seqs_buffer_length; + thread_data[i].do_pairing=1; + sem_post(&thread_data[i].processor_trigger_sem); + } + + // wait for the processing to be done + for(int32_t i=0;iopt->num_threads;i++) { + sem_wait(&thread_data[i].processor_done_sem); + thread_data[i].do_pairing=0; } // estimate pairing parameters for(i=0;iopt->num_threads) { - // NB: we will write data as threads process the data. This is to - // facilitate SAM/BAM writing, which may be slow, especially for - // BAM. - int32_t tid = (i % driver->opt->num_threads); - while((*(*thread_data)[tid].buffer_idx) <= i) { - usleep(1000*1000); // sleep - } - } -#endif // only for paired ends if(NULL != records[i] && 2 == records[i]->n @@ -1854,24 +1794,6 @@ tmap_map_driver_infer_pairing(tmap_seqs_io_t *io_in, records[i] = NULL; } -#ifdef HAVE_LIBPTHREAD - // join threads - if(1 < driver->opt->num_threads) { - // join threads - for(i=0;iopt->num_threads;i++) { - if(0 != pthread_join((*threads)[i], NULL)) { - tmap_error("error joining threads", Exit, ThreadError); - } - // free the buffer index - free((*thread_data)[i].buffer_idx); - (*thread_data)[i].buffer_idx = NULL; - } - free((*threads)); (*threads) = NULL; - free(*(thread_data)); (*thread_data) = NULL; - free((*attr)); (*attr) = NULL; - } -#endif - if(isize_num < 8) { tmap_error("failed to infer the insert size distribution (too few reads): turning pairing off", Warn, OutOfRange); driver->opt->pairing = -1; @@ -1944,20 +1866,51 @@ tmap_map_driver_infer_pairing(tmap_seqs_io_t *io_in, } #ifdef HAVE_LIBPTHREAD -typedef struct { - tmap_seqs_io_t *io_in; - tmap_sam_io_t *io_out; - tmap_seqs_t **seqs_buffer; - int32_t seqs_buffer_length; - int32_t reads_queue_size; -} tmap_map_driver_thread_io_data_t; static void * tmap_map_driver_thread_io_worker (void *arg) { - tmap_map_driver_thread_io_data_t *d = (tmap_map_driver_thread_io_data_t*) arg; - d->seqs_buffer_length = tmap_seqs_io_read_buffer (d->io_in, d->seqs_buffer, d->reads_queue_size, d->io_out->fp->header->header); - return d; + tmap_map_driver_thread_io_data_t *d = (tmap_map_driver_thread_io_data_t*) arg; + while (1) + { + sem_wait(&d->reader_trigger_sem); + if (d->dismantle) + break; + d->seqs_buffer_length = tmap_seqs_io_read_buffer (d->io_in, d->seqs_buffer, d->reads_queue_size, d->io_out->fp->header->header); + sem_post(&d->reader_done_sem); + } + // return d; + return NULL; +} + +static void * +tmap_map_driver_thread_writer_worker (void *arg) +{ + tmap_map_driver_thread_writer_data_t *data = (tmap_map_driver_thread_writer_data_t*) arg; + while(1) + { + sem_wait(&data->writer_trigger_sem); + if (data->dismantle) + break; + for(int i=0;iseqs_buffer_length;i++) { + // write + for(int j=0;jbams[i]->n;j++) { // for each end + for(int k=0;kbams[i]->bams[j]->n;k++) { // for each hit + bam1_t *b = NULL; + b = data->bams[i]->bams[j]->bams[k]; // that's a lot of BAMs + if(NULL == b) tmap_bug(); + if(samwrite(data->io_out->fp, b) <= 0) { + tmap_error("Error writing the SAM file", Exit, WriteFileError); + } + } + } + tmap_map_bams_destroy(data->bams[i]); + data->bams[i] = NULL; + } + sem_post(&data->writer_done_sem); + } + // return data; + return NULL; } #endif @@ -1988,6 +1941,35 @@ uint8_t fill_sw_overrides (tmap_refseq_t* refseq, tmap_map_driver_t *driver) } +static uint32_t find_if_realigner_or_context_is_needed +( + uint8_t driver_realign_flag, + uint8_t driver_context_flag, + tmap_map_locopt_t* local_options, + uint32_t local_options_cnt, + uint8_t* realignment_needed, + uint8_t* context_needed) +{ + if (!context_needed || !realignment_needed) + return 0; + if (context_needed) *context_needed = 0; + if (realignment_needed) *realignment_needed = 0; + if (realignment_needed && driver_realign_flag) + *realignment_needed = 1; + if (context_needed && driver_context_flag) + *context_needed = 1; + for (tmap_map_locopt_t* sent = local_options + local_options_cnt; local_options != sent; ++local_options) + { + if (realignment_needed && !*realignment_needed && local_options->do_realign.over && local_options->do_realign.value) + *realignment_needed = 1; + if (!context_needed && *context_needed && local_options->do_hp_weight.over && local_options->do_hp_weight.value) + *context_needed = 1; + if ((!context_needed || *context_needed) && (!realignment_needed || *realignment_needed)) + break; + } + return 1; +} + void tmap_map_driver_core (tmap_map_driver_t *driver) { @@ -2002,31 +1984,34 @@ tmap_map_driver_core (tmap_map_driver_t *driver) #endif tmap_map_record_t **records=NULL; // buffer for the mapped data tmap_map_bams_t **bams=NULL;// buffer for the mapped BAM data + tmap_map_bams_t **bams_to_write=NULL;// copy of buffer for the writer thread to access tmap_index_t *index = NULL; // reference indes - tmap_map_stats_t *stat = NULL; // alignment statistics local_ovrs = 0; // count of local (per-amplicon) logging overrides #ifdef HAVE_LIBPTHREAD - pthread_attr_t *attr = NULL; - pthread_attr_t attr_io; - pthread_t *threads = NULL; - pthread_t *thread_io = NULL; - tmap_map_driver_thread_data_t *thread_data=NULL; + pthread_attr_t attr; + pthread_t thread_reader; + pthread_t thread_writer; + pthread_t *threads = tmap_calloc(driver->opt->num_threads, sizeof(pthread_t), "threads"); + tmap_map_driver_thread_data_t *thread_data=tmap_calloc(driver->opt->num_threads, sizeof(tmap_map_driver_thread_data_t), "thread_data"); tmap_map_driver_thread_io_data_t thread_io_data; + tmap_map_driver_thread_writer_data_t thread_writer_data; tmap_rand_t **rand = NULL; // random # generator for each thread - tmap_map_stats_t **stats = NULL; // alignment statistics for each thread + tmap_map_stats_t **statss = NULL; // alignment statistics for each thread #else tmap_rand_t *rand = NULL; // random # generator + tmap_map_stats_t *stats = NULL; // alignment statistics #endif time_t start_time = time (NULL); + tmap_map_stats_t* stat = tmap_map_stats_init (); // if (driver->opt->report_stats) // tmap_file_stdout = tmap_file_fdopen (fileno (stdout), "wb", TMAP_FILE_NO_COMPRESSION); // DVK - realignment #ifdef HAVE_LIBPTHREAD - struct RealignProxy** realigner = NULL; - struct RealignProxy** context = NULL; + struct RealignProxy** realigners = NULL; + struct RealignProxy** contexts = NULL; #else struct RealignProxy* realigner = NULL; struct RealignProxy* context = NULL; @@ -2071,7 +2056,7 @@ tmap_map_driver_core (tmap_map_driver_t *driver) // initialize the driver->options and print any relevant information tmap_map_driver_do_init(driver, index->refseq); if (!tmap_refseq_read_bed(index->refseq, driver->opt->bed_file, driver->opt->use_param_ovr, driver->opt->use_bed_read_ends_stat, &local_ovrs)) - tmap_error ("Bed file read error", Exit, OutOfRange ); + tmap_error ("Bed file read error", Exit, OutOfRange); if (local_ovrs && !driver->opt->realign_log) tmap_warning ("Amplicon-specific logging will have no effect since log file is not specified on command line (%s option)", "--log"); @@ -2097,17 +2082,18 @@ tmap_map_driver_core (tmap_map_driver_t *driver) #endif } records = tmap_malloc(sizeof(tmap_map_record_t*)*reads_queue_size, "records"); - bams = tmap_malloc(sizeof(tmap_map_bams_t*)*reads_queue_size, "bams"); + bams = tmap_calloc(reads_queue_size,sizeof(tmap_map_bams_t*), "bams"); + bams_to_write = tmap_calloc(reads_queue_size, sizeof(tmap_map_bams_t*), "bams_to_write"); - stat = tmap_map_stats_init(); -#ifdef HAVE_LIBPTHREAD - stats = tmap_malloc(driver->opt->num_threads * sizeof(tmap_map_stats_t*), "stats"); + #ifdef HAVE_LIBPTHREAD + statss = tmap_malloc(driver->opt->num_threads * sizeof(tmap_map_stats_t*), "statss"); rand = tmap_malloc(driver->opt->num_threads * sizeof(tmap_rand_t*), "rand"); for(i=0;iopt->num_threads;i++) { - stats[i] = tmap_map_stats_init(); + statss[i] = tmap_map_stats_init(); rand[i] = tmap_rand_init(i); } #else + stats = tmap_map_stats_init(); rand = tmap_rand_init(13); #endif @@ -2129,37 +2115,54 @@ tmap_map_driver_core (tmap_map_driver_t *driver) // Note: this needs to be initialized only if --do-realign is specified, // !!! or if --do-repeat-clip is specified, as repeat clipping uses some of the structures in realigner for data holding { + // determine if we need realigner or context + uint8_t context_needed = 0, realignment_needed = 0; + find_if_realigner_or_context_is_needed (driver->opt->do_realign, driver->opt->do_hp_weight, index->refseq->parmem, index->refseq->parmem_used, &realignment_needed, &context_needed); #ifdef HAVE_LIBPTHREAD - realigner = tmap_malloc (driver->opt->num_threads * sizeof (struct RealignProxy*), "realigner"); - context = tmap_malloc (driver->opt->num_threads * sizeof (struct RealignProxy*), "context"); + realigners = tmap_malloc (driver->opt->num_threads * sizeof (struct RealignProxy*), "realigner"); + contexts = tmap_malloc (driver->opt->num_threads * sizeof (struct RealignProxy*), "context"); for (i = 0; i != driver->opt->num_threads; ++i) { - realigner [i] = realigner_create (); - realigner_set_scores (realigner [i], driver->opt->realign_mat_score, driver->opt->realign_mis_score, driver->opt->realign_gip_score, driver->opt->realign_gep_score); - realigner_set_bandwidth (realigner [i], driver->opt->realign_bandwidth); - realigner_set_clipping (realigner [i], (enum CLIPTYPE) driver->opt->realign_cliptype); - - context [i] = context_aligner_create (); - realigner_set_scores (context [i], driver->opt->context_mat_score, driver->opt->context_mis_score, -driver->opt->context_gip_score, -driver->opt->context_gep_score); - realigner_set_bandwidth (context [i], driver->opt->context_extra_bandwidth); - realigner_set_gap_scale_mode (context [i], driver->opt->gap_scale_mode); - realigner_set_debug (context [i], driver->opt->debug_log); - if (driver->opt->debug_log && logfile) // WARNING! not a thread-safve operation. Disabled through cmd line options check for multithreaded runs - realigner_set_log (context [i], fileno (logfile)); + realigners [i] = NULL; + if (realignment_needed) + { + realigners [i] = realigner_create_spec (driver->opt->realign_maxlen, driver->opt->realign_maxclip); + realigner_set_scores (realigners [i], driver->opt->realign_mat_score, driver->opt->realign_mis_score, driver->opt->realign_gip_score, driver->opt->realign_gep_score); + realigner_set_bandwidth (realigners [i], driver->opt->realign_bandwidth); + realigner_set_clipping (realigners [i], (enum CLIPTYPE) driver->opt->realign_cliptype); + } + contexts [i] = NULL; + if (context_needed) + { + contexts [i] = context_aligner_create (); + realigner_set_scores (contexts [i], driver->opt->context_mat_score, driver->opt->context_mis_score, -driver->opt->context_gip_score, -driver->opt->context_gep_score); + realigner_set_bandwidth (contexts [i], driver->opt->context_extra_bandwidth); + realigner_set_gap_scale_mode (contexts [i], driver->opt->gap_scale_mode); + realigner_set_debug (contexts [i], driver->opt->debug_log); + if (driver->opt->debug_log && logfile) // WARNING! not a thread-safve operation. Disabled through cmd line options check for multithreaded runs + realigner_set_log (contexts [i], fileno (logfile)); + } + } +#else + realigner = NULL; + if (realignment_needed) + { + realigner = realigner_create (); + realigner_set_scores (realigner, driver->opt->realign_mat_score, driver->opt->realign_mis_score, driver->opt->realign_gip_score, driver->opt->realign_gep_score); + realigner_set_bandwidth (realigner, driver->opt->realign_bandwidth); + realigner_set_clipping (realigner, (enum CLIPTYPE) driver->opt->realign_cliptype); + } + context = NULL; + if (context_needed) + { + context = context_aligner_create (); + realigner_set_scores (context, driver->opt->context_mat_score, driver->opt->context_mis_score, driver->opt->context_gip_score, driver->opt->context_gep_score); + realigner_set_bandwidth (context, driver->opt->context_extra_bandwidth); + realigner_set_gap_scale_mode (context, driver->opt->gap_scale_mode); + realigner_set_debug (context, driver->opt->context_debug_log); + if (driver->opt->debug_log && logfile) + realigner_set_log (context, fileno (logfile)); } - #else - realigner = realigner_create (); - realigner_set_scores (realigner, driver->opt->realign_mat_score, driver->opt->realign_mis_score, driver->opt->realign_gip_score, driver->opt->realign_gep_score); - realigner_set_bandwidth (realigner, driver->opt->realign_bandwidth); - realigner_set_clipping (realigner, (enum CLIPTYPE) driver->opt->realign_cliptype); - - context = context_aligner_create (); - realigner_set_scores (context, driver->opt->context_mat_score, driver->opt->context_mis_score, driver->opt->context_gip_score, driver->opt->context_gep_score); - realigner_set_bandwidth (context, driver->opt->context_extra_bandwidth); - realigner_set_gap_scale_mode (context, driver->opt->gap_scale_mode); - realigner_set_debug (context, driver->opt->context_debug_log); - if (driver->opt->debug_log && logfile) - realigner_set_log (context, fileno (logfile)); #endif } @@ -2189,36 +2192,90 @@ tmap_map_driver_core (tmap_map_driver_t *driver) header = NULL; // pairing - seqs_buffer_length = tmap_map_driver_infer_pairing(io_in, io_out->fp->header->header, seqs_buffer, records, - bams, seqs_buffer_length, reads_queue_size, - index, driver, stat, -#ifdef ENABLE_TMAP_DEBUG_FUNCTIONS - rand_core, -#endif + seqs_loaded = 1; + int writer_spawned = 0; + // main processing loop + tmap_progress_print("processing reads"); + thread_writer_data.bams = bams_to_write; + #ifdef HAVE_LIBPTHREAD - &attr, &threads, &thread_data, rand, stats, realigner, context -#endif - ); - if(0 == seqs_buffer_length) { + if (0 != sem_init(&thread_io_data.reader_trigger_sem,0,0)) + tmap_error ("error creating semaphore", Exit, ThreadError); + if (0 != sem_init(&thread_io_data.reader_done_sem,0,0)) + tmap_error ("error creating semaphore", Exit, ThreadError); + // launch a new thread that loads in the reads + if (0 != pthread_attr_init(&attr)) + tmap_error ("error initializing thread attribute", Exit, ThreadError); + thread_io_data.io_in = io_in; + thread_io_data.io_out = io_out; + thread_io_data.seqs_buffer_length = 0; + thread_io_data.reads_queue_size = reads_queue_size; + thread_io_data.seqs_buffer = seqs_buffer_next; + thread_io_data.dismantle = 0; + if(0 != pthread_create(&thread_reader, &attr, tmap_map_driver_thread_io_worker, &thread_io_data)) + tmap_error ("error creating threads", Exit, ThreadError); + + int32_t seqCntr=0; + + // create threads + for(int32_t i=0;iopt->num_threads;i++) + { + thread_data[i].sam_header = io_out->fp->header->header; + thread_data[i].seqs_buffer = seqs_buffer; + thread_data[i].seqs_buffer_length = seqs_buffer_length; + thread_data[i].records = records; + thread_data[i].bams = bams; + thread_data[i].index = index; + thread_data[i].driver = driver; + thread_data[i].stat = statss ? statss [i] : NULL; + thread_data[i].rand = rand [i]; + // DVK - realigner + thread_data[i].realigner = realigners [i]; + thread_data[i].context = contexts [i]; + thread_data[i].do_pairing = 0; + thread_data[i].tid = i; + thread_data[i].seqCntr = &seqCntr; + if (0 != sem_init(&thread_data[i].processor_trigger_sem,0,0)) + tmap_error ("error creating semaphore", Exit, ThreadError); + if (0 != sem_init(&thread_data[i].processor_done_sem,0,0)) + tmap_error ("error creating semaphore", Exit, ThreadError); + thread_data[i].dismantle = 0; + if(0 != pthread_create(&threads[i], &attr, tmap_map_driver_core_thread_worker, &thread_data[i])) + tmap_error ("error creating threads", Exit, ThreadError); + } + + // pthread_attr_init(&attr); // DK: according to pthread specs, calling pthread_init_attr on already initialized attributes has undefined behavior + //populate buffer with what's needed + thread_writer_data.seqs_buffer_length = seqs_buffer_length; + thread_writer_data.io_out = io_out; + if (0 != sem_init(&thread_writer_data.writer_trigger_sem,0,0)) + tmap_error ("error creating semaphore", Exit, ThreadError); + if (0 != sem_init(&thread_writer_data.writer_done_sem,0,0)) + tmap_error ("error creating semaphore", Exit, ThreadError); + bams_to_write = bams; + bams = thread_writer_data.bams; + thread_writer_data.bams = bams_to_write; + thread_writer_data.dismantle = 0; + //spawn new writer thread + if(0 != pthread_create(&thread_writer, &attr, tmap_map_driver_thread_writer_worker, &thread_writer_data)) + tmap_error ("error creating writer thread", Exit, ThreadError); + + { tmap_progress_print("loading reads"); - seqs_buffer_length = tmap_seqs_io_read_buffer(io_in, seqs_buffer, reads_queue_size, io_out->fp->header->header); + seqs_buffer_length = tmap_seqs_io_read_buffer (io_in, seqs_buffer, reads_queue_size, io_out->fp->header->header); tmap_progress_print2("loaded %d reads", seqs_buffer_length); } - seqs_loaded = 1; - // main processing loop - tmap_progress_print("processing reads"); + tmap_map_driver_infer_pairing(seqs_buffer, records, seqs_buffer_length, driver, thread_data); + + #endif + while(1) { // get the reads if(0 == seqs_loaded) { tmap_progress_print("loading reads"); #ifdef HAVE_LIBPTHREAD - // join the thread that loads in the reads - if(0 != pthread_join((*thread_io), NULL)) { - tmap_error("error joining IO thread", Exit, ThreadError); - } - free(thread_io); - thread_io = NULL; + sem_wait(&thread_io_data.reader_done_sem); // swap buffers seqs_buffer_length = thread_io_data.seqs_buffer_length; seqs_buffer_next = seqs_buffer; // temporarily store this here @@ -2228,92 +2285,54 @@ tmap_map_driver_core (tmap_map_driver_t *driver) seqs_buffer_length = tmap_seqs_io_read_buffer (io_in, seqs_buffer, reads_queue_size, io_out->fp->header->header); #endif seqs_loaded = 1; + tmap_progress_print2("loaded %d reads", seqs_buffer_length); } if(0 == seqs_buffer_length) { // are there any more? break; } - #ifdef HAVE_LIBPTHREAD - // launch a new thread that loads in the reads - pthread_attr_init(&attr_io); - pthread_attr_setdetachstate(&attr_io, PTHREAD_CREATE_JOINABLE); - thread_io = tmap_malloc(sizeof(pthread_t), "thread_io"); - thread_io_data.io_in = io_in; - thread_io_data.io_out = io_out; - thread_io_data.seqs_buffer_length = 0; - thread_io_data.reads_queue_size = reads_queue_size; - thread_io_data.seqs_buffer = seqs_buffer_next; - if(0 != pthread_create(thread_io, &attr_io, tmap_map_driver_thread_io_worker, &thread_io_data)) { - tmap_error("error creating threads", Exit, ThreadError); + // start reading the next chunk of data + sem_post(&thread_io_data.reader_trigger_sem); + + // start processing the next chunk of sequences + seqCntr=0; + for(int32_t i=0;iopt->num_threads;i++) { + thread_data[i].seqs_buffer = seqs_buffer; + thread_data[i].seqs_buffer_length = seqs_buffer_length; + thread_data[i].bams = bams; + sem_post(&thread_data[i].processor_trigger_sem); } -#endif - // create the threads - if(0 == tmap_map_driver_create_threads(io_out->fp->header->header, seqs_buffer, records, - bams, seqs_buffer_length, index, driver, stat, -#ifdef ENABLE_TMAP_DEBUG_FUNCTIONS - rand_core, -#endif -#ifdef HAVE_LIBPTHREAD - &attr, &threads, &thread_data, rand, stats, realigner, context, -#endif - 0)) { - break; + // wait for the processing to be done + for(int32_t i=0;iopt->num_threads;i++) { + sem_wait(&thread_data[i].processor_done_sem); } - /* - if(-1 != driver->opt->reads_queue_size) { - tmap_progress_print("writing alignments"); - } - */ +#endif + - // write data - for(i=0;iopt->num_threads) { - // NB: we will write data as threads process the data. This is to - // facilitate SAM/BAM writing, which may be slow, especially for - // BAM. - int32_t tid = (i % driver->opt->num_threads); - while((*thread_data[tid].buffer_idx) <= i) { - usleep(1000*1000); // sleep - } - } -#endif - // write - for(j=0;jn;j++) { // for each end - for(k=0;kbams[j]->n;k++) { // for each hit - bam1_t *b = NULL; - b = bams[i]->bams[j]->bams[k]; // that's a lot of BAMs - if(NULL == b) tmap_bug(); - if(samwrite(io_out->fp, b) <= 0) { - tmap_error("Error writing the SAM file", Exit, WriteFileError); - } - } - } - tmap_map_bams_destroy(bams[i]); - bams[i] = NULL; + //join previous writer thread + if(writer_spawned){ + sem_wait(&thread_writer_data.writer_done_sem); } + thread_writer_data.seqs_buffer_length = seqs_buffer_length; + bams_to_write = bams; + bams = thread_writer_data.bams; + thread_writer_data.bams = bams_to_write; + sem_post(&thread_writer_data.writer_trigger_sem); -#ifdef HAVE_LIBPTHREAD - // join threads - if(1 < driver->opt->num_threads) { - // join threads - for(i=0;iopt->num_threads;i++) { - if(0 != pthread_join(threads[i], NULL)) { - tmap_error("error joining threads", Exit, ThreadError); - } - // add the stats - tmap_map_stats_add (stat, stats[i]); - tmap_map_stats_zero (stats[i]); - // free the buffer index - free(thread_data[i].buffer_idx); - } - free(threads); threads = NULL; - free(thread_data); thread_data = NULL; - free(attr); attr = NULL; + writer_spawned=1; + + // merge thread statistics + for(i=0;iopt->num_threads;i++) + { + // add the stats + tmap_map_stats_add (stat, statss[i]); + tmap_map_stats_zero (statss[i]); } + #endif // TODO: should we flush when writing SAM and processing one read at a time? @@ -2342,6 +2361,64 @@ tmap_map_driver_core (tmap_map_driver_t *driver) seqs_loaded = 0; } + if(writer_spawned){ + sem_wait(&thread_writer_data.writer_done_sem); + } + + + if(1 < driver->opt->num_threads) + { + // merge last iteration statistics? seems like this is futile; statss [i] at this time should always be zeroed + for(i=0;iopt->num_threads;i++) + { + tmap_map_stats_add (stat, statss [i]); + tmap_map_stats_zero (statss[i]); + } + } + + tmap_progress_print2 ("dismantling threads"); + // dismantle reader thread + thread_io_data.dismantle = 1; + sem_post (&thread_io_data.reader_trigger_sem); + if (0 != pthread_join (thread_reader, NULL)) + tmap_error ("error joining reader thread", Exit, ThreadError); + tmap_progress_print2 (" reader joined"); + // dismantle writer thread + thread_writer_data.dismantle = 1; + sem_post(&thread_writer_data.writer_trigger_sem); + if (0 != pthread_join (thread_writer, NULL)) + tmap_error ("error joining writer thread", Exit, ThreadError); + tmap_progress_print2 (" writer joined"); + // dismantle worker threads + for (i = 0; i < driver->opt->num_threads; ++i) + { + thread_data [i].dismantle = 1; + sem_post (&thread_data [i].processor_trigger_sem); + if (0 != pthread_join (threads [i], NULL)) + tmap_error ("error joining worker thread", Exit, ThreadError); + } + tmap_progress_print2 (" all workers joined"); + // destroy semaphores + if (0 != sem_destroy (&thread_writer_data.writer_done_sem)) + tmap_error ("error destroying semaphore", Exit, ThreadError); + if (0 != sem_destroy (&thread_writer_data.writer_trigger_sem)) + tmap_error ("error destroying semaphore", Exit, ThreadError); + for (i = 0; i < driver->opt->num_threads; ++i) + { + if (0 != sem_destroy (&thread_data [i].processor_done_sem)) + tmap_error ("error destroying semaphore", Exit, ThreadError); + if (0 != sem_destroy (&thread_data [i].processor_trigger_sem)) + tmap_error ("error destroying semaphore", Exit, ThreadError); + } + if (0 != sem_destroy (&thread_io_data.reader_done_sem)) + tmap_error ("error destroying semaphore", Exit, ThreadError); + if (0 != sem_destroy (&thread_io_data.reader_trigger_sem)) + tmap_error ("error destroying semaphore", Exit, ThreadError); + tmap_progress_print2 (" semaphores dismantled"); + if (0 != pthread_attr_destroy (&attr)) + tmap_error ("error destroying thread attributes", Exit, ThreadError); + tmap_progress_print2 (" thread attributes dismantled"); + if(-1 == driver->opt->reads_queue_size) { tmap_progress_print2("processed %d reads", n_reads_processed); @@ -2504,7 +2581,7 @@ tmap_map_driver_core (tmap_map_driver_t *driver) tmap_file_fprintf (tmap_file_stderr, " Ends repaired: %8llu %8llu\n", stat->ends_REPAiRed [0], stat->ends_REPAiRed [1]); - tmap_file_fprintf (tmap_file_stderr, " Ends clipped: %8llu %8llu\n", + tmap_file_fprintf (tmap_file_stderr, " Ends clipped: %8llu %8llu\n", stat->ends_REPAiR_clipped [0], stat->ends_REPAiR_clipped [1]); tmap_file_fprintf (tmap_file_stderr, " Ends extended: %8llu %8llu\n", @@ -2530,24 +2607,24 @@ tmap_map_driver_core (tmap_map_driver_t *driver) tmap_file_fprintf (tmap_file_stderr, "No tail repeat clipping performed\n"); else { - tmap_file_fprintf (tmap_file_stderr, " Alignments tail-clipped: %llu", stat->num_tailclipped); + tmap_file_fprintf (tmap_file_stderr, "Alignments tail-clipped: %llu", stat->num_tailclipped); if (stat->num_seen_tailclipped) - tmap_file_fprintf (tmap_file_stderr, " (%.2f%% seen)", ((double) stat->num_tailclipped) * 100 / stat->num_seen_tailclipped); - tmap_file_fprintf (tmap_file_stderr, "\n"); - tmap_file_fprintf (tmap_file_stderr, " Tail-clipped bases: %llu", stat->bases_tailclipped); + tmap_file_fprintf (tmap_file_stderr, " (%.2f%% seen)", ((double) stat->num_tailclipped) * 100 / stat->num_seen_tailclipped); + tmap_file_fprintf (tmap_file_stderr, "\n"); + tmap_file_fprintf (tmap_file_stderr, " Tail-clipped bases: %llu", stat->bases_tailclipped); if (stat->bases_seen_tailclipped) - tmap_file_fprintf (tmap_file_stderr, " (%.2f%% seen)", ((double) stat->bases_tailclipped) * 100 / stat->bases_seen_tailclipped); - tmap_file_fprintf (tmap_file_stderr, "\n"); - tmap_file_fprintf (tmap_file_stderr, "Completely clipped reads: %llu", stat->num_fully_tailclipped); + tmap_file_fprintf (tmap_file_stderr, " (%.2f%% seen)", ((double) stat->bases_tailclipped) * 100 / stat->bases_seen_tailclipped); + tmap_file_fprintf (tmap_file_stderr, "\n"); + tmap_file_fprintf (tmap_file_stderr, " Fully clipped reads: %llu", stat->num_fully_tailclipped); if (stat->num_seen_tailclipped) - tmap_file_fprintf (tmap_file_stderr, " (%.2f%% clipped)", ((double) stat->num_fully_tailclipped) * 100 / stat->num_tailclipped); - tmap_file_fprintf (tmap_file_stderr, ", contain %llu bases", stat->bases_fully_tailclipped); + tmap_file_fprintf (tmap_file_stderr, " (%.2f%% clipped)", ((double) stat->num_fully_tailclipped) * 100 / stat->num_tailclipped); + tmap_file_fprintf (tmap_file_stderr, ", contain %llu bases", stat->bases_fully_tailclipped); if (stat->bases_tailclipped) - tmap_file_fprintf (tmap_file_stderr, " (%.2f%% clipped)", ((double) stat->bases_fully_tailclipped) * 100 / stat->bases_tailclipped); - tmap_file_fprintf (tmap_file_stderr, "\n"); + tmap_file_fprintf (tmap_file_stderr, " (%.2f%% clipped)", ((double) stat->bases_fully_tailclipped) * 100 / stat->bases_tailclipped); + tmap_file_fprintf (tmap_file_stderr, "\n"); if (stat->num_seen_tailclipped) { - tmap_file_fprintf (tmap_file_stderr, " Average bases clipped:\n"); + tmap_file_fprintf (tmap_file_stderr, " Average bases clipped:\n"); tmap_file_fprintf (tmap_file_stderr, " per read: %.1f\n", ((double) stat->bases_tailclipped) / stat->num_seen_tailclipped); if (stat->num_tailclipped) tmap_file_fprintf (tmap_file_stderr, " per clipped read: %.1f\n", ((double) stat->bases_tailclipped) / stat->num_tailclipped); @@ -2559,7 +2636,31 @@ tmap_map_driver_core (tmap_map_driver_t *driver) tmap_file_fprintf (tmap_file_stderr, "No alignment filtering performed\n"); else { - tmap_file_fprintf (tmap_file_stderr, " Filtered alignments: %llu\n", stat->num_filtered_als); + tmap_file_fprintf (tmap_file_stderr, "Filtered alignments: %llu\n", stat->num_filtered_als); + } + tmap_file_fprintf (tmap_file_stderr, "Candidate evaluation stats:\n"); + + tmap_file_fprintf (tmap_file_stderr, " Primary VSW (S#%d) calls: %llu\n", driver->opt->vsw_type, stat->vect_sw_calls); + tmap_file_fprintf (tmap_file_stderr, " Fallback VSW (S#%d) calls: %llu\n", driver->opt->vsw_fallback, stat->fallback_vsw_calls); + tmap_file_fprintf (tmap_file_stderr, " Fallback N-VSW (S#2) calls: %llu\n", stat->fallback_sw_calls); + tmap_file_fprintf (tmap_file_stderr, " DP matrix extensions: %llu\n", stat->read_clipping_extensions); + tmap_file_fprintf (tmap_file_stderr, " VSW overflows: %llu\n", stat->overflows); + tmap_file_fprintf (tmap_file_stderr, " VSW failures: %llu\n", stat->vswfails); + tmap_file_fprintf (tmap_file_stderr, " Total SW failures: %llu\n", stat->totswfails); + if (driver->opt->vsw_type == 4) + { + tmap_file_fprintf (tmap_file_stderr, " Non-standard base fallbacks in forward scoring: %llu\n", stat->nonstd_base_fallbacks_fwd); + tmap_file_fprintf (tmap_file_stderr, " Non-standard base fallbacks in reverse scoring: %llu\n", stat->nonstd_base_fallbacks_rev); + } + tmap_file_fprintf (tmap_file_stderr, " Symmetrically scored VSW: %llu\n", stat->symmetric_scores); + tmap_file_fprintf (tmap_file_stderr, " Corrected asymmetries: %llu\n", stat->asymmetric_scores_corrected); + tmap_file_fprintf (tmap_file_stderr, " Unrecoverable asymmetries %llu\n", stat->asymmetric_scores_failed); + if (index->refseq->bed_exist && driver->opt->use_param_ovr && driver->opt->ovr_candeval) + { + tmap_file_fprintf (tmap_file_stderr, " Amplicon searches: %llu, successful %llu, failed %llu\n", stat->amplicon_searches, stat->amplicon_search_successes, stat->amplicon_searches - stat->amplicon_search_successes); + tmap_file_fprintf (tmap_file_stderr, " Multi-amplicon overlaps: %llu\n", stat->amplicon_overlaps); + tmap_file_fprintf (tmap_file_stderr, " Overrides used: %llu\n", stat->candeval_overrides); + tmap_file_fprintf (tmap_file_stderr, " Multiple overrides %llu\n", stat->multiple_candeval_overrides); } } @@ -2590,11 +2691,13 @@ tmap_map_driver_core (tmap_map_driver_t *driver) #ifdef HAVE_LIBPTHREAD for (i = 0; i != driver->opt->num_threads; ++i) { - realigner_destroy (realigner [i]); - realigner_destroy (context [i]); + if(realigners [i]) + realigner_destroy (realigners [i]); + if (contexts [i]) + realigner_destroy (contexts [i]); } - free (realigner); - free (context); + free (realigners); + free (contexts); #else realigner_destroy (realigner); @@ -2607,17 +2710,20 @@ tmap_map_driver_core (tmap_map_driver_t *driver) free(records); free(bams); - tmap_map_stats_destroy(stat); + free(bams_to_write); + tmap_map_stats_destroy (stat); #ifdef HAVE_LIBPTHREAD for(i=0;iopt->num_threads;i++) { - tmap_map_stats_destroy(stats[i]); - tmap_rand_destroy(rand[i]); + tmap_map_stats_destroy (statss [i]); + tmap_rand_destroy (rand[i]); } - free(stats); - free(rand); - free(thread_io); + free (statss); + free (rand); + free (thread_data); + free (threads); #else - tmap_rand_destroy(rand); + tmap_rand_destroy (rand); + tmap_map_stats_destroy (stats); #endif #ifdef ENABLE_TMAP_DEBUG_FUNCTIONS tmap_rand_destroy(rand_core); diff --git a/Analysis/TMAP/src/map/tmap_map_driver.h b/Analysis/TMAP/src/map/tmap_map_driver.h index 794ec777..4daaab61 100644 --- a/Analysis/TMAP/src/map/tmap_map_driver.h +++ b/Analysis/TMAP/src/map/tmap_map_driver.h @@ -154,66 +154,6 @@ tmap_map_driver_run(tmap_map_driver_t *driver); void tmap_map_driver_destroy(tmap_map_driver_t *driver); -/*! - Driver data to be passed to a thread - */ -typedef struct { - sam_header_t *sam_header; /*!< the SAM Header */ - tmap_seqs_t **seqs_buffer; /*!< the buffers of sequences */ - int32_t seqs_buffer_length; /*!< the buffers length */ - int32_t *buffer_idx; /*!< the current zero-based index into the buffer */ - tmap_map_record_t **records; /*!< the alignments for each sequence */ - tmap_map_bams_t **bams; /*!< the BAM alignments for each sequence */ - tmap_index_t *index; /*!< pointer to the reference index */ - tmap_map_driver_t *driver; /*!< the main driver object */ - tmap_map_stats_t *stat; /*!< the driver statistics */ - tmap_rand_t *rand; /*!< the random number generator */ - // DVK - realigner - struct RealignProxy *realigner; /*!< post-processing realigner engine */ - struct RealignProxy *context; /*!< post-processing context-dependent realignment engine */ - int32_t do_pairing; /*!< 1 if we are performing pairing paramter calculation, 0 otherwise */ - int32_t tid; /*!< the zero-based thread id */ -} tmap_map_driver_thread_data_t; - -/*! - The core worker routine of mapall - @param sam_header the SAM Header - @param seqs_buffer the buffer of sequences - @param records the records to return - @param bams the bams to return - @param seqs_buffer_length the number of sequences in the buffer - @param buffer_idx the current zero-based index into the buffer - @param index the reference index - @param driver the driver - @param stat the driver statistics - @param rand the random number generator - @param do_pairing 1 if we are performing pairing paramter calculation, 0 otherwise - @param tid the thread ids - */ -void -tmap_map_driver_core_worker(sam_header_t *sam_header, - tmap_seqs_t **seqs_buffer, - tmap_map_record_t **records, - tmap_map_bams_t **bams, - int32_t seqs_buffer_length, - int32_t *buffer_idx, - tmap_index_t *index, - tmap_map_driver_t *driver, - tmap_map_stats_t* stat, - tmap_rand_t *rand, - // DVK - realign - struct RealignProxy *realigner, - struct RealignProxy *context, - int32_t do_pairing, - int32_t tid); - -/*! - A wrapper around the core function of mapall - @param arg the worker arguments in the type: tmap_map_driver_thread_data_t - @return the worker arguments - */ -void * -tmap_map_driver_core_thread_worker(void *arg); /*! the core routine for mapping data with or without threads diff --git a/Analysis/TMAP/src/map/util/tmap_map_locopt.c b/Analysis/TMAP/src/map/util/tmap_map_locopt.c index 896fab5e..b9ec303c 100644 --- a/Analysis/TMAP/src/map/util/tmap_map_locopt.c +++ b/Analysis/TMAP/src/map/util/tmap_map_locopt.c @@ -13,6 +13,7 @@ void tmap_map_locopt_init (tmap_map_locopt_t* locopt) locopt->gapl_len.over = 0; locopt->bw.over = 0; locopt->softclip_type.over = 0; + locopt->score_thr.over = 0; locopt->end_repair.over = 0; locopt->end_repair_he.over = 0; locopt->end_repair_le.over = 0; diff --git a/Analysis/TMAP/src/map/util/tmap_map_locopt.h b/Analysis/TMAP/src/map/util/tmap_map_locopt.h index aaf6dd0e..2846bad9 100644 --- a/Analysis/TMAP/src/map/util/tmap_map_locopt.h +++ b/Analysis/TMAP/src/map/util/tmap_map_locopt.h @@ -38,6 +38,7 @@ typedef struct __tmap_map_locopt_t tmap_map_opt_ovr_i_t gapl_len; /*!< the number of extra bases to add when searching for long indels (-K, --gap-long-length) */ tmap_map_opt_ovr_i_t bw; /*!< the extra bases to add before and after the target during Smith-Waterman (-w,--band-width) */ tmap_map_opt_ovr_i_t softclip_type; /*!< soft clip type (-g,--softclip-type) */ + tmap_map_opt_ovr_i_t score_thr; /*!< the score threshold (match-score-scaled) (-T,--score-thres) */ tmap_map_opt_ovr_i_t end_repair; // /*!< specifies if and how to perform end repair on higher coordinate end of the amplicon (0 - disabled, 1 - prefer mismatches, 2 - prefer indels) (--end-repair) */ tmap_map_opt_ovr_i_t end_repair_he; // /*!< specifies to perform 5' end repair on higher coordinate end of the amplicon (0 - disabled, 1 - prefer mismatches, 2 - prefer indels) (--end-repair) */ tmap_map_opt_ovr_i_t end_repair_le; /*!< specifies to perform 5' end repair on lower coordinate end of the amplicon (0 - disabled, 1 - prefer mismatches, 2 - prefer indels) (--end-repair) */ diff --git a/Analysis/TMAP/src/map/util/tmap_map_opt.c b/Analysis/TMAP/src/map/util/tmap_map_opt.c index bcad6d68..79f37e85 100644 --- a/Analysis/TMAP/src/map/util/tmap_map_opt.c +++ b/Analysis/TMAP/src/map/util/tmap_map_opt.c @@ -110,10 +110,11 @@ static char *tmap_map_opt_input_types[] = {"INT", "FLOAT", "NUM", "FILE", "STRIN #define __tmap_map_opt_option_print_func_tf_init(_name) \ static void tmap_map_opt_option_print_func_##_name(void *arg) { \ tmap_map_opt_t *opt = (tmap_map_opt_t*)arg; \ - tmap_file_fprintf(tmap_file_stderr, "%s[%s%s%s]%s", KMAG, KYEL, (1 == opt->_name) ? "true" : "false", KMAG, KNRM); \ + /* tmap_file_fprintf(tmap_file_stderr, "%s[%s%s%s]%s", KMAG, KYEL, (1 == opt->_name) ? "true" : "false", KMAG, KNRM); */ \ } -// verbosity + + // verbosity #define __tmap_map_opt_option_print_func_verbosity_init() \ static void tmap_map_opt_option_print_func_verbosity(void *arg) { \ tmap_file_fprintf(tmap_file_stderr, "%s[%s%s%s]%s", KMAG, KYEL, (1 == tmap_progress_get_verbosity()) ? "true" : "false", KMAG, KNRM); \ @@ -188,9 +189,11 @@ __tmap_map_opt_option_print_func_chars_init(fn_sam, "stdout") __tmap_map_opt_option_print_func_int64_init(bam_start_vfo) __tmap_map_opt_option_print_func_int64_init(bam_end_vfo) __tmap_map_opt_option_print_func_tf_init(use_param_ovr) +__tmap_map_opt_option_print_func_tf_init(ovr_candeval) __tmap_map_opt_option_print_func_tf_init(use_bed_in_end_repair) __tmap_map_opt_option_print_func_tf_init(use_bed_in_mapq) __tmap_map_opt_option_print_func_tf_init(use_bed_read_ends_stat) +__tmap_map_opt_option_print_func_int_init(amplicon_scope) __tmap_map_opt_option_print_func_int_init(score_match) __tmap_map_opt_option_print_func_int_init(pen_mm) __tmap_map_opt_option_print_func_int_init(pen_gapo) @@ -232,11 +235,19 @@ __tmap_map_opt_option_print_func_double_init(repair_identity_drop_limit) __tmap_map_opt_option_print_func_int_init(repair_max_primer_zone_dist) __tmap_map_opt_option_print_func_int_init(repair_clip_ext) + + __tmap_map_opt_option_print_func_int_init(shm_key) #ifdef ENABLE_TMAP_DEBUG_FUNCTIONS __tmap_map_opt_option_print_func_double_init(sample_reads) #endif __tmap_map_opt_option_print_func_int_init(vsw_type) +__tmap_map_opt_option_print_func_int_init(vsw_fallback) +__tmap_map_opt_option_print_func_tf_init(confirm_vsw_corr) +__tmap_map_opt_option_print_func_tf_init(candidate_ext) +__tmap_map_opt_option_print_func_tf_init(correct_failed_vsw) +__tmap_map_opt_option_print_func_tf_init(use_nvsw_on_nonstd_bases) + __tmap_map_opt_option_print_func_verbosity_init() __tmap_map_opt_option_print_func_tf_init(do_realign) @@ -246,6 +257,8 @@ __tmap_map_opt_option_print_func_int_init(realign_gip_score) __tmap_map_opt_option_print_func_int_init(realign_gep_score) __tmap_map_opt_option_print_func_int_init(realign_bandwidth) __tmap_map_opt_option_print_func_int_init(realign_cliptype) +__tmap_map_opt_option_print_func_int_init(realign_maxlen) +__tmap_map_opt_option_print_func_int_init(realign_maxclip) __tmap_map_opt_option_print_func_tf_init(report_stats) __tmap_map_opt_option_print_func_chars_init(realign_log, "") @@ -513,7 +526,7 @@ tmap_map_opt_init_helper(tmap_map_opt_t *opt) "3 - all alignments", NULL}; static char *vsw_type[] = { - "NB: currently only #1, #4, and #6 have been tested", + "NB: currently only #1, #2, #4, and #6 have been tested", "1 - lh3/ksw.c/nh13", "2 - simple VSW", "3 - SHRiMP2 VSW [not working]", @@ -605,6 +618,12 @@ tmap_map_opt_init_helper(tmap_map_opt_t *opt) NULL, tmap_map_opt_option_print_func_use_param_ovr, TMAP_MAP_ALGO_GLOBAL); + tmap_map_opt_options_add(opt->options, "ovr-candeval", no_argument, 0, 0, + TMAP_MAP_OPT_TYPE_NONE, + "use location-specific parameters overriding at candidate evaluation stage", + NULL, + tmap_map_opt_option_print_func_ovr_candeval, + TMAP_MAP_ALGO_GLOBAL); tmap_map_opt_options_add(opt->options, "no-bed-er", no_argument, 0, 0, TMAP_MAP_OPT_TYPE_NONE, "use of amplicon edge coordinates from BED file in end repair", @@ -623,6 +642,12 @@ tmap_map_opt_init_helper(tmap_map_opt_t *opt) NULL, tmap_map_opt_option_print_func_use_bed_read_ends_stat, TMAP_MAP_ALGO_GLOBAL); + tmap_map_opt_options_add(opt->options, "ampl-scope", required_argument, 0, 0, + TMAP_MAP_OPT_TYPE_INT, + "read padding used for amplicon search", + NULL, + tmap_map_opt_option_print_func_amplicon_scope, + TMAP_MAP_ALGO_GLOBAL); tmap_map_opt_options_add(opt->options, "score-match", required_argument, 0, 'A', TMAP_MAP_OPT_TYPE_INT, "score for a match", @@ -750,11 +775,11 @@ tmap_map_opt_init_helper(tmap_map_opt_t *opt) tmap_map_opt_option_print_func_rand_read_name, TMAP_MAP_ALGO_GLOBAL); tmap_map_opt_options_add(opt->options, "prefix-exclude", required_argument, 0, 0, - TMAP_MAP_OPT_TYPE_INT, - "specify how many letters of prefix of name to be excluded when do randomize by name", - NULL, - tmap_map_opt_option_print_func_prefix_exclude, - TMAP_MAP_ALGO_GLOBAL); + TMAP_MAP_OPT_TYPE_INT, + "specify how many letters of prefix of name to be excluded when do randomize by name", + NULL, + tmap_map_opt_option_print_func_prefix_exclude, + TMAP_MAP_ALGO_GLOBAL); tmap_map_opt_options_add(opt->options, "suffix-exclude", required_argument, 0, 0, TMAP_MAP_OPT_TYPE_INT, "specify how many letters of suffix of name to be excluded when do randomize by name", @@ -887,6 +912,36 @@ tmap_map_opt_init_helper(tmap_map_opt_t *opt) vsw_type, tmap_map_opt_option_print_func_vsw_type, TMAP_MAP_ALGO_GLOBAL); + tmap_map_opt_options_add(opt->options, "vsw-fallback", required_argument, 0, 'H', + TMAP_MAP_OPT_TYPE_INT, + "the fallback vectorized smith-waterman algorithm", + NULL, + tmap_map_opt_option_print_func_vsw_fallback, + TMAP_MAP_ALGO_GLOBAL); + tmap_map_opt_options_add(opt->options, "confirm-vsw-corr", no_argument, 0, 0, + TMAP_MAP_OPT_TYPE_NONE, + "confirm corrections of assymetric VSW scores with standard SW", + NULL, + tmap_map_opt_option_print_func_confirm_vsw_corr, + TMAP_MAP_ALGO_GLOBAL); + tmap_map_opt_options_add(opt->options, "no-candidate-ext", no_argument, 0, 0, + TMAP_MAP_OPT_TYPE_NONE, + "do not extend reference zone for partially aligned candidates", + NULL, + tmap_map_opt_option_print_func_candidate_ext, + TMAP_MAP_ALGO_GLOBAL); + tmap_map_opt_options_add(opt->options, "no-vsw-fallback", no_argument, 0, 0, + TMAP_MAP_OPT_TYPE_NONE, + "do not use fallback alignment method if primary method fails", + NULL, + tmap_map_opt_option_print_func_correct_failed_vsw, + TMAP_MAP_ALGO_GLOBAL); + tmap_map_opt_options_add(opt->options, "no-nonstd-bases", no_argument, 0, 0, + TMAP_MAP_OPT_TYPE_NONE, + "do not process candidate locations containing non-standard nucleotides", + NULL, + tmap_map_opt_option_print_func_use_nvsw_on_nonstd_bases, + TMAP_MAP_ALGO_GLOBAL); tmap_map_opt_options_add(opt->options, "help", no_argument, 0, 'h', TMAP_MAP_OPT_TYPE_NONE, "print this message", @@ -943,6 +998,18 @@ tmap_map_opt_init_helper(tmap_map_opt_t *opt) realignment_clip_type, tmap_map_opt_option_print_func_realign_cliptype, TMAP_MAP_ALGO_GLOBAL); + tmap_map_opt_options_add(opt->options, "r-maxlen", required_argument, 0, 0, + TMAP_MAP_OPT_TYPE_INT, + "realignment maximal supported sequence length", + NULL, + tmap_map_opt_option_print_func_realign_maxlen, + TMAP_MAP_ALGO_GLOBAL); + tmap_map_opt_options_add(opt->options, "r-maxclip", required_argument, 0, 0, + TMAP_MAP_OPT_TYPE_INT, + "realignment maximal supported clip length", + NULL, + tmap_map_opt_option_print_func_realign_maxclip, + TMAP_MAP_ALGO_GLOBAL); tmap_map_opt_options_add(opt->options, "stats", no_argument, 0, 0, TMAP_MAP_OPT_TYPE_NONE, @@ -1491,9 +1558,11 @@ tmap_map_opt_init(int32_t algo_id) opt->bam_start_vfo = 0; opt->bam_end_vfo = 0; opt->use_param_ovr = 0; + opt->ovr_candeval = 0; opt->use_bed_in_end_repair = 1; opt->use_bed_in_mapq = 1; opt->use_bed_read_ends_stat = 0; + opt->amplicon_scope = TMAP_MAP_OPT_AMPLICON_SCOPE; opt->score_match = TMAP_MAP_OPT_SCORE_MATCH; opt->pen_mm = TMAP_MAP_OPT_PEN_MM; opt->pen_gapo = TMAP_MAP_OPT_PEN_GAPO; @@ -1507,7 +1576,7 @@ tmap_map_opt_init(int32_t algo_id) opt->unroll_banding = 0; opt->long_hit_mult = 3.0; opt->score_thr = 8; - opt->reads_queue_size = 262144; + opt->reads_queue_size = 65535; opt->num_threads = tmap_detect_cpus(); opt->num_threads_autodetected = 1; opt->aln_output_mode = TMAP_MAP_OPT_ALN_MODE_RAND_BEST; @@ -1539,6 +1608,11 @@ tmap_map_opt_init(int32_t algo_id) opt->sample_reads = 1.0; #endif opt->vsw_type = 4; + opt->vsw_fallback = 1; + opt->confirm_vsw_corr = 0; + opt->candidate_ext = 1; + opt->correct_failed_vsw = 1; + opt->use_nvsw_on_nonstd_bases = 1; opt->do_realign = 0; opt->realign_mat_score = TMAP_MAP_OPT_REALIGN_SCORE_MATCH; @@ -1547,6 +1621,8 @@ tmap_map_opt_init(int32_t algo_id) opt->realign_gep_score = TMAP_MAP_OPT_REALIGN_SCORE_GE; opt->realign_bandwidth = TMAP_MAP_OPT_REALIGN_BW; opt->realign_cliptype = 2; + opt->realign_maxlen = TMAP_MAP_OPT_REALIGN_MAXLEN; + opt->realign_maxclip = TMAP_MAP_OPT_REALIGN_MAXCLIP; opt->report_stats = 0; opt->realign_log = NULL; // tail repeat clipping @@ -1925,9 +2001,12 @@ tmap_map_opt_parse(int argc, char *argv[], tmap_map_opt_t *opt) else if(0 == c && 0 == strcmp("bam-end-vfo", options[option_index].name)) { opt->bam_end_vfo = strtol(optarg,NULL,0); } - else if((0 == c && 0 == strcmp("par-ovr", options[option_index].name))) { + else if(0 == c && 0 == strcmp("par-ovr", options[option_index].name)) { opt->use_param_ovr = 1; } + else if(0 == c && 0 == strcmp("ovr-candeval", options[option_index].name)) { + opt->ovr_candeval = 1; + } else if((0 == c && 0 == strcmp("no-bed-er", options[option_index].name))) { opt->use_bed_in_end_repair = 0; } @@ -1937,6 +2016,9 @@ tmap_map_opt_parse(int argc, char *argv[], tmap_map_opt_t *opt) else if((0 == c && 0 == strcmp("repair", options[option_index].name))) { opt->use_bed_read_ends_stat = 1; } + else if (0 == c && 0 == strcmp("ampl-scope", options[option_index].name)) { + opt->amplicon_scope = atoi(optarg); + } else if(c == 'A' || (0 == c && 0 == strcmp("score-match", options[option_index].name))) { opt->score_match = atoi(optarg); } @@ -1958,6 +2040,21 @@ tmap_map_opt_parse(int argc, char *argv[], tmap_map_opt_t *opt) else if(c == 'H' || (0 == c && 0 == strcmp("vsw-type", options[option_index].name))) { opt->vsw_type = atoi(optarg); } + else if(0 == c && 0 == strcmp("vsw-fallback", options[option_index].name)) { + opt->vsw_fallback = atoi(optarg); + } + else if(0 == c && 0 == strcmp("confirm-vsw-corr", options[option_index].name)) { + opt->confirm_vsw_corr = 1; + } + else if(0 == c && 0 == strcmp("no-candidate-ext", options[option_index].name)) { + opt->candidate_ext = 0; + } + else if(0 == c && 0 == strcmp("no-vsw-fallback", options[option_index].name)) { + opt->correct_failed_vsw = 0; + } + else if(0 == c && 0 == strcmp("no-nonstd-bases", options[option_index].name)) { + opt->use_nvsw_on_nonstd_bases = 0; + } else if(c == 'I' || (0 == c && 0 == strcmp("use-seq-equal", options[option_index].name))) { opt->seq_eq = 1; } @@ -2117,6 +2214,12 @@ tmap_map_opt_parse(int argc, char *argv[], tmap_map_opt_t *opt) else if (0 == c && 0 == strcmp ("r-clip", options [option_index].name)) { opt->realign_cliptype = atoi (optarg); } + else if (0 == c && 0 == strcmp ("r-maxlen", options [option_index].name)) { + opt->realign_maxlen = atoi (optarg); + } + else if (0 == c && 0 == strcmp ("r-maxclip", options [option_index].name)) { + opt->realign_maxclip = atoi (optarg); + } else if (0 == c && 0 == strcmp ("stats", options [option_index].name)) { opt->report_stats = 1; } @@ -2460,25 +2563,25 @@ tmap_map_opt_check_global(tmap_map_opt_t *opt_a, tmap_map_opt_t *opt_b) tmap_error("option -A was specified outside of the common options", Exit, CommandLineArgument); } if(opt_a->pen_mm != opt_b->pen_mm) { - tmap_error("option -M was specified outside of the common options", Exit, CommandLineArgument); + tmap_error("option -M was specified outside of the common options", Warn, CommandLineArgument); } if(opt_a->pen_gapo != opt_b->pen_gapo) { - tmap_error("option -O was specified outside of the common options", Exit, CommandLineArgument); + tmap_error("option -O was specified outside of the common options", Warn, CommandLineArgument); } if(opt_a->pen_gape != opt_b->pen_gape) { - tmap_error("option -E was specified outside of the common options", Exit, CommandLineArgument); + tmap_error("option -E was specified outside of the common options", Warn, CommandLineArgument); } if(opt_a->pen_gapl != opt_b->pen_gapl) { - tmap_error("option -G was specified outside of the common options", Exit, CommandLineArgument); + tmap_error("option -G was specified outside of the common options", Warn, CommandLineArgument); } if(opt_a->gapl_len != opt_b->gapl_len) { - tmap_error("option -K was specified outside of the common options", Exit, CommandLineArgument); + tmap_error("option -K was specified outside of the common options", Warn, CommandLineArgument); } if(opt_a->bw != opt_b->bw) { - tmap_error("option -w was specified outside of the common options", Exit, CommandLineArgument); + tmap_error("option -w was specified outside of the common options", Warn, CommandLineArgument); } if(opt_a->softclip_type != opt_b->softclip_type) { - tmap_error("option -g was specified outside of the common options", Exit, CommandLineArgument); + tmap_error("option -g was specified outside of the common options", Warn, CommandLineArgument); } if(opt_a->dup_window != opt_b->dup_window) { tmap_error("option -W was specified outside of the common options", Exit, CommandLineArgument); @@ -2490,7 +2593,7 @@ tmap_map_opt_check_global(tmap_map_opt_t *opt_a, tmap_map_opt_t *opt_b) tmap_error("option -U was specified outside of the common options", Exit, CommandLineArgument); } if(opt_a->score_thr != opt_b->score_thr) { - tmap_error("option -T was specified outside of the common options", Exit, CommandLineArgument); + tmap_error("option -T was specified outside of the common options", Exit, CommandLineArgument); } if(opt_a->reads_queue_size != opt_b->reads_queue_size) { tmap_error("option -q was specified outside of the common options", Exit, CommandLineArgument); @@ -2530,6 +2633,9 @@ tmap_map_opt_check_global(tmap_map_opt_t *opt_a, tmap_map_opt_t *opt_b) if(opt_a->vsw_type != opt_b->vsw_type) { tmap_error("option -H was specified outside of the common options", Exit, CommandLineArgument); } + if(opt_a->vsw_fallback != opt_b->vsw_fallback) { + tmap_error("option --vsw-fallback was specified outside of the common options", Exit, CommandLineArgument); + } if(opt_a->long_hit_mult != opt_b->long_hit_mult) { tmap_error("option --long-hit-mult was specified outside of the common options", Exit, CommandLineArgument); } @@ -2668,9 +2774,15 @@ tmap_map_opt_check(tmap_map_opt_t *opt) tmap_error_cmd_check_int64(opt->bam_start_vfo, 0, INT64_MAX, "--bam-start-vfo"); tmap_error_cmd_check_int64(opt->bam_end_vfo, 0, INT64_MAX, "--bam-end-vfo"); tmap_error_cmd_check_int(opt->use_param_ovr, 0, 1, "--par-ovr"); + tmap_error_cmd_check_int(opt->ovr_candeval, 0, 1, "--ovr-candeval"); + tmap_error_cmd_check_int(opt->confirm_vsw_corr, 0, 1, "--confirm-vsw-corr"); + tmap_error_cmd_check_int(opt->candidate_ext, 0, 1, "--no-candidate-ext"); + tmap_error_cmd_check_int(opt->correct_failed_vsw, 0, 1, "--no-err-fallback"); + tmap_error_cmd_check_int(opt->use_nvsw_on_nonstd_bases, 0, 1, "--no-nonstd-bases"); tmap_error_cmd_check_int(opt->use_bed_in_end_repair, 0, 1, "--no-bed-er"); tmap_error_cmd_check_int(opt->use_bed_in_mapq, 0, 1, "--no-bed-mapq"); tmap_error_cmd_check_int(opt->use_bed_read_ends_stat, 0, 1, "--repair"); + tmap_error_cmd_check_int(opt->amplicon_scope, 0, INT32_MAX, "--ampl-scope"); tmap_error_cmd_check_int(opt->score_match, 1, INT32_MAX, "-A"); tmap_error_cmd_check_int(opt->pen_mm, 1, INT32_MAX, "-M"); tmap_error_cmd_check_int(opt->pen_gapo, 1, INT32_MAX, "-O"); @@ -2722,6 +2834,7 @@ tmap_map_opt_check(tmap_map_opt_t *opt) // Warn users switch(opt->vsw_type) { case 1: + case 2: case 4: case 6: break; @@ -2729,7 +2842,18 @@ tmap_map_opt_check(tmap_map_opt_t *opt) tmap_error("the option -H value has not been extensively tested; proceed with caution", Warn, CommandLineArgument); break; } - + tmap_error_cmd_check_int(opt->vsw_fallback, 1, 10, "-H"); + // Warn users + switch(opt->vsw_fallback) { + case 1: + case 2: + case 4: + case 6: + break; + default: + tmap_error("the option --vsw-fallback value has not been extensively tested; proceed with caution", Warn, CommandLineArgument); + break; + } // flowspace options tmap_error_cmd_check_int(opt->fscore, 0, INT32_MAX, "-X"); tmap_error_cmd_check_int(opt->softclip_key, 0, 1, "-y"); @@ -2758,6 +2882,8 @@ tmap_map_opt_check(tmap_map_opt_t *opt) tmap_error_cmd_check_int(opt->realign_gep_score, -127, 128, "--r-gep"); tmap_error_cmd_check_int(opt->realign_bandwidth, 0, 256, "--r-bw"); tmap_error_cmd_check_int(opt->realign_cliptype, 0, 4, "--r-clip"); + tmap_error_cmd_check_int(opt->realign_maxlen, 0, 4096, "--r-maxlen"); + tmap_error_cmd_check_int(opt->realign_maxclip, 0, 256, "--r-maxclip"); // stats report tmap_error_cmd_check_int(opt->report_stats, 0, 1, "--stats"); @@ -2902,9 +3028,15 @@ tmap_map_opt_copy_global(tmap_map_opt_t *opt_dest, tmap_map_opt_t *opt_src) opt_dest->bam_start_vfo = opt_src->bam_start_vfo; opt_dest->bam_end_vfo = opt_src->bam_end_vfo; opt_dest->use_param_ovr = opt_src->use_param_ovr; + opt_dest->confirm_vsw_corr = opt_src->confirm_vsw_corr; + opt_dest->candidate_ext = opt_src->candidate_ext; + opt_dest->correct_failed_vsw = opt_src->correct_failed_vsw; + opt_dest->use_nvsw_on_nonstd_bases= opt_src->use_nvsw_on_nonstd_bases; + opt_dest->ovr_candeval = opt_src->ovr_candeval; opt_dest->use_bed_in_end_repair = opt_src->use_bed_in_end_repair; opt_dest->use_bed_in_mapq = opt_src->use_bed_in_mapq; opt_dest->use_bed_read_ends_stat = opt_src->use_bed_read_ends_stat; + opt_dest->amplicon_scope = opt_src->amplicon_scope; opt_dest->score_match = opt_src->score_match; opt_dest->pen_mm = opt_src->pen_mm; opt_dest->pen_gapo = opt_src->pen_gapo; @@ -2958,6 +3090,7 @@ tmap_map_opt_copy_global(tmap_map_opt_t *opt_dest, tmap_map_opt_t *opt_src) opt_dest->sample_reads = opt_src->sample_reads; #endif opt_dest->vsw_type = opt_src->vsw_type; + opt_dest->vsw_fallback = opt_src->vsw_fallback; // realignment control opt_dest->do_realign = opt_src->do_realign; @@ -3037,9 +3170,11 @@ tmap_map_opt_print(tmap_map_opt_t *opt) fprintf(stderr, "bam_start_vfo=%ld\n", opt->bam_start_vfo); fprintf(stderr, "bam_end_vfo=%ld\n", opt->bam_end_vfo); fprintf(stderr, "use_param_ovr=%d\n", opt->use_param_ovr); + fprintf(stderr, "ovr_candeval=%d\n", opt->ovr_candeval); fprintf(stderr, "use_bed_in_end_repair=%d\n", opt->use_bed_in_end_repair); fprintf(stderr, "use_bed_in_mapq=%d\n", opt->use_bed_in_mapq); fprintf(stderr, "use_bed_read_ends_stat=%d\n", opt->use_bed_read_ends_stat); + fprintf(stderr, "amplicon_scope=%d\n", opt->amplicon_scope); fprintf(stderr, "score_match=%d\n", opt->score_match); fprintf(stderr, "pen_mm=%d\n", opt->pen_mm); fprintf(stderr, "pen_gapo=%d\n", opt->pen_gapo); @@ -3089,6 +3224,11 @@ tmap_map_opt_print(tmap_map_opt_t *opt) fprintf(stderr, "sample_reads=%lf\n", opt->sample_reads); #endif fprintf(stderr, "vsw_type=%d\n", opt->vsw_type); + fprintf(stderr, "vsw_fallback=%d\n", opt->vsw_fallback); + fprintf(stderr, "confirm_vsw_corr=%d\n", opt->confirm_vsw_corr); + fprintf(stderr, "candidate_ext=%d\n", opt->candidate_ext); + fprintf(stderr, "correct_failed_vsw=%d\n", opt->correct_failed_vsw); + fprintf(stderr, "use_nvsw_on_nonstd_bases=%d\n", opt->use_nvsw_on_nonstd_bases); fprintf(stderr, "min_seq_len=%d\n", opt->min_seq_len); fprintf(stderr, "max_seq_len=%d\n", opt->max_seq_len); fprintf(stderr, "seed_length=%d\n", opt->seed_length); diff --git a/Analysis/TMAP/src/map/util/tmap_map_opt.h b/Analysis/TMAP/src/map/util/tmap_map_opt.h index 1b63625e..f580b2f3 100644 --- a/Analysis/TMAP/src/map/util/tmap_map_opt.h +++ b/Analysis/TMAP/src/map/util/tmap_map_opt.h @@ -17,6 +17,10 @@ extern "C" The default offset for homopolymer errors. */ #define TMAP_MAP_OPT_FSW_OFFSET 2 +/*! + The default padding for the read when searching for overlapping amplicons + */ +#define TMAP_MAP_OPT_AMPLICON_SCOPE 0 /*! The default match score. */ @@ -58,6 +62,8 @@ extern "C" #define TMAP_MAP_OPT_REALIGN_SCORE_GE -2 #define TMAP_MAP_OPT_REALIGN_BW 50 #define TMAP_MAP_OPT_REALIGN_CLIPTYPE 2 +#define TMAP_MAP_OPT_REALIGN_MAXLEN 500 +#define TMAP_MAP_OPT_REALIGN_MAXCLIP 50 #define TMAP_MAP_OPT_CONTEXT_SCORE_MATCH ((double) TMAP_MAP_OPT_SCORE_MATCH) #define TMAP_MAP_OPT_CONTEXT_SCORE_MM ((double) -TMAP_MAP_OPT_PEN_MM) @@ -227,9 +233,11 @@ typedef struct __tmap_map_opt_t { int64_t bam_start_vfo; /*!< starting virtual file offset (--bam-start-vfo) */ int64_t bam_end_vfo; /*!< ending virtual file offset (--bam-end-vfo) */ int32_t use_param_ovr; /*!< use parameters overwrite if given in BED file */ + int32_t ovr_candeval; /*!< use parameters overwrites in candidate evaluation */ int32_t use_bed_in_end_repair; /*!< use coordinates of amplicon edges in end repair */ int32_t use_bed_in_mapq; /*!< use coordinates of amplicons mapq computing */ int32_t use_bed_read_ends_stat; /*use read ends statisitcs from BED if provided */ + int32_t amplicon_scope; /*padding to the read when searching for overlapping amplions */ int32_t score_match; /*!< the match score (-A,--score-match) */ int32_t pen_mm; /*!< the mismatch penalty (-M,--pen-mismatch) */ int32_t pen_gapo; /*!< the indel open penalty (-O,--pen-gap-open) */ @@ -276,7 +284,14 @@ typedef struct __tmap_map_opt_t { #ifdef ENABLE_TMAP_DEBUG_FUNCTIONS double sample_reads; /*!< sample the reads at this fraction (-x,--sample-reads) */ #endif + + // candidate evaluation - hit SW scoring, initial zone boundaries int32_t vsw_type; /*!< the vectorized smith waterman algorithm (-H,--vsw-type) */ + int32_t vsw_fallback; /*!< the smith waterman algorithm used as fallback (used when the main one fails or if failure pre-conditions is detected)*/ + int32_t confirm_vsw_corr; /*!< use non-vectorized SW to confirm VSW assymetric score corrections */ + int32_t candidate_ext; /*!< extend candidate alignment zone to capture full read footprint */ + int32_t correct_failed_vsw; /*!< fall back to non-vectorized (slow) SW algorithm if vectorized fails*/ + int32_t use_nvsw_on_nonstd_bases; /*!< fall back to non-vectorized (slow) SW algorithm if non-standard bases are present in aligned zone*/ // DVK: realignment control int32_t do_realign; /*!< perform realignment after mapping */ @@ -286,6 +301,8 @@ typedef struct __tmap_map_opt_t { int32_t realign_gep_score; /*!< realignment gap extension score */ int32_t realign_bandwidth; /*!< realignment DP matrix band width */ int32_t realign_cliptype; /*!< realignment clipping type: 0: none, 1: semiglobal, 2: semiglobal+soft clip bead end, 3: semiglobal + soft clip key end, 4: local alignment */ + int32_t realign_maxlen; /*!< realignment maximal alignment length supproted (should be set to a minimal reasonable value to avoid excessive memory use)*/ + int32_t realign_maxclip; /*!< realignment maximal clip length supproted*/ int32_t do_hp_weight; /*!< perform realignment with context-specific gap scores */ // int32_t context_noclip; /*!< perform realignment with context-specific gap scores */ diff --git a/Analysis/TMAP/src/map/util/tmap_map_stats.c b/Analysis/TMAP/src/map/util/tmap_map_stats.c index 2057c9c1..15a7aacd 100644 --- a/Analysis/TMAP/src/map/util/tmap_map_stats.c +++ b/Analysis/TMAP/src/map/util/tmap_map_stats.c @@ -103,6 +103,25 @@ tmap_map_stats_add(tmap_map_stats_t *dest, tmap_map_stats_t *src) dest->bases_fully_tailclipped += src->bases_fully_tailclipped; dest->num_filtered_als += src->num_filtered_als; + + dest->read_clipping_extensions += src->read_clipping_extensions; + dest->nonstd_base_fallbacks_fwd += src->nonstd_base_fallbacks_fwd; + dest->nonstd_base_fallbacks_rev += src->nonstd_base_fallbacks_rev; + dest->vect_sw_calls += src->vect_sw_calls; + dest->fallback_vsw_calls += src->fallback_vsw_calls; + dest->fallback_sw_calls += src->fallback_sw_calls; + dest->overflows += src->overflows; + dest->vswfails += src->vswfails; + dest->totswfails += src->totswfails; + dest->symmetric_scores += src->symmetric_scores; + dest->asymmetric_scores_corrected += src->asymmetric_scores_corrected; + dest->asymmetric_scores_failed += src->asymmetric_scores_failed; + + dest->amplicon_searches += src->amplicon_searches; + dest->amplicon_search_successes += src->amplicon_search_successes; + dest->amplicon_overlaps += src->amplicon_overlaps; + dest->candeval_overrides += src->candeval_overrides; + dest->multiple_candeval_overrides += src->multiple_candeval_overrides; } void @@ -239,4 +258,23 @@ tmap_map_stats_print(tmap_map_stats_t *s) fprintf (stderr, "num_filtered_als=%llu\n", (unsigned long long int)s->num_filtered_als); + fprintf (stderr, "read_clipping_extensions=%llu\n", (unsigned long long int)s->read_clipping_extensions); + fprintf (stderr, "vect_sw_calls=%llu\n", (unsigned long long int)s->vect_sw_calls); + fprintf (stderr, "fallback_vsw_calls=%llu\n", (unsigned long long int)s->fallback_vsw_calls); + fprintf (stderr, "fallback_sw_calls=%llu\n", (unsigned long long int)s->fallback_sw_calls); + + fprintf (stderr, "nonstd_base_fallbacks_fwd=%llu\n", (unsigned long long int)s->nonstd_base_fallbacks_fwd); + fprintf (stderr, "nonstd_base_fallbacks_rev=%llu\n", (unsigned long long int)s->nonstd_base_fallbacks_rev); + fprintf (stderr, "overflows=%llu\n", (unsigned long long int)s->overflows); + fprintf (stderr, "symmetric_scores=%llu\n", (unsigned long long int)s->symmetric_scores); + fprintf (stderr, "asymmetric_scores_corrected=%llu\n", (unsigned long long int)s->asymmetric_scores_corrected); + fprintf (stderr, "asymmetric_scores_failed=%llu\n", (unsigned long long int)s->asymmetric_scores_failed); + + fprintf (stderr, "amplicon_searches=%llu\n", (unsigned long long int)s->amplicon_searches); + fprintf (stderr, "amplicon_search_successes=%llu\n", (unsigned long long int)s->amplicon_search_successes); + fprintf (stderr, "amplicon_overlaps=%llu\n", (unsigned long long int)s->amplicon_overlaps); + fprintf (stderr, "candeval_overrides=%llu\n", (unsigned long long int)s->candeval_overrides); + fprintf (stderr, "multiple_candeval_overrides=%llu\n", (unsigned long long int)s->multiple_candeval_overrides); + + } diff --git a/Analysis/TMAP/src/map/util/tmap_map_stats.h b/Analysis/TMAP/src/map/util/tmap_map_stats.h index fc8bce28..dcc72780 100644 --- a/Analysis/TMAP/src/map/util/tmap_map_stats.h +++ b/Analysis/TMAP/src/map/util/tmap_map_stats.h @@ -81,6 +81,24 @@ typedef struct uint64_t bases_fully_tailclipped; // number of filtered alignments uint64_t num_filtered_als; + // statistics on candidate evaluation + uint64_t vect_sw_calls; + uint64_t fallback_vsw_calls; + uint64_t fallback_sw_calls; + uint64_t read_clipping_extensions; + uint64_t nonstd_base_fallbacks_fwd; + uint64_t nonstd_base_fallbacks_rev; + uint64_t overflows; + uint64_t vswfails; + uint64_t totswfails; + uint64_t symmetric_scores; + uint64_t asymmetric_scores_corrected; + uint64_t asymmetric_scores_failed; + uint64_t amplicon_searches; + uint64_t amplicon_search_successes; + uint64_t amplicon_overlaps; + uint64_t candeval_overrides; + uint64_t multiple_candeval_overrides; } tmap_map_stats_t; /*! diff --git a/Analysis/TMAP/src/map/util/tmap_map_util.c b/Analysis/TMAP/src/map/util/tmap_map_util.c index e8f31585..8bdc20fd 100644 --- a/Analysis/TMAP/src/map/util/tmap_map_util.c +++ b/Analysis/TMAP/src/map/util/tmap_map_util.c @@ -4,8 +4,10 @@ #include #include #include +#include #include "../../util/tmap_alloc.h" #include "../../util/tmap_error.h" +#include "../../util/tmap_bsearch.h" #include "../../util/tmap_histo.h" #include "../../util/tmap_sam_convert.h" #include "../../util/tmap_progress.h" @@ -24,7 +26,6 @@ #include "tmap_map_util.h" #include "tmap_map_align_util.h" #include "../../sw/tmap_sw.h" -#include "../../util/tmap_histo.h" // #define CONCURRENT_PARAMETERS_CACHE 1 #ifdef CONCURRENT_PARAMETERS_CACHE @@ -104,11 +105,11 @@ tmap_map_get_amplicon int32_t seqid, uint32_t start, uint32_t end, + uint32_t strand, uint32_t *ampl_start, uint32_t *ampl_end, tmap_map_locopt_t** locopt, - tmap_map_endstat_p_t* read_ends, - uint32_t strand + tmap_map_endstat_p_t* read_ends ) { uint32_t *srh; @@ -196,6 +197,264 @@ tmap_map_get_amplicon return 0; } +typedef struct __tmap_map_amplicon_info +{ + uint32_t ampl_start; + uint32_t ampl_end; + tmap_map_locopt_t* locopt; + tmap_map_endstat_p_t read_ends; +} +tmap_map_amplicon_info; + +typedef struct __candeval_overrides_s +{ + tmap_map_amplicon_info* source; + int32_t softclip_type; + int32_t max_adapter_bases_for_soft_clipping; + tmap_vsw_opt_t vsw; +} +candeval_overrides_s; + +uint32_t candeval_overrides_same (candeval_overrides_s* p1, candeval_overrides_s* p2) +{ + return p1->softclip_type == p2->softclip_type && + p1->max_adapter_bases_for_soft_clipping == p2->max_adapter_bases_for_soft_clipping && + p1->vsw.score_match == p2->vsw.score_match && + p1->vsw.pen_mm == p2->vsw.pen_mm && + p1->vsw.pen_gapo == p2->vsw.pen_gapo && + p1->vsw.pen_gape == p2->vsw.pen_gape && + p1->vsw.score_thres == p2->vsw.score_thres; +} + +#define AMPL_INFO_INIT_CAPACITY 0 +static uint32_t capacity_snapper (uint32_t desired_capacity) +{ + // use closest higher degree of 2, but not less then AMPL_INFO_INIT_CAPACITY + + assert (desired_capacity <= INT32_MAX); // for the logic below to work, the upper bit should be 0 + uint8_t exp = 0; + if (desired_capacity == 0) + return 0; + if (desired_capacity == 1) + return 1; + while (desired_capacity) + { + desired_capacity >>= 1; + ++exp; + } + uint32_t capacity = 1 << exp; +#if AMPL_INFO_INIT_CAPACITY > 0 + if (capacity < AMPL_INFO_INIT_CAPACITY) + capacity = AMPL_INFO_INIT_CAPACITY; +#endif + return capacity; +} + +static void init_amplicon_info (tmap_map_amplicon_info** ampl_info, uint32_t* capacity, uint32_t preallocate) +{ + assert (ampl_info); + assert (capacity); + preallocate = capacity_snapper (preallocate); + if (preallocate) + *ampl_info = (tmap_map_amplicon_info*) tmap_calloc (preallocate, sizeof (tmap_map_amplicon_info), "amplicon_info"); + else + *ampl_info = NULL; + *capacity = preallocate; +} +static void manage_amplicon_info (tmap_map_amplicon_info** ampl_info, uint32_t* capacity, uint32_t needed_size) +{ + assert (ampl_info); + assert (capacity); + if (needed_size >= *capacity) + { + uint32_t new_capacity = capacity_snapper (needed_size); + *ampl_info = tmap_realloc (*ampl_info, new_capacity * sizeof (tmap_map_amplicon_info), "amplicon_info"); + } +} +static void destroy_amplicon_info (tmap_map_amplicon_info** ampl_info, uint32_t* capacity) +{ + assert (ampl_info); + assert (capacity); + free (*ampl_info); + *ampl_info = NULL; + *capacity = 0; +} + +// checks if amplicon overrides any of the candidate evaluation parameters; +// it yes, returns true and fills the passed in 'overrides' structure with the correct parameters (the non-overriden filled with default values) +static uint32_t ampl_candeval_parameters_from_locopt (tmap_map_opt_t* stage_opts, tmap_map_locopt_t* locopt, uint8_t strand, candeval_overrides_s* overrides) +{ + uint32_t rv = 0; + + // preset to defaults + overrides->softclip_type = stage_opts->softclip_type; + overrides->max_adapter_bases_for_soft_clipping = stage_opts->max_adapter_bases_for_soft_clipping; + overrides->vsw.score_match = stage_opts->score_match; + overrides->vsw.pen_mm = stage_opts->pen_mm; + overrides->vsw.pen_gapo = stage_opts->pen_gapo; + overrides->vsw.pen_gape = stage_opts->pen_gape; + overrides->vsw.score_thres = stage_opts->score_thr; + overrides->source = NULL; + + if (!locopt) + return rv; + + // softclip_type + if (locopt->softclip_type.over && locopt->softclip_type.value != stage_opts->softclip_type) + { + overrides->softclip_type = locopt->softclip_type.value; + rv = 1; + } + // "-J" parameter (--max-adapter-bases-for-soft-clipping) may be overriden for high or low amplicon end or for both. End-based spec takes over. + if (locopt->max_adapter_bases_for_soft_clipping_he.over && strand == 0) // read's 3' mapped to the higher end and overriden + { + if (locopt->max_adapter_bases_for_soft_clipping_he.value != stage_opts->max_adapter_bases_for_soft_clipping) + { + overrides->max_adapter_bases_for_soft_clipping = locopt->max_adapter_bases_for_soft_clipping_he.value; + rv = 1; + } + } + else if (locopt->max_adapter_bases_for_soft_clipping_le.over && strand == 1) // read's 3' mapped to the lower end and overriden + { + if (locopt->max_adapter_bases_for_soft_clipping_le.value != stage_opts->max_adapter_bases_for_soft_clipping) + { + overrides->max_adapter_bases_for_soft_clipping = locopt->max_adapter_bases_for_soft_clipping_le.value; + rv = 1; + } + } + else if (locopt->max_adapter_bases_for_soft_clipping.over) + { + if (locopt->max_adapter_bases_for_soft_clipping.value != stage_opts->max_adapter_bases_for_soft_clipping) + { + overrides->max_adapter_bases_for_soft_clipping = locopt->max_adapter_bases_for_soft_clipping.value; + rv = 1; + } + } + // score_match + if (locopt->score_match.over && locopt->score_match.value != stage_opts->score_match) + { + overrides->vsw.score_match = locopt->score_match.value; + rv = 1; + } + // pen_mm + if (locopt->pen_mm.over && locopt->pen_mm.value != stage_opts->pen_mm) + { + overrides->vsw.pen_mm = locopt->pen_mm.value; + rv = 1; + } + // pen_gapo + if (locopt->pen_gapo.over && locopt->pen_gapo.value != stage_opts->pen_gapo) + { + overrides->vsw.pen_gapo = locopt->pen_gapo.value; + rv = 1; + } + // pen_gape + if (locopt->pen_gape.over && locopt->pen_gape.value != stage_opts->pen_gape) + { + overrides->vsw.pen_gape = locopt->pen_gape.value; + rv = 1; + } + // score_thres + if (locopt->score_thr.over && locopt->score_thr.value != stage_opts->score_thr) + { + overrides->vsw.score_thres = locopt->score_thr.value; + rv = 1; + } + return rv; +} + +static uint32_t ampl_candeval_parameters (tmap_map_opt_t* stage_opts, tmap_map_amplicon_info* amplinfo, uint8_t strand, candeval_overrides_s* overrides) +{ + uint32_t rv = ampl_candeval_parameters_from_locopt (stage_opts, amplinfo->locopt, strand, overrides); + if (rv) + overrides->source = amplinfo; + return rv; +} + +// same as above using sam as a data source for overrides +static uint32_t ampl_candeval_parameters_from_sam (tmap_map_opt_t* stage_opts, tmap_map_sam_t* sam, candeval_overrides_s* overrides) +{ + return ampl_candeval_parameters_from_locopt (stage_opts, sam->param_ovr, sam->strand, overrides); +} + +// finds amplions intersecting with given start-end interval +// fills in the array of tmap_map_ampliocn_info at the address pointed by touched_ampls; +// allocates or re-allocates this array (updating address at touched_ampls), in this case updates touched_ampls_capacity +// returns number of touched_amplsactually filled in +// (always replaces whatever content is in the passed **touched_amplicons +int +tmap_map_get_overlapping_amplicons +( + tmap_refseq_t *refseq, + int32_t seqid, + uint32_t start, + uint32_t end, + uint32_t allowance, + tmap_map_amplicon_info** touched_ampls, // pointer to the array of ampliocn info structures, NULL if not allocated yest + uint32_t* touched_ampls_capacity) // capacity (allocated size) of touched_ampls array (for ammortized re-allocation and re-use) +{ + if (!refseq->bed_exist || refseq->bednum [seqid] == 0) + return 0; + + // find all amplions where ampl_ends are above start and ampl_starts are below end + + // WARNING: the code below assumes that both ampl_starts AND ampl_ends arrays are sorted + // This is true for current implementation: the BED loading code discards all fully contained amplicons, recording only the outermost ones. + // When we switch to handling inner amplicons as well, we'll need to add another level of indirection when searching for the ampl_ends, as the original bed-derived array may be unordered. + + start += allowance; + end = (allowance > end)?0:(end - allowance); + + // find first amplicon with ampl_end equal or above start + uint32_t* ampl_starts = refseq->bedstart [seqid]; + uint32_t* ampl_ends = refseq->bedend [seqid]; + uint32_t ampl_no = refseq->bednum [seqid]; + + uint32_t* first_ampl = (uint32_t*) tmap_binary_search (&start, ampl_ends, ampl_no, sizeof (*ampl_ends), lt_uint32); + uint32_t first_idx = first_ampl - ampl_ends; + if (first_idx == ampl_no) + return 0; + + // find last amplicon with ampl_start equal or above end. This is a sentinel, excluded from overlapped list + uint32_t* last_ampl = (uint32_t*) tmap_binary_search (&end, ampl_starts, ampl_no, sizeof (*ampl_starts), lt_uint32); + uint32_t last_idx = last_ampl - ampl_starts; + if (last_idx == 0) + return 0; + + if (first_idx == last_idx) + return 0; + + // reallocate result storage if needed + manage_amplicon_info (touched_ampls, touched_ampls_capacity, last_idx - first_idx); + + // fill in results + uint32_t ampl_idx; + tmap_map_amplicon_info* cur_ainfo = *touched_ampls; + for (ampl_idx = first_idx; ampl_idx != last_idx; ++ampl_idx, ++cur_ainfo) + { + cur_ainfo->ampl_start = ampl_starts [ampl_idx]; + cur_ainfo->ampl_end = ampl_ends [ampl_idx]; + if (refseq->parovr && refseq->parovr [seqid] && refseq->parovr [seqid][ampl_idx] != UINT32_MAX) + cur_ainfo->locopt = refseq->parmem + refseq->parovr [seqid][ampl_idx]; + else + cur_ainfo->locopt = NULL; + if (refseq->read_ends && refseq->read_ends [seqid] && refseq->read_ends [seqid][ampl_idx].index != UINT32_MAX) + { + tmap_map_endstat_t* src = refseq->read_ends [seqid] + ampl_idx; + cur_ainfo->read_ends.positions = refseq->endposmem + src->index; + cur_ainfo->read_ends.starts_count = src->starts_count; + cur_ainfo->read_ends.ends_count = src->ends_count; + } + else + { + cur_ainfo->read_ends.positions = NULL; + cur_ainfo->read_ends.starts_count = 0; + cur_ainfo->read_ends.ends_count = 0; + } + } + return last_idx - first_idx; +} + // use softclip settings from tmap parameters // disallow 3' softclip, if @@ -206,15 +465,15 @@ tmap_map_get_amplicon static void tmap_map_util_set_softclip ( - tmap_map_opt_t *opt, + int32_t softclip_type, tmap_seq_t *seq, int32_t max_adapter_bases_for_soft_clipping, int32_t *softclip_start, int32_t *softclip_end ) { - (*softclip_start) = (TMAP_MAP_OPT_SOFT_CLIP_LEFT == opt->softclip_type || TMAP_MAP_OPT_SOFT_CLIP_ALL == opt->softclip_type) ? 1 : 0; - (*softclip_end) = (TMAP_MAP_OPT_SOFT_CLIP_RIGHT == opt->softclip_type || TMAP_MAP_OPT_SOFT_CLIP_ALL == opt->softclip_type) ? 1 : 0; + (*softclip_start) = (TMAP_MAP_OPT_SOFT_CLIP_LEFT == softclip_type || TMAP_MAP_OPT_SOFT_CLIP_ALL == softclip_type) ? 1 : 0; + (*softclip_end) = (TMAP_MAP_OPT_SOFT_CLIP_RIGHT == softclip_type || TMAP_MAP_OPT_SOFT_CLIP_ALL == softclip_type) ? 1 : 0; // check if the ZB tag is present... if (TMAP_SEQ_TYPE_SAM == seq->type || TMAP_SEQ_TYPE_BAM == seq->type) // SAM/BAM { @@ -1197,7 +1456,7 @@ tmap_map_util_mapq(tmap_map_sams_t *sams, int32_t seq_len, tmap_map_opt_t *opt, uint32_t end = start+tmp_sam.target_len-1; uint32_t ampl_start, ampl_end; if (tmp_sam.score != best_score) continue; - if (tmap_map_get_amplicon(refseq, tmp_sam.seqid, start, end, &l_start, &l_end, NULL, NULL, tmp_sam.strand)) + if (tmap_map_get_amplicon(refseq, tmp_sam.seqid, start, end, tmp_sam.strand, &l_start, &l_end, NULL, NULL)) { /* if (abs(ampl_start-start) < 15 && abs(ampl_end-end) < 15) { @@ -1462,6 +1721,7 @@ tmap_map_util_sw_gen_score_helper ( tmap_refseq_t *refseq, tmap_map_sams_t *sams, + tmap_seq_t *origseq, tmap_seq_t *seq, tmap_map_sams_t *sams_tmp, int32_t *idx, @@ -1474,364 +1734,491 @@ tmap_map_util_sw_gen_score_helper uint32_t end_pos, int32_t *target_mem, uint8_t **target, - int32_t softclip_start, - int32_t softclip_end, + // int32_t softclip_start, + // int32_t softclip_end, int32_t prev_n_best, int32_t max_seed_band, // NB: this may be modified as banding is unrolled int32_t prev_score, // NB: must be greater than or equal to the scoring threshold tmap_vsw_opt_t *vsw_opt, tmap_rand_t *rand, - tmap_map_opt_t *opt + tmap_map_opt_t *opt, + tmap_map_amplicon_info** amplicons, + uint32_t* amplicons_capacity, + tmap_map_stats_t *stat // statistics + ) { - tmap_map_sam_t tmp_sam; - uint8_t *query; - uint32_t qlen; - int32_t tlen, overflow = 0, is_long_hit = 0; - - // choose a random one within the window - if(start == end) { - tmp_sam = sams->sams[start]; - } - else { - int32_t r = (int32_t)(tmap_rand_get(rand) * (end - start + 1)); - r += start; - tmp_sam = sams->sams[r]; - } - - if(0 < opt->long_hit_mult && seq_len * opt->long_hit_mult <= end_pos - start_pos + 1) { - is_long_hit = 1; - } - - // update the query sequence - query = (uint8_t*)tmap_seq_get_bases(seq)->s; - qlen = tmap_seq_get_bases_length(seq); + tmap_map_sam_t tmp_sam; + uint8_t *query; + uint32_t qlen; + int32_t tlen, overflow = 0, is_long_hit = 0; - // add in band width - // one-based - if(start_pos < opt->bw) { - start_pos = 1; - } - else { - start_pos -= opt->bw - 1; - } - end_pos += opt->bw - 1; - if(refseq->annos[sams->sams[end].seqid].len < end_pos) { - end_pos = refseq->annos[sams->sams[end].seqid].len; // one-based - } + // choose a random one within the window + if (start == end) + { + tmp_sam = sams->sams [start]; + } + else + { + int32_t r = (int32_t) (tmap_rand_get (rand) * (end - start + 1)); + r += start; + tmp_sam = sams->sams [r]; + } - // get the target sequence - tlen = end_pos - start_pos + 1; - if((*target_mem) < tlen) { // more memory? - (*target_mem) = tlen; - tmap_roundup32((*target_mem)); - (*target) = tmap_realloc((*target), sizeof(uint8_t)*(*target_mem), "target"); - } - // NB: IUPAC codes are turned into mismatches - if(NULL == tmap_refseq_subseq2(refseq, sams->sams[end].seqid+1, start_pos, end_pos, (*target), 1, NULL)) { - tmap_error("bug encountered", Exit, OutOfRange); - } + if (0 < opt->long_hit_mult && seq_len * opt->long_hit_mult <= end_pos - start_pos + 1) + is_long_hit = 1; - // reverse compliment the target - if(1 == strand) { - tmap_reverse_compliment_int((*target), tlen); - } + // update the query sequence + query = (uint8_t*) tmap_seq_get_bases (seq)->s; + qlen = tmap_seq_get_bases_length (seq); - // Debugging -#ifdef TMAP_VSW_DEBUG - int j; - fprintf(stderr, "seqid:%u start_pos=%u end_pos=%u strand=%d\n", sams->sams[end].seqid+1, start_pos, end_pos, strand); - for(j=0;jbw) + start_pos = 1; + else + start_pos -= opt->bw - 1; - // initialize the bounds - tmp_sam.result.query_start = tmp_sam.result.query_end = 0; - tmp_sam.result.target_start = tmp_sam.result.target_end = 0; - - /** - * Discussion on choosing alignments. - * - * In general, we would like to choose the alignment using the *most* number - * of query bases. The complication comes when using soft-clipping. - * - * When no soft-clipping occurs, then the whole query will be used. - * - * When there is only soft-clipping at the 3' end of the query (end of the - * read), we can search for the alignment with the greatest query end when - * searching in the 5'->3' direction. Since the query start is fixed, as there - * is no 5' start-clipping, we are then guaranteed to find the alignment with - * the most number of query bases if we fix the query end when we align in the - * 3'->5' direction. - * - * When there is only soft-clipping at the 5' end of the query (start of the - * read), we can search for the alignment with the greatest query end when - * searching in the 5'->3' direction, as the query end is fixed. Then, when - * aligning in the 3'->5' direction, we can search for the alignment with the - * smallest query start (which in the 3'->5' direction is the one with the one - * with the largest query end). - * - * We cannot guarantee anything if we are allowing soft-clipping on both the - * 5' and 3' ends. - */ - - // NB: this aligns in the sequencing direction - // DVK: bug #11386 - { - const int16_t TARGET_EDGE_ALLOWANCE = 4; - const int16_t MAX_TARGET_LEN_FOR_VSW = 32000; - int8_t target_causes_read_clipping; - int8_t first_run = 1; - int32_t score = 0, prev_score = 0; - uint32_t new_end_pos, new_start_pos; - tmap_vsw_result_t result; - do - { - // initial assumption - target_causes_read_clipping = 0; + end_pos += opt->bw - 1; + if (refseq->annos [sams->sams [end].seqid].len < end_pos) + end_pos = refseq->annos [sams->sams [end].seqid].len; // one-based - // initialize the bounds - why? - result.query_start = result.query_end = 0; - result.target_start = result.target_end = 0; - score = tmap_vsw_process_fwd(vsw, query, qlen, (*target), tlen, - &result, &overflow, opt->score_thr, 1); + // get the target sequence + tlen = end_pos - start_pos + 1; + if ((*target_mem) < tlen) + { // more memory? + (*target_mem) = tlen; + tmap_roundup32 ((*target_mem)); + (*target) = tmap_realloc ((*target), sizeof (uint8_t)*(*target_mem), "target"); + } + // NB: IUPAC codes are turned into mismatches + if (NULL == tmap_refseq_subseq2 (refseq, sams->sams [end].seqid+1, start_pos, end_pos, (*target), 1, NULL)) + { + tmap_error ("bug encountered", Exit, OutOfRange); + } - if (1 == overflow) - return INT32_MIN; + // reverse compliment the target + if (1 == strand) + tmap_reverse_compliment_int ((*target), tlen); - if (!first_run && score <= prev_score) // check for zone edge crossing on first run always, then only if score is improved - break; // if score did not improve, get out and keep last result/score in tmp_sam - // query clip may be recoverable if it has 3' clip and alignment goes to target zone end - new_end_pos = end_pos; - new_start_pos = start_pos; - if (tlen - result.target_end < TARGET_EDGE_ALLOWANCE && qlen > result.query_end) + // #define DEBUG_VSW_ASSYMETRY + #ifdef DEBUG_VSW_ASSYMETRY + { + int j; + // fprintf (stderr, "seqid:%u start_pos=%u end_pos=%u strand=%d\n", sams->sams [end].seqid+1, start_pos, end_pos, strand); + for (j = 0; j < qlen; j++) + { + if (query [j] >= 4) { - // extend target if possible - new_end_pos += qlen - result.query_end + TARGET_EDGE_ALLOWANCE; - if(refseq->annos[sams->sams[end].seqid].len < new_end_pos) - { - new_end_pos = refseq->annos[sams->sams[end].seqid].len; // one-based - } + tmap_warning ("QUERY [%d] = %d\n", j, query [j]); + // query [j] = 0; } - // similarly process 5' clips - if (result.target_start < TARGET_EDGE_ALLOWANCE && result.query_start > 0) + // fputc ("ACGTN" [query [j]], stderr); + } + // fputc ('\n', stderr); + for (j = 0; j < tlen; j++) + { + if ((*target) [j] >= 4) { - if (result.query_start + TARGET_EDGE_ALLOWANCE > new_start_pos) - new_start_pos -= result.query_start + TARGET_EDGE_ALLOWANCE; - else - new_start_pos = 1; + tmap_warning ("TARGET [%d] = %d\n", j, (*target) [j]); + // (*target) [j] = 0; } - if (new_end_pos > end_pos || new_start_pos < start_pos ) - { - end_pos = new_end_pos; - start_pos = new_start_pos; - // get the target sequence - tlen = end_pos - start_pos + 1; - if((*target_mem) < tlen) - { // more memory? - (*target_mem) = tlen; - tmap_roundup32((*target_mem)); - (*target) = tmap_realloc((*target), sizeof(uint8_t)*(*target_mem), "target"); - } - // NB: IUPAC codes are turned into mismatches - if(NULL == tmap_refseq_subseq2(refseq, sams->sams[end].seqid+1, start_pos, end_pos, (*target), 1, NULL)) - tmap_error("bug encountered", Exit, OutOfRange); + // fputc ("ACGTN" [(*target) [j]], stderr); + } + // fputc ('\n', stderr); + } + #endif - // reverse compliment the target - if (1 == strand) - tmap_reverse_compliment_int((*target), tlen); + // initialize the bounds + tmp_sam.result.query_start = tmp_sam.result.query_end = 0; + tmp_sam.result.target_start = tmp_sam.result.target_end = 0; - target_causes_read_clipping = 1; - } - tmp_sam.score = score; - tmp_sam.result = result; - prev_score = score; - first_run = 0; - if (start_pos + MAX_TARGET_LEN_FOR_VSW < end_pos) - break; - } - while (target_causes_read_clipping); + /** + * Discussion on choosing alignments. + * + * In general, we would like to choose the alignment using the *most* number + * of query bases. The complication comes when using soft-clipping. + * + * When no soft-clipping occurs, then the whole query will be used. + * + * When there is only soft-clipping at the 3' end of the query (end of the + * read), we can search for the alignment with the greatest query end when + * searching in the 5'->3' direction. Since the query start is fixed, as there + * is no 5' start-clipping, we are then guaranteed to find the alignment with + * the most number of query bases if we fix the query end when we align in the + * 3'->5' direction. + * + * When there is only soft-clipping at the 5' end of the query (start of the + * read), we can search for the alignment with the greatest query end when + * searching in the 5'->3' direction, as the query end is fixed. Then, when + * aligning in the 3'->5' direction, we can search for the alignment with the + * smallest query start (which in the 3'->5' direction is the one with the one + * with the largest query end). + * + * We cannot guarantee anything if we are allowing soft-clipping on both the + * 5' and 3' ends. + */ - } + // NB: this aligns in the sequencing direction + // DVK: bug #11386 + { + const int16_t TARGET_EDGE_ALLOWANCE = 4; + const int16_t MAX_TARGET_LEN_FOR_VSW = 32000; + int8_t target_causes_read_clipping; + uint32_t clipping_extensions = 0; + int8_t first_run = 1; + int32_t score = 0, prev_score = 0; + uint32_t new_end_pos, new_start_pos; + tmap_vsw_result_t result; + uint32_t amplicons_no = 0; + uint32_t ampl_found = 0; + tmap_map_amplicon_info best_ampl; + memset (&best_ampl, 0, sizeof (best_ampl)); + do + { + // initial assumption + target_causes_read_clipping = 0; + ampl_found = 0; - if (1 < tmp_sam.result.n_best) - { - // What happens if soft-clipping or not soft-clipping causes two - // alignments to be equally likely? So while we could set the scores to be - // similar, we can also down-weight the score a little bit. - tmp_sam.score_subo = tmp_sam.score - opt->pen_gapo - opt->pen_gape; - //tmp_sam.score_subo = tmp_sam.score - 1; - } - if (1 == is_long_hit) - { - // if we have many seeds that span a large tandem repeat, then we should - // downweight the sub-optimal score - tmp_sam.score_subo = tmp_sam.score - opt->pen_gapo - opt->pen_gape; - } + // initialize the bounds - why? + result.query_start = result.query_end = 0; + result.target_start = result.target_end = 0; + // handle amplicons - find if parameters overriding is needed + if (opt->use_param_ovr && opt->ovr_candeval) + { + // find amplicons + amplicons_no = tmap_map_get_overlapping_amplicons (refseq, sams->sams [end].seqid, start_pos, end_pos, opt->amplicon_scope, amplicons, amplicons_capacity); + ++stat->amplicon_searches; + if (amplicons_no) + ++stat->amplicon_search_successes; + if (amplicons_no > 1) + ++stat->amplicon_overlaps; + } - if(opt->score_thr <= tmp_sam.score) { // NB: we could also specify 'prev_score <= tmp_sam.score' - int32_t add_current = 1; // yes, by default - - // Save local variables - // TODO: do we need to save this data in this fashion? - int32_t t_end = end; - int32_t t_start = start; - int32_t t_end_pos = end_pos; - uint32_t t_start_pos = start_pos; - - if(1 == opt->unroll_banding // unrolling is turned on - && 0 <= max_seed_band // do we have enough bases to unrooll - && 1 < end - start + 1 // are there enough seeds in this group - && ((prev_n_best < 0 && 1 < tmp_sam.result.n_best) // we need to do a first timeunroll - || (prev_n_best == tmp_sam.result.n_best))) { // unroll was not successful, try again - uint32_t start_pos_prev=0; - uint32_t start_pos_cur=0, end_pos_cur=0; - uint32_t unrolled = 0; - - while(0 == unrolled) { - - // Reset local variables - start = t_start; - end = t_end; - - //fprintf(stderr, "max_seed_band=%d start=%d end=%d\n", max_seed_band, start, end); - // NB: band based on EXACT start position - int32_t n = end + 1; - end = start; - while(start < n) { - int32_t cur_score; - // reset start and end position - if(start == end) { - tmap_map_util_sw_get_start_and_end_pos(&sams->sams[start], seq_len, strand, &start_pos, &end_pos); - start_pos_prev = start_pos; - } - if(end + 1 < n) { - if(sams->sams[end].strand == sams->sams[end+1].strand - && sams->sams[end].seqid == sams->sams[end+1].seqid) { - tmap_map_util_sw_get_start_and_end_pos(&sams->sams[end+1], seq_len, strand, &start_pos_cur, &end_pos_cur); + // make list of distinct overrides that do not match stage params + candeval_overrides_s* overrides = (candeval_overrides_s*) alloca (sizeof (candeval_overrides_s) * amplicons_no); + int overrides_no = 0; + for (tmap_map_amplicon_info *ainfo = *amplicons, *sent = *amplicons + amplicons_no; ainfo != sent; ++ainfo) + { + // set parameters overrides: fill in first unoccupied slot in 'overrides' + uint32_t differs = ampl_candeval_parameters (opt, ainfo, strand, overrides + overrides_no); + if (!differs) // matched default and thus was not recorded + continue; + // check if matches any prior one; increment overrides_no only if unique + uint32_t match_found = 0; + for (candeval_overrides_s* older_override = overrides, *older_sent = overrides + overrides_no; older_override != older_sent && ! match_found; ++older_override) + if (candeval_overrides_same (older_override, overrides + overrides_no)) + match_found = 1; + if (!match_found) + ++overrides_no; + } + // if no amplicons found (or no overriding ordered), use global params to compute score + if (!overrides_no) + { + score = tmap_vsw_process_fwd (vsw, query, qlen, (*target), tlen, + &result, &overflow, opt->score_thr, 1, opt->confirm_vsw_corr, opt->correct_failed_vsw, opt->use_nvsw_on_nonstd_bases, stat); + } + else // run for every override + { + ++stat->candeval_overrides; + if (overrides_no > 1) + ++stat->multiple_candeval_overrides; + int32_t softclip_start, softclip_end; + // save default parameters + tmap_vsw_opt_t orig_vsw_opt = *(vsw->opt); + int32_t orig_softclip_start = vsw->query_start_clip, orig_softclip_end = vsw->query_end_clip; + // run for every override + int32_t best_score = INT32_MIN; + candeval_overrides_s* best_params = NULL; + for (candeval_overrides_s* override = overrides, *ovr_sent = overrides + overrides_no; override != ovr_sent; ++override) + { + tmap_map_util_set_softclip (override->softclip_type, origseq, override->max_adapter_bases_for_soft_clipping, &softclip_start, &softclip_end); + tmap_vsw_set_params (vsw, softclip_start, softclip_end, &(override->vsw)); + score = tmap_vsw_process_fwd (vsw, query, qlen, (*target), tlen, + &result, &overflow, opt->score_thr, 1, opt->confirm_vsw_corr, opt->correct_failed_vsw, opt->use_nvsw_on_nonstd_bases, stat); + if (score > best_score) + { + best_score = score; + best_params = override; + ampl_found = 1; + } + } + if (ampl_found) + { + // pick the best (highest) one + score = best_score; + // remember what was the best amplicon (best_ampl) + best_ampl = *best_params->source; + } + // reset vsw parameters to orig + tmap_vsw_set_params (vsw, orig_softclip_start, orig_softclip_end, &(orig_vsw_opt)); + } + if (1 == overflow) + return INT32_MIN; + if (!first_run && score <= prev_score) // check for zone edge crossing on first run always, then only if score is improved + break; // if score did not improve, get out and keep last result/score in tmp_sam + + // query clip may be recoverable if it has 3' clip and alignment goes to target zone end + new_end_pos = end_pos; + new_start_pos = start_pos; + if (tlen - result.target_end < TARGET_EDGE_ALLOWANCE && qlen > result.query_end) + { + // extend target if possible + new_end_pos += qlen - result.query_end + TARGET_EDGE_ALLOWANCE; + if (refseq->annos [sams->sams [end].seqid].len < new_end_pos) + { + new_end_pos = refseq->annos [sams->sams [end].seqid].len; // one-based + } + } + // similarly process 5' clips + if (result.target_start < TARGET_EDGE_ALLOWANCE && result.query_start > 0) + { + if (result.query_start + TARGET_EDGE_ALLOWANCE > new_start_pos) + new_start_pos -= result.query_start + TARGET_EDGE_ALLOWANCE; + else + new_start_pos = 1; + } + if (opt->candidate_ext && (new_end_pos > end_pos || new_start_pos < start_pos)) + { + end_pos = new_end_pos; + start_pos = new_start_pos; + // get the target sequence + tlen = end_pos - start_pos + 1; + if ((*target_mem) < tlen) + { // more memory? + (*target_mem) = tlen; + tmap_roundup32 ((*target_mem)); + (*target) = tmap_realloc ((*target), sizeof (uint8_t) * (*target_mem), "target"); + } + // NB: IUPAC codes are turned into mismatches + if (NULL == tmap_refseq_subseq2 (refseq, sams->sams [end].seqid + 1, start_pos, end_pos, (*target), 1, NULL)) + tmap_error ("bug encountered", Exit, OutOfRange); - // fprintf(stderr, "start_pos_cur=%u start_pos_prev=%u max_seed_band=%d\n", - // start_pos_cur, start_pos_prev, max_seed_band); + // reverse compliment the target + if (1 == strand) + tmap_reverse_compliment_int ((*target), tlen); + target_causes_read_clipping = 1; + ++clipping_extensions; + } + prev_score = score; + first_run = 0; + if (start_pos + MAX_TARGET_LEN_FOR_VSW < end_pos) + break; + } + while (target_causes_read_clipping); + stat->read_clipping_extensions += clipping_extensions; + tmp_sam.score = score; + tmp_sam.result = result; + if (ampl_found) // found the best scoring out of (one or more) overlapping amplicons + { + tmp_sam.ampl_start = best_ampl.ampl_start; + tmp_sam.ampl_end = best_ampl.ampl_end; + tmp_sam.param_ovr = best_ampl.locopt; + tmp_sam.read_ends = best_ampl.read_ends; + } + else if (amplicons_no == 1) // regardless of how good/bad the match is and whether overrides were defined, if there is only one overlapping amplicon, bind it + { + tmp_sam.ampl_start = (*amplicons)->ampl_start; + tmp_sam.ampl_end = (*amplicons)->ampl_end; + tmp_sam.param_ovr = (*amplicons)->locopt; + tmp_sam.read_ends = (*amplicons)->read_ends; + } + else + { + tmp_sam.ampl_start = 0; + tmp_sam.ampl_end = 0; + tmp_sam.param_ovr = NULL; + tmp_sam.read_ends.positions = NULL, tmp_sam.read_ends.starts_count = 0, tmp_sam.read_ends.ends_count = 0; + } + } - // consider start positions only - if(start_pos_cur - start_pos_prev <= max_seed_band) { // consider start positions only - end++; - if(end_pos < end_pos_cur) { - end_pos = end_pos_cur; - } - start_pos_prev = start_pos_cur; - continue; // there may be more to add - } } } // do not recurse if we did not unroll if(0 < max_seed_band && t_start == start && t_end == end) { // we did not unroll any max_seed_band = (max_seed_band >> 1); break; } - unrolled = 1; // we are going to unroll + if (1 < tmp_sam.result.n_best) + { + // What happens if soft-clipping or not soft-clipping causes two + // alignments to be equally likely? So while we could set the scores to be + // similar, we can also down-weight the score a little bit. + tmp_sam.score_subo = tmp_sam.score - opt->pen_gapo - opt->pen_gape; + //tmp_sam.score_subo = tmp_sam.score - 1; + } + if (1 == is_long_hit) + { + // if we have many seeds that span a large tandem repeat, then we should + // downweight the sub-optimal score + tmp_sam.score_subo = tmp_sam.score - opt->pen_gapo - opt->pen_gape; + } - // TODO: we could hash the alignment result, as unrolling may - // cause many more SWs - // recurse - cur_score = tmap_map_util_sw_gen_score_helper(refseq, sams, seq, sams_tmp, idx, start, end, + if (opt->score_thr <= tmp_sam.score) + { // NB: we could also specify 'prev_score <= tmp_sam.score' + int32_t add_current = 1; // yes, by default + + // Save local variables + // TODO: do we need to save this data in this fashion? + int32_t t_end = end; + int32_t t_start = start; + int32_t t_end_pos = end_pos; + uint32_t t_start_pos = start_pos; + + if ( 1 == opt->unroll_banding // unrolling is turned on + && 0 <= max_seed_band // do we have enough bases to unrooll + && 1 < end - start + 1 // are there enough seeds in this group + && ( (prev_n_best < 0 && 1 < tmp_sam.result.n_best) // we need to do a first time unroll + || (prev_n_best == tmp_sam.result.n_best))) + { // unroll was not successful, try again + uint32_t start_pos_prev=0; + uint32_t start_pos_cur=0, end_pos_cur=0; + uint32_t unrolled = 0; + + while (0 == unrolled) + { + // Reset local variables + start = t_start; + end = t_end; + + //fprintf (stderr, "max_seed_band=%d start=%d end=%d\n", max_seed_band, start, end); + // NB: band based on EXACT start position + int32_t n = end + 1; + end = start; + while (start < n) + { + int32_t cur_score; + // reset start and end position + if (start == end) + { + tmap_map_util_sw_get_start_and_end_pos (&sams->sams [start], seq_len, strand, &start_pos, &end_pos); + start_pos_prev = start_pos; + } + if (end + 1 < n) + { + if ( sams->sams [end].strand == sams->sams [end+1].strand + && sams->sams [end].seqid == sams->sams [end+1].seqid) + { + tmap_map_util_sw_get_start_and_end_pos (&sams->sams [end+1], seq_len, strand, &start_pos_cur, &end_pos_cur); + + // consider start positions only + if (start_pos_cur - start_pos_prev <= max_seed_band) + { // consider start positions only + end++; + if (end_pos < end_pos_cur) + end_pos = end_pos_cur; + start_pos_prev = start_pos_cur; + continue; // there may be more to add + } + } + } // do not recurse if we did not unroll if (0 < max_seed_band && t_start == start && t_end == end) { // we did not unroll any max_seed_band = (max_seed_band >> 1); break; } + unrolled = 1; // we are going to unroll + + // TODO: we could hash the alignment result, as unrolling may + // cause many more SWs + + // recurse + cur_score = tmap_map_util_sw_gen_score_helper (refseq, sams, origseq, seq, sams_tmp, idx, start, end, strand, vsw, seq_len, start_pos, end_pos, target_mem, target, - softclip_start, softclip_end, + // softclip_start, softclip_end, tmp_sam.result.n_best, (max_seed_band <= 0) ? -1 : (max_seed_band >> 1), tmp_sam.score, - vsw_opt, rand, opt); - - if(cur_score == tmp_sam.score) add_current = 0; // do not add the current alignment, we found it during unrolling - // update start/end - end++; - start = end; - } - } - } - - // Reset local variables - // TODO: do we need to reset this data in this fashion? - end = t_end; - start = t_start; - end_pos = t_end_pos; - start_pos = t_start_pos; + vsw_opt, rand, opt, + amplicons, + amplicons_capacity, + stat + ); + + if (cur_score == tmp_sam.score) + add_current = 0; // do not add the current alignment, we found it during unrolling + // update start/end + end++; + start = end; + } + } + } - if(1 == add_current) { - tmap_map_sam_t *s = NULL; + // Reset local variables + // TODO: do we need to reset this data in this fashion? + end = t_end; + start = t_start; + end_pos = t_end_pos; + start_pos = t_start_pos; - if(sams_tmp->n <= (*idx)) { - tmap_map_sams_realloc(sams_tmp, (*idx)+1); - //tmap_error("bug encountered", Exit, OutOfRange); - } + if (1 == add_current) + { + tmap_map_sam_t *s = NULL; - s = &sams_tmp->sams[(*idx)]; - // shallow copy previous data - (*s) = tmp_sam; - //s->result = tmp_sam.result; + if (sams_tmp->n <= (*idx)) + { + tmap_map_sams_realloc (sams_tmp, (*idx)+1); + //tmap_error ("bug encountered", Exit, OutOfRange); + } - // nullify the cigar - s->n_cigar = 0; - s->cigar = NULL; + s = &sams_tmp->sams [(*idx)]; + // shallow copy previous data + (*s) = tmp_sam; + //s->result = tmp_sam.result; - // adjust target length and position NB: query length is implicitly - // stored in s->query_end (consider on the next pass) - s->pos = start_pos - 1; // zero-based - s->target_len = s->result.target_end + 1; + // nullify the cigar + s->n_cigar = 0; + s->cigar = NULL; - if(1 == strand) { - if(s->pos + tlen <= s->result.target_end) s->pos = 0; - else s->pos += tlen - s->result.target_end - 1; - } + // adjust target length and position NB: query length is implicitly + // stored in s->query_end (consider on the next pass) + s->pos = start_pos - 1; // zero-based + s->target_len = s->result.target_end + 1; - /* - fprintf(stderr, "strand=%d pos=%d n_best=%d %d-%d %d-%d %d\n", - strand, - s->pos, - s->result.n_best, - s->query_start, - s->query_end, - s->target_start, - s->result.target_end, - s->target_len); - */ + if (1 == strand) + { + if (s->pos + tlen <= s->result.target_end) s->pos = 0; + else s->pos += tlen - s->result.target_end - 1; + } - // # of seeds - s->n_seeds = (end - start + 1); - // update aux data - tmap_map_sam_malloc_aux(s); - switch(s->algo_id) { + /* + fprintf (stderr, "strand=%d pos=%d n_best=%d %d-%d %d-%d %d\n", + strand, + s->pos, + s->result.n_best, + s->query_start, + s->query_end, + s->target_start, + s->result.target_end, + s->target_len); + */ + + // # of seeds + s->n_seeds = (end - start + 1); + // update aux data + tmap_map_sam_malloc_aux (s); + switch (s->algo_id) + { case TMAP_MAP_ALGO_MAP1: - (*s->aux.map1_aux) = (*tmp_sam.aux.map1_aux); - break; + (*s->aux.map1_aux) = (*tmp_sam.aux.map1_aux); + break; case TMAP_MAP_ALGO_MAP2: - (*s->aux.map2_aux) = (*tmp_sam.aux.map2_aux); - break; + (*s->aux.map2_aux) = (*tmp_sam.aux.map2_aux); + break; case TMAP_MAP_ALGO_MAP3: - (*s->aux.map3_aux) = (*tmp_sam.aux.map3_aux); - break; + (*s->aux.map3_aux) = (*tmp_sam.aux.map3_aux); + break; case TMAP_MAP_ALGO_MAP4: - (*s->aux.map4_aux) = (*tmp_sam.aux.map4_aux); - break; + (*s->aux.map4_aux) = (*tmp_sam.aux.map4_aux); + break; case TMAP_MAP_ALGO_MAPVSW: - (*s->aux.map_vsw_aux) = (*tmp_sam.aux.map_vsw_aux); - break; + (*s->aux.map_vsw_aux) = (*tmp_sam.aux.map_vsw_aux); + break; default: - tmap_error("bug encountered", Exit, OutOfRange); - break; - } - (*idx)++; - } - } - return tmp_sam.score; + tmap_error ("bug encountered", Exit, OutOfRange); + break; + } + (*idx)++; + } + } + return tmp_sam.score; } -typedef struct +typedef struct __tmap_map_util_gen_score_t { uint32_t seqid; int8_t strand; @@ -1852,7 +2239,9 @@ tmap_map_util_sw_gen_score tmap_seq_t **seqs, tmap_rand_t *rand, tmap_map_opt_t *opt, - int32_t *num_after_grouping + int32_t *num_after_grouping, + tmap_map_stats_t *stat // statistics + ) { int32_t i, j; @@ -1871,31 +2260,40 @@ tmap_map_util_sw_gen_score int32_t num_groups = 0, num_groups_filtered = 0; double stage_seed_freqc = opt->stage_seed_freqc; int32_t max_group_size = 0, repr_hit, filter_ok = 0; + tmap_map_amplicon_info *amplicons = NULL; + uint32_t amplicons_capacity = 0; + // tmap_map_amplicon_info chosen_amplicon; - if(NULL != num_after_grouping) (*num_after_grouping) = 0; + if (NULL != num_after_grouping) (*num_after_grouping) = 0; - if(0 == sams->n) { + if (0 == sams->n) { return sams; } // the final mappings will go here - sams_tmp = tmap_map_sams_init(sams); - tmap_map_sams_realloc(sams_tmp, sams->n); + sams_tmp = tmap_map_sams_init (sams); + tmap_map_sams_realloc (sams_tmp, sams->n); + + init_amplicon_info (&licons, &licons_capacity, 0); + + // sort by strand / chr/pos / score + tmap_sort_introsort (tmap_map_sam_sort_coord, sams->n, sams->sams); - // sort by strand/chr/pos/score - tmap_sort_introsort(tmap_map_sam_sort_coord, sams->n, sams->sams); - tmap_map_util_set_softclip(opt, seq, opt->max_adapter_bases_for_soft_clipping, &softclip_start, &softclip_end); + // ! This may be re-set later (in _helper) for the hits located in the overriding amplions + tmap_map_util_set_softclip (opt->softclip_type, seq, opt->max_adapter_bases_for_soft_clipping, &softclip_start, &softclip_end); - // initialize opt - vsw_opt = tmap_vsw_opt_init(opt->score_match, opt->pen_mm, opt->pen_gapo, opt->pen_gape, opt->score_thr); + // initialize opt for initial vsw set up - the parameters set here can be overriden later in tmap_map_util_sw_gen_score_helper, if the hit position appears to be within overriden amplicon + vsw_opt = tmap_vsw_opt_init (opt->score_match, opt->pen_mm, opt->pen_gapo, opt->pen_gape, opt->score_thr); // init seqs - seq_len = tmap_seq_get_bases_length(seqs[0]); + seq_len = tmap_seq_get_bases_length (seqs [0]); + // seq_len = tmap_seq_get_bases_length (seq); // forward - vsw = tmap_vsw_init((uint8_t*)tmap_seq_get_bases(seqs[0])->s, seq_len, softclip_start, softclip_end, opt->vsw_type, vsw_opt); + vsw = tmap_vsw_init ((uint8_t*)tmap_seq_get_bases (seqs [0])->s, seq_len, softclip_start, softclip_end, opt->vsw_type, opt->vsw_fallback, vsw_opt); + // vsw = tmap_vsw_init ((uint8_t*)tmap_seq_get_bases (seq)->s, seq_len, softclip_start, softclip_end, opt->vsw_type, vsw_opt); // pre-allocate groups - groups = tmap_calloc(sams->n, sizeof(tmap_map_util_gen_score_t), "groups"); + groups = tmap_calloc (sams->n, sizeof (tmap_map_util_gen_score_t), "groups"); // determine groups num_groups = num_groups_filtered = 0; @@ -1903,41 +2301,41 @@ tmap_map_util_sw_gen_score start_pos = end_pos = 0; best_subo_score = INT32_MIN; // track the best sub-optimal hit repr_hit = 0; - while(end < sams->n) { + while (end < sams->n) { uint32_t seqid; uint8_t strand; - // get the strand/start/end positions - seqid = sams->sams[end].seqid; - strand = sams->sams[end].strand; + // get the strand / start/end positions + seqid = sams->sams [end].seqid; + strand = sams->sams [end].strand; //first pass, setup start and end - if(start == end) { - tmap_map_util_sw_get_start_and_end_pos(&sams->sams[start], seq_len, strand, &start_pos, &end_pos); + if (start == end) { + tmap_map_util_sw_get_start_and_end_pos (&sams->sams [start], seq_len, strand, &start_pos, &end_pos); end_pos_prev = end_pos; - repr_hit = sams->sams[end].repr_hit; + repr_hit = sams->sams [end].repr_hit; } // sub-optimal score - if(best_subo_score < sams->sams[end].score_subo) { - best_subo_score = sams->sams[end].score_subo; + if (best_subo_score < sams->sams [end].score_subo) { + best_subo_score = sams->sams [end].score_subo; } // check if the hits can be banded - //fprintf(stderr, "end=%d seqid: %d start: %d end: %d\n", end, sams->sams[end].seqid, sams->sams[end].pos, (sams->sams[end].pos + sams->sams[end].target_len)); - if(end + 1 < sams->n) { - //fprintf(stderr, "%d seed start: %d end: %d next start: %d next end: %d\n", end, sams->sams[end].pos, (sams->sams[end].pos + sams->sams[end].target_len), sams->sams[end+1].pos, (sams->sams[end+1].pos + sams->sams[end+1].target_len)); - if(sams->sams[end].strand == sams->sams[end+1].strand - && sams->sams[end].seqid == sams->sams[end+1].seqid) { - tmap_map_util_sw_get_start_and_end_pos(&sams->sams[end+1], seq_len, strand, &start_pos_cur, &end_pos_cur); - - if(start_pos_cur <= end_pos_prev // NB: beware of unsigned int underflow + //fprintf (stderr, "end=%d seqid: %d start: %d end: %d\n", end, sams->sams [end].seqid, sams->sams [end].pos, (sams->sams [end].pos + sams->sams [end].target_len)); + if (end + 1 < sams->n) { + //fprintf (stderr, "%d seed start: %d end: %d next start: %d next end: %d\n", end, sams->sams [end].pos, (sams->sams [end].pos + sams->sams [end].target_len), sams->sams [end + 1].pos, (sams->sams [end + 1].pos + sams->sams [end + 1].target_len)); + if (sams->sams [end].strand == sams->sams [end + 1].strand + && sams->sams [end].seqid == sams->sams [end + 1].seqid) { + tmap_map_util_sw_get_start_and_end_pos (&sams->sams [end + 1], seq_len, strand, &start_pos_cur, &end_pos_cur); + + if (start_pos_cur <= end_pos_prev // NB: beware of unsigned int underflow || (start_pos_cur - end_pos_prev) <= opt->max_seed_band) { end++; - if(end_pos < end_pos_cur) { + if (end_pos < end_pos_cur) { end_pos = end_pos_cur; } end_pos_prev = end_pos_cur; - repr_hit |= sams->sams[end].repr_hit; // representitive hit + repr_hit |= sams->sams [end].repr_hit; // representitive hit continue; // there may be more to add } @@ -1947,25 +2345,25 @@ tmap_map_util_sw_gen_score // add a group num_groups++; // update - groups[num_groups-1].seqid = seqid; - groups[num_groups-1].strand = strand; - groups[num_groups-1].start = start; - groups[num_groups-1].end = end; - groups[num_groups-1].start_pos = start_pos; - groups[num_groups-1].end_pos = end_pos; - groups[num_groups-1].filtered = 0; // assume not filtered, not guilty - groups[num_groups-1].repr_hit = repr_hit; - if(max_group_size < end - start + 1) { + groups [num_groups-1].seqid = seqid; + groups [num_groups-1].strand = strand; + groups [num_groups-1].start = start; + groups [num_groups-1].end = end; + groups [num_groups-1].start_pos = start_pos; + groups [num_groups-1].end_pos = end_pos; + groups [num_groups-1].filtered = 0; // assume not filtered, not guilty + groups [num_groups-1].repr_hit = repr_hit; + if (max_group_size < end - start + 1) { max_group_size = end - start + 1; } - // update start/end + // update start / end end++; start = end; } // resize - if(num_groups < sams->n) { - groups = tmap_realloc(groups, num_groups * sizeof(tmap_map_util_gen_score_t), "groups"); + if (num_groups < sams->n) { + groups = tmap_realloc (groups, num_groups * sizeof (tmap_map_util_gen_score_t), "groups"); } // filter groups @@ -1975,11 +2373,11 @@ tmap_map_util_sw_gen_score { num_groups_filtered = 0; - for(i=0;i(sams->n * opt->seed_freqc ) comes from /* @@ -1991,13 +2389,13 @@ tmap_map_util_sw_gen_score * if a region has ≥fC q-hits, only then it is processed further. " */ /* - fprintf(stderr, "repr_hit=%d size=%d freq=%lf\n", + fprintf (stderr, "repr_hit=%d size=%d freq=%lf\n", group->repr_hit, (group->end - group->start + 1), ( sams->n * stage_seed_freqc)); */ - if(0 == group->repr_hit && (group->end - group->start + 1) > ( sams->n * stage_seed_freqc) ) + if (0 == group->repr_hit && (group->end - group->start + 1) > ( sams->n * stage_seed_freqc) ) { group->filtered = 0; } @@ -2009,23 +2407,23 @@ tmap_map_util_sw_gen_score } /* - fprintf(stderr, "stage_seed_freqc=%lf num_groups=%d num_groups_filtered=%d\n", + fprintf (stderr, "stage_seed_freqc=%lf num_groups=%d num_groups_filtered=%d\n", stage_seed_freqc, num_groups, num_groups_filtered); */ - if(opt->stage_seed_freqc_min_groups <= num_groups + if (opt->stage_seed_freqc_min_groups <= num_groups && (num_groups - num_groups_filtered) < opt->stage_seed_freqc_min_groups) { stage_seed_freqc /= 2.0; // reset - for(i=0;ifiltered = 0; } num_groups_filtered = 0; - if(stage_seed_freqc < 1.0 / sams->n) + if (stage_seed_freqc < 1.0 / sams->n) { // the filter will accept all hits break; } @@ -2036,35 +2434,35 @@ tmap_map_util_sw_gen_score break; } } - while(1); + while (1); - if(num_groups < opt->stage_seed_freqc_min_groups) + if (num_groups < opt->stage_seed_freqc_min_groups) { // if too few groups, always keep // reset - for(i=0;ifiltered = 0; } num_groups_filtered = 0; } - else if(0 == filter_ok) + else if (0 == filter_ok) { // we could not find an effective filter int32_t cur_max; // Try filtering based on retaining the groups with most number of seeds. cur_max = (max_group_size * 2) - 1; // NB: this will be reduced // Assume all are filtered num_groups_filtered = num_groups; - while(num_groups - num_groups_filtered < opt->stage_seed_freqc_min_groups) + while (num_groups - num_groups_filtered < opt->stage_seed_freqc_min_groups) { // too many groups were filtered num_groups_filtered = 0; // halve the minimum group size cur_max /= 2; // go through the groups - for(i=0;iend - group->start + 1 < cur_max) + tmap_map_util_gen_score_t *group = &groups [i]; + if (group->end - group->start + 1 < cur_max) { // filter if there were too few seeds group->filtered = 1; num_groups_filtered++; @@ -2078,27 +2476,27 @@ tmap_map_util_sw_gen_score } /* - for(i=j=0;ifiltered && 0 == group->repr_hit) continue; + for (i=j=0;ifiltered && 0 == group->repr_hit) continue; j++; } - fprintf(stderr, "num_groups=%d num_groups_filtered=%d j=%d\n", num_groups, num_groups_filtered, j); + fprintf (stderr, "num_groups=%d num_groups_filtered=%d j=%d\n", num_groups, num_groups_filtered, j); */ /* - fprintf(stderr, "final sams->n=%d num_groups=%d num_groups_filtered=%d\n", + fprintf (stderr, "final sams->n=%d num_groups=%d num_groups_filtered=%d\n", sams->n, num_groups, num_groups_filtered); */ // process unfiltered... - for(i=j=0;istart, group->end, group->end - group->start + 1, @@ -2109,9 +2507,9 @@ tmap_map_util_sw_gen_score group->repr_hit, group->filtered); */ - if(1 == group->filtered && 0 == group->repr_hit) continue; + if (1 == group->filtered && 0 == group->repr_hit) continue; /* - fprintf(stderr, "start=%d end=%d num=%d seqid=%u strand=%d start_pos=%u end_pos=%u filtered=%d\n", + fprintf (stderr, "start=%d end=%d num=%d seqid=%u strand=%d start_pos=%u end_pos=%u filtered=%d\n", group->start, group->end, group->end - group->start + 1, @@ -2123,41 +2521,45 @@ tmap_map_util_sw_gen_score */ // generate the score - tmap_map_util_sw_gen_score_helper(refseq, sams, seqs[0], sams_tmp, &j, group->start, group->end, + tmap_map_util_sw_gen_score_helper (refseq, sams, seq, seqs [0], sams_tmp, &j, group->start, group->end, group->strand, vsw, seq_len, group->start_pos, group->end_pos, &target_mem, &target, - softclip_start, softclip_end, + // softclip_start, softclip_end, -1, // this is our first call opt->max_seed_band, // NB: this may be modified as banding is unrolled opt->score_thr-1, - vsw_opt, rand, opt); + vsw_opt, rand, opt, + &licons, + &licons_capacity, + stat + ); // save the number of groups - if(NULL != num_after_grouping) (*num_after_grouping)++; + if (NULL != num_after_grouping) (*num_after_grouping)++; } - //fprintf(stderr, "unfiltered # = %d\n", j); + //fprintf (stderr, "unfiltered # = %d\n", j); // only if we applied the freqc filter - if(0 < stage_seed_freqc && 0 < opt->stage_seed_freqc_rand_repr) + if (0 < stage_seed_freqc && 0 < opt->stage_seed_freqc_rand_repr) { // check if we filtered too many groups, and so if we should keep // representative hits. /* - fprintf(stderr, "Should we get representatives %lf < %lf\n", + fprintf (stderr, "Should we get representatives %lf < %lf\n", opt->stage_seed_freqc_group_frac, (double)num_groups_filtered / num_groups); */ - if(opt->stage_seed_freqc_group_frac <= (double)num_groups_filtered / num_groups) + if (opt->stage_seed_freqc_group_frac <= (double)num_groups_filtered / num_groups) { int32_t best_score = INT32_MIN, best_score_filt = INT32_MIN; double pr = 0.0; int32_t k, l, c, n; // get the best score from a group that passed the filter - for(k=0;ksams[k].score) + if (best_score < sams_tmp->sams [k].score) { - best_score = sams_tmp->sams[k].score; + best_score = sams_tmp->sams [k].score; } } @@ -2166,49 +2568,57 @@ tmap_map_util_sw_gen_score // pick the one with the most # of seeds c = l = -1; - for(i=0;ifiltered) continue; - if(c < group->end - group->start + 1) + tmap_map_util_gen_score_t *group = &groups [i]; + if (0 == group->filtered) continue; + if (c < group->end - group->start + 1) { c = group->end - group->start + 1; l = i; } } - if(0 <= l) + if (0 <= l) { - tmap_map_util_gen_score_t *group = &groups[l]; + tmap_map_util_gen_score_t *group = &groups [l]; // generate the score - tmap_map_util_sw_gen_score_helper(refseq, sams, seqs[0], sams_tmp, &j, group->start, group->end, + tmap_map_util_sw_gen_score_helper (refseq, sams, seq, seqs [0], sams_tmp, &j, group->start, group->end, group->strand, vsw, seq_len, group->start_pos, group->end_pos, &target_mem, &target, - softclip_start, softclip_end, + // softclip_start, softclip_end, -1, // this is our first call opt->max_seed_band, // NB: this may be modified as banding is unrolled opt->score_thr-1, - vsw_opt, rand, opt); + vsw_opt, rand, opt, + &licons, + &licons_capacity, + stat + ); group->filtered = 0; // no longer filtered } // now, choose uniformly - pr = num_groups / (1+opt->stage_seed_freqc_rand_repr); - for(i=c=n=0;istage_seed_freqc_rand_repr); + for (i=c=n=0;ifiltered) continue; - if(pr < c) + tmap_map_util_gen_score_t *group = &groups [i]; + if (0 == group->filtered) continue; + if (pr < c) { - if(n == opt->stage_seed_freqc_rand_repr) break; + if (n == opt->stage_seed_freqc_rand_repr) break; // generate the score - tmap_map_util_sw_gen_score_helper(refseq, sams, seqs[0], sams_tmp, &j, group->start, group->end, + tmap_map_util_sw_gen_score_helper (refseq, sams, seq, seqs [0], sams_tmp, &j, group->start, group->end, group->strand, vsw, seq_len, group->start_pos, group->end_pos, &target_mem, &target, - softclip_start, softclip_end, + // softclip_start, softclip_end, -1, // this is our first call opt->max_seed_band, // NB: this may be modified as banding is unrolled opt->score_thr-1, - vsw_opt, rand, opt); + vsw_opt, rand, opt, + &licons, + &licons_capacity, + stat + ); group->filtered = 0; // no longer filtered n++; // reset @@ -2217,64 +2627,69 @@ tmap_map_util_sw_gen_score } // get the best from the filtered - for(;ksams[k].score) + if (best_score_filt < sams_tmp->sams [k].score) { - best_score_filt = sams_tmp->sams[k].score; + best_score_filt = sams_tmp->sams [k].score; } } /* - fprintf(stderr, "best_score=%d best_score_filt=%d\n", + fprintf (stderr, "best_score=%d best_score_filt=%d\n", best_score, best_score_filt); */ // check if we should redo ALL the filtered groups - if(best_score < best_score_filt) + if (best_score < best_score_filt) { // NB: do not redo others... - for(i=0;ifiltered) continue; + tmap_map_util_gen_score_t *group = &groups [i]; + if (0 == group->filtered) continue; // generate the score - tmap_map_util_sw_gen_score_helper(refseq, sams, seqs[0], sams_tmp, &j, group->start, group->end, + tmap_map_util_sw_gen_score_helper (refseq, sams, seq, seqs [0], sams_tmp, &j, group->start, group->end, group->strand, vsw, seq_len, group->start_pos, group->end_pos, &target_mem, &target, - softclip_start, softclip_end, + // softclip_start, softclip_end, -1, // this is our first call opt->max_seed_band, // NB: this may be modified as banding is unrolled opt->score_thr-1, - vsw_opt, rand, opt); + vsw_opt, rand, opt, + &licons, + &licons_capacity, + stat + ); } } } } // realloc - tmap_map_sams_realloc(sams_tmp, j); + tmap_map_sams_realloc (sams_tmp, j); // sub-optimal score - for(i=0;in;i++) + for (i=0;in;i++) { - if(best_subo_score < sams_tmp->sams[i].score_subo) + if (best_subo_score < sams_tmp->sams [i].score_subo) { - best_subo_score = sams_tmp->sams[i].score_subo; + best_subo_score = sams_tmp->sams [i].score_subo; } } // update the sub-optimal - for(i=0;in;i++) + for (i=0;in;i++) { - sams_tmp->sams[i].score_subo = best_subo_score; + sams_tmp->sams [i].score_subo = best_subo_score; } // free memory - tmap_map_sams_destroy(sams); - free(target); - tmap_vsw_opt_destroy(vsw_opt); - tmap_vsw_destroy(vsw); - free(groups); + tmap_map_sams_destroy (sams); + free (target); + destroy_amplicon_info (&licons, &licons_capacity); + tmap_vsw_opt_destroy (vsw_opt); + tmap_vsw_destroy (vsw); + free (groups); return sams_tmp; } @@ -2457,6 +2872,7 @@ tmap_map_util_one_gap int *is_ins, // 1 == Ins, 0 == Del int *softclip, // length of prefix softclip int pad, // the extension on either size of target buffer that is safe to access. This function checks this many bases as continuation of M segment as if no indel was present + int matched_bases, int *extra_match // number of consecutive matches after M segment end (check relation with pad. Are these bases in the pad??) ) { @@ -2536,7 +2952,7 @@ tmap_map_util_one_gap if (j == tlen) { *indel_size = qlen-q; - *is_ins = 1; + *is_ins = 1; } else { @@ -2558,6 +2974,7 @@ tmap_map_util_one_gap break; (*extra_match) += 1; } + if (*extra_match >= matched_bases) return 0; // cannot have leading indel, total duplication or no extra anchor, TS-18181 int total_anchor = ((qlen < tlen-i)? qlen: tlen-i) + (*extra_match); if (total_anchor < min_size) continue; if (total_anchor < 15 && *indel_size > 3 * (qlen + (*extra_match))) // reject indels 3 or more times longer than query + matching 'pad' @@ -2796,7 +3213,7 @@ tmap_map_util_end_repair return repaired; // check if we allow soft-clipping on the 5' end - tmap_map_util_set_softclip (opt, seq, max_adapter_bases_for_soft_clipping, &softclip_start, &softclip_end); + tmap_map_util_set_softclip (opt->softclip_type, seq, max_adapter_bases_for_soft_clipping, &softclip_start, &softclip_end); int8_t o_strand = strand; if (end_repair > 2) // Modern End-Repair, invoked when --end-repair parameter is above 2 (and denotes percent of mismatches above which to trim the alignment) { @@ -3029,7 +3446,7 @@ tmap_map_util_end_repair int min_anchor = min_anchor_large_indel_rescue; int half_anchor = min_anchor / 2; if (refseq->bed_exist && use_bed_in_end_repair && total_scl >= half_anchor && s->ampl_start != 0) - // tmap_map_get_amplicon (refseq, s->seqid, start_o, end_o, &l_start, &l_end, NULL, o_strand)) // DK: if bed exists and coords use in end repair enabled, the amplicon coords are cached within *s (tmap_map_sam_t) + // tmap_map_get_amplicon (refseq, s->seqid, start_o, end_o, o_strand, &l_start, &l_end, NULL)) // DK: if bed exists and coords use in end repair enabled, the amplicon coords are cached within *s (tmap_map_sam_t) { //total_scl is desired to be larger than 5 //fprintf(stderr, "%d %d %d qlen=%d\n", ampl_start, ampl_end, total_scl, qlen); @@ -3049,11 +3466,13 @@ tmap_map_util_end_repair int buffer = half_buffer + 3; uint32_t start, end; uint32_t pad_s, pad_e, pad; + uint32_t matched_bases; pad_s = pad_e = pad = 0; if (strand == 0) { start = s->pos + s->target_len + 1 - s_pos_adj; end = s->ampl_end + half_buffer; + matched_bases = start-s->pos-1; pad_s = 100; if (pad_s > qlen - total_scl) pad_s = qlen - total_scl; @@ -3069,6 +3488,7 @@ tmap_map_util_end_repair else start = s->ampl_start - half_buffer; end = s->pos + s_pos_adj; + matched_bases = s->pos+s->target_len-end; pad_e = 100; if (pad_e > qlen - total_scl) pad_e = qlen - total_scl; @@ -3076,6 +3496,7 @@ tmap_map_util_end_repair pad_e = refseq->annos [s->seqid].len - end; pad = pad_e; } + // effectively matched_bases = s->target_len-s_pos_adj; The target_len is the reference length after softclipping tlen = end - start + 1; //fprintf(stderr, "%d %d %d %d %d\n", start, end, tlen, min_anchor, pad); //if (tlen >= min_anchor) @@ -3110,6 +3531,7 @@ tmap_map_util_end_repair &is_ins, // 1==I, 0==D &softclip, // size of softclip pad, // size of pad on either side of target // DK: what if assymetric, like at the end of chromosome? + matched_bases, // tell the rountine how many bases the rest of cigar matched to the ref &extra_match)) // { free (target); @@ -4805,6 +5227,7 @@ int find_alignment_start ( tmap_map_sam_t* src_sam, // source: raw (position-only) mapping tmap_map_sam_t* dest_sam, // destination: refined (aligned) mapping + tmap_seq_t* seq, // // needed to set overriden softclip tmap_seq_t** seqs, // array of size 4 that contains pre-computed inverse / complement combinations tmap_refseq_t* refseq, // reference server int32_t softclip_start, // is 5' softclip allowed @@ -4832,6 +5255,16 @@ int find_alignment_start // uint8_t *query_rc = NULL; int32_t qlen = src_sam->result.query_end + 1; // adjust based on the query end; +// #define DEBUG_VSW_ASSYMETRY +#ifdef DEBUG_VSW_ASSYMETRY + { + for (int dd = 0; dd != qlen; ++dd) + if (query_rc [dd] >= 4) + { + tmap_warning ("QUERY Base [%d] is %d\n", dd, query_rc [dd]); + } + } +#endif // do not band when generating the cigar tmap_map_sam_t tmp_sam; // TODO: actually, only the .pos, .score and .result members change; it would be cleaner to use only them tmp_sam = *src_sam; @@ -4843,24 +5276,52 @@ int find_alignment_start // reverse compliment the target_buf if(0 == src_sam->strand) tmap_reverse_compliment_int (target->data, target->data_len); +#ifdef DEBUG_VSW_ASSYMETRY + { + for (int dd = 0; dd != target->data_len; ++dd) + if (target->data [dd] >= 4) + { + tmap_warning ("TAGET Base [%d] is %d\n", dd, target->data [dd]); + } + } +#endif + + // check if the amplicon was found and has overrides + candeval_overrides_s override; + ampl_candeval_parameters_from_sam (opt, src_sam, &override); + // save default parameters + tmap_vsw_opt_t orig_vsw_opt = *(vsw->opt); + int32_t orig_softclip_start = vsw->query_start_clip, orig_softclip_end = vsw->query_end_clip; + + tmap_map_util_set_softclip (override.softclip_type, seq, override.max_adapter_bases_for_soft_clipping, &softclip_start, &softclip_end); + // tmap_vsw_set_params (vsw, softclip_start, softclip_end, &(override.vsw)); + + //DK: since we compute in reverse direction, softclip_end is at the start and softclip_start is at the end of the alignment! + tmap_vsw_set_params (vsw, softclip_end, softclip_start, &(override.vsw)); + // NB: if match/mismatch penalties are on the opposite strands, we may // have wrong scores // NB: this aligns in the opposite direction than sequencing (3'->5') int32_t overflow; + int32_t orig_score = tmp_sam.score; tmp_sam.score = tmap_vsw_process_rev (vsw, query_rc, qlen, target->data, target->data_len, &tmp_sam.result, &overflow, opt->score_thr, - (1 == softclip_end && 1 == softclip_start) ? 0 : 1); // NB: to guarantee correct soft-clipping if both ends are clipped + (1 == softclip_end && 1 == softclip_start) ? 0 : 1, opt->confirm_vsw_corr, opt->correct_failed_vsw, opt->use_nvsw_on_nonstd_bases, stat); // NB: to guarantee correct soft-clipping if both ends are clipped if(1 == overflow) - tmap_bug(); + tmap_bug (); - // reverse back compliment the target_buf + // reset vsw parameters to orig + tmap_vsw_set_params (vsw, orig_softclip_start, orig_softclip_end, &(orig_vsw_opt)); + + // reverse-compliment the target_buf back if(0 == tmp_sam.strand) tmap_reverse_compliment_int (target->data, target->data_len); - if (tmp_sam.score < opt->score_thr) // this could happen if VSW fails. Just skip the damned, with no warning ?!? - return 0; // TODO: may beed warning or error report here + if (tmp_sam.score < opt->score_thr) // this could happen if VSW fails. + // The score error is reported in tmap_vsw_process_rev, no need to repeat it here (the overflows are not reported on stderr but reported in stats) + return 0; if (0 == tmp_sam.strand) { @@ -5137,7 +5598,7 @@ void salvage_long_indel_at_edges ( int32_t long_gap = pen_gapl; //ZZ: check amplicon // uint32_t ampl_start = 0, ampl_end = 0; - // if (tmap_map_get_amplicon (refseq, dest_sam->seqid, dest_sam->pos, dest_sam->pos + dest_sam->target_len, &l_start, &l_end, NULL, dest_sam->strand)) + // if (tmap_map_get_amplicon (refseq, dest_sam->seqid, dest_sam->pos, dest_sam->pos + dest_sam->target_len, dest_sam->strand, &l_start, &l_end, NULL)) if (dest_sam->ampl_end != 0) { // ampl_exist = 1; @@ -5327,7 +5788,7 @@ void salvage_long_indel_at_edges ( // DK : if both suffix and prefix branches are executed, and the read hits the amplicon, the ampl_exist is 1 here // so tmap_map_get_amplicon is not executed and 0 is used as the value of ampl_end // Removing ampl_exist check clause from here. - // if (ampl_exist || tmap_map_get_amplicon (refseq, dest_sam->seqid, dest_sam->pos, dest_sam->pos + dest_sam->target_len, &l_start, &l_end, NULL, dest_sam->strand)) + // if (ampl_exist || tmap_map_get_amplicon (refseq, dest_sam->seqid, dest_sam->pos, dest_sam->pos + dest_sam->target_len, dest_sam->strand, &l_start, &l_end, NULL)) if (dest_sam->ampl_end != 0) { // ampl_exist = 1; @@ -5768,7 +6229,7 @@ void end_repair ( max_adapter_bases_for_soft_clipping = dest_sam->param_ovr->max_adapter_bases_for_soft_clipping.value; } } - tmap_map_util_set_softclip (opt, seq, max_adapter_bases_for_soft_clipping, &softclip_start, &softclip_end); // this is done within end_repair anyway; doing redundant call here to check for ins instead of softclp inend_repair_helper + tmap_map_util_set_softclip (opt->softclip_type, seq, max_adapter_bases_for_soft_clipping, &softclip_start, &softclip_end); // this is done within end_repair anyway; doing redundant call here to check for ins instead of softclp inend_repair_helper int32_t r3 = end_repair_helper (dest_sam, seqs, seq, refseq, target, path_buf, path_buf_sz, softclip_start, softclip_end, opt, /* stage_swpar, */ stat, 0); max_adapter_bases_for_soft_clipping = opt->max_adapter_bases_for_soft_clipping; @@ -5789,7 +6250,7 @@ void end_repair ( max_adapter_bases_for_soft_clipping = dest_sam->param_ovr->max_adapter_bases_for_soft_clipping.value; } } - tmap_map_util_set_softclip (opt, seq, max_adapter_bases_for_soft_clipping, &softclip_start, &softclip_end); // this is done within end_repair anyway; doing redundant call here to check for ins instead of softclp inend_repair_helper + tmap_map_util_set_softclip (opt->softclip_type, seq, max_adapter_bases_for_soft_clipping, &softclip_start, &softclip_end); // this is done within end_repair anyway; doing redundant call here to check for ins instead of softclp inend_repair_helper int32_t r5 = end_repair_helper (dest_sam, seqs, seq, refseq, target, path_buf, path_buf_sz, softclip_start, softclip_end, opt, /* stage_swpar, */ stat, 1); // update alignment box (dest_sam->result), as it may be used downstream @@ -5887,7 +6348,7 @@ tmap_map_util_find_align_starts ( tmap_map_sams_realloc (sams_tmp, sams->n); // pre-allocate for same number of mappings // set softclip flags, rule-based - tmap_map_util_set_softclip (opt, seq, opt->max_adapter_bases_for_soft_clipping, &softclip_start, &softclip_end); + tmap_map_util_set_softclip (opt->softclip_type, seq, opt->max_adapter_bases_for_soft_clipping, &softclip_start, &softclip_end); // initialize opt vsw_opt = tmap_vsw_opt_init (opt->score_match, opt->pen_mm, opt->pen_gapo, opt->pen_gape, opt->score_thr); @@ -5896,7 +6357,7 @@ tmap_map_util_find_align_starts ( orig_query_len = tmap_seq_get_bases_length (seqs [0]); // reverse compliment query - vsw = tmap_vsw_init ((uint8_t*) tmap_seq_get_bases(seqs[1])->s, orig_query_len, softclip_end, softclip_start, opt->vsw_type, vsw_opt); + vsw = tmap_vsw_init ((uint8_t*) tmap_seq_get_bases(seqs[1])->s, orig_query_len, softclip_end, softclip_start, opt->vsw_type, opt->vsw_fallback, vsw_opt); for (end = 0, i = 0; end < sams->n; ++end) // for each placement { @@ -5906,6 +6367,7 @@ tmap_map_util_find_align_starts ( if (find_alignment_start ( src_sam, // source: raw (position-only) mapping dest_sam, // destination: refined (aligned) mapping + seq, seqs, // array of size 4 that contains pre-computed inverse / complement combinations refseq, // reference server softclip_start, // is 5' softclip allowed @@ -5946,29 +6408,47 @@ void tmap_map_find_amplicons for (i = 0; i < sams->n; ++i) // for each placement { tmap_map_sam_t* dest_sam = sams->sams + i; - locopt = NULL, ampl_start = 0, ampl_end = 0; - ends.positions = NULL, ends.starts_count = 0, ends.ends_count = 0; - if (tmap_map_get_amplicon (refseq, dest_sam->seqid, dest_sam->pos, dest_sam->pos + dest_sam->target_len, &l_start, &l_end, &locopt, &ends, dest_sam->strand)) - { - dest_sam->ampl_start = ampl_start; - dest_sam->ampl_end = ampl_end; - dest_sam->param_ovr = locopt; - // - // check if override sw parameters for stage are already cached; cache if not - // - // !!! TS-17814: do not do this here - causes race condition. Protecting against that causes seralization bottleneck - // do not uncomment the line that follows without #defining CONCURRENT_PARAMETERS_CACHE - // - // cache_sw_overrides (locopt, stage_ord, stage_opt, def_sw_par); - // - dest_sam->read_ends = ends; - } - else + // only try to assign amplions for the not yet assigned ones + // (if parameters overriding in candidate evaluation is enabled, the amplicons are already assigned) +// #define DEBUG_AMPLFIND_COMPARE +#ifndef DEBUG_AMPLFIND_COMPARE + if (dest_sam->ampl_start == 0 && dest_sam->ampl_end == 0) +#endif { - dest_sam->ampl_start = 0; - dest_sam->ampl_end = 0; - dest_sam->param_ovr = NULL; - dest_sam->read_ends.positions = NULL, dest_sam->read_ends.starts_count = 0, dest_sam->read_ends.ends_count = 0; + locopt = NULL, ampl_start = 0, ampl_end = 0; + ends.positions = NULL, ends.starts_count = 0, ends.ends_count = 0; + + if (tmap_map_get_amplicon (refseq, dest_sam->seqid, dest_sam->pos, dest_sam->pos + dest_sam->target_len, dest_sam->strand, &l_start, &l_end, &locopt, &ends)) + { +#ifdef DEBUG_AMPLFIND_COMPARE + if (dest_sam->ampl_start != 0 || dest_sam->ampl_end != 0) + { + if (dest_sam->ampl_start != ampl_start || dest_sam->ampl_end != ampl_end) + tmap_warning ("Old amplicon find gives result different than new: old: %d-%d, new %d-%d\n", ampl_start, ampl_end, dest_sam->ampl_start, dest_sam->ampl_end); + } +#endif + dest_sam->ampl_start = ampl_start; + dest_sam->ampl_end = ampl_end; + dest_sam->param_ovr = locopt; + // + // check if override sw parameters for stage are already cached; cache if not + // + // !!! TS-17814: do not do this here - causes race condition. Protecting against that causes seralization bottleneck + // do not uncomment the line that follows without #defining CONCURRENT_PARAMETERS_CACHE + // + // cache_sw_overrides (locopt, stage_ord, stage_opt, def_sw_par); + // + dest_sam->read_ends = ends; + } +#if 0 // this is redundant now + else + { + dest_sam->ampl_start = 0; + dest_sam->ampl_end = 0; + dest_sam->param_ovr = NULL; + dest_sam->read_ends.positions = NULL, dest_sam->read_ends.starts_count = 0, dest_sam->read_ends.ends_count = 0; + } +#endif } } } diff --git a/Analysis/TMAP/src/map/util/tmap_map_util.h b/Analysis/TMAP/src/map/util/tmap_map_util.h index af910a31..e78c7980 100644 --- a/Analysis/TMAP/src/map/util/tmap_map_util.h +++ b/Analysis/TMAP/src/map/util/tmap_map_util.h @@ -431,7 +431,9 @@ tmap_map_util_sw_gen_score tmap_seq_t **seqs, tmap_rand_t *rand, tmap_map_opt_t *opt, - int32_t *num_after_grouping + int32_t *num_after_grouping, + tmap_map_stats_t *stat // statistics + ); void tmap_map_util_populate_sw_par_iupac_direct @@ -740,11 +742,11 @@ tmap_map_get_amplicon int32_t seqid, uint32_t start, uint32_t end, + uint32_t strand, uint32_t *ampl_start, uint32_t *ampl_end, tmap_map_locopt_t** overrides, - tmap_map_endstat_p_t* ends, - uint32_t strand + tmap_map_endstat_p_t* ends ); uint8_t diff --git a/Analysis/TMAP/src/realign/Realign.cpp b/Analysis/TMAP/src/realign/Realign.cpp index db22f15b..19831366 100644 --- a/Analysis/TMAP/src/realign/Realign.cpp +++ b/Analysis/TMAP/src/realign/Realign.cpp @@ -74,14 +74,14 @@ void Realigner::InitializeRealigner(unsigned int reserve_size, unsigned int clip isForwardStrandRead_ = true; verbose_ = false; invalid_cigar_in_input = false; - + alignment_bandwidth_ = 20; q_limit_minus_.reserve(reserve_size); q_limit_plus_.reserve(reserve_size); - clipped_anchors_.cigar_left.reserve(50); - clipped_anchors_.cigar_right.reserve(50); - clipped_anchors_.md_left.reserve(50); - clipped_anchors_.md_right.reserve(50); + clipped_anchors_.cigar_left.reserve(clipping_size); + clipped_anchors_.cigar_right.reserve(clipping_size); + clipped_anchors_.md_left.reserve(clipping_size); + clipped_anchors_.md_right.reserve(clipping_size); pretty_tseq_.reserve(reserve_size); pretty_qseq_.reserve(reserve_size); diff --git a/Analysis/TMAP/src/seq/tmap_sam.c b/Analysis/TMAP/src/seq/tmap_sam.c index 70f410e6..6680df1c 100644 --- a/Analysis/TMAP/src/seq/tmap_sam.c +++ b/Analysis/TMAP/src/seq/tmap_sam.c @@ -143,7 +143,8 @@ tmap_sam_get_zb(tmap_sam_t *sam) { uint8_t *tag = NULL; // ZB - if(NULL == sam->b) tmap_bug(); + if(NULL == sam->b) + tmap_bug(); tag = bam_aux_get(sam->b, "ZB"); if(NULL != tag) return bam_aux2i(tag); else return -1; diff --git a/Analysis/TMAP/src/seq/tmap_seq.c b/Analysis/TMAP/src/seq/tmap_seq.c index 1df60f79..373c8c52 100644 --- a/Analysis/TMAP/src/seq/tmap_seq.c +++ b/Analysis/TMAP/src/seq/tmap_seq.c @@ -7,6 +7,8 @@ #include "tmap_sff.h" #include "tmap_seq.h" +seq_update_cache_t update_cache; + tmap_seq_t * tmap_seq_init(int8_t type) { @@ -333,6 +335,8 @@ tmap_seq_update(tmap_seq_t *seq, int32_t idx, sam_header_t *header) sam_header_records_t *records = NULL; sam_header_record_t **record_list = NULL; int32_t n = 0; + int32_t use_cache = 0; + // Read Group switch(seq->type) { @@ -347,6 +351,19 @@ tmap_seq_update(tmap_seq_t *seq, int32_t idx, sam_header_t *header) tmap_error("type is unrecognized", Exit, OutOfRange); break; } + + if(update_cache.rg_id == NULL){ + update_cache.rg_id = rg_id; + } + else{ + if(update_cache.rg_id == rg_id){ + use_cache=1; + } + else{ + update_cache.rg_id=rg_id; + } + } + if(NULL == rg_id) { // did not find in SAM/BAM // NB: assume that it is from the ith record in the header records = sam_header_get_records(header, "RG"); @@ -358,7 +375,10 @@ tmap_seq_update(tmap_seq_t *seq, int32_t idx, sam_header_t *header) if(NULL == seq->rg_record) tmap_bug(); } } - else { // found in SAM/BAM + else if(use_cache){ + seq->rg_record = update_cache.rg_record; + } + else{// found in SAM/BAM n = 0; record_list = sam_header_get_record(header, "RG", "ID", rg_id, &n); if(0 == n) { @@ -370,25 +390,36 @@ tmap_seq_update(tmap_seq_t *seq, int32_t idx, sam_header_t *header) tmap_error("Found more than one @RG.ID in the SAM/BAM Header", Exit, OutOfRange); } seq->rg_record = record_list[0]; + update_cache.rg_record = record_list[0]; free(record_list); // NB: shallow copied } - // Program Group // NB: assumes the last item in the header - records = sam_header_get_records(header, "PG"); - if(NULL != records && 0 < records->n) { // it exists - seq->pg_record = records->records[records->n-1]; // copy over - } - else { - seq->pg_record = NULL; + if(update_cache.pg_record == NULL){ + records = sam_header_get_records(header, "PG"); + if(NULL != records && 0 < records->n) { // it exists + update_cache.pg_record = records->records[records->n-1]; // copy over + } + else { + update_cache.pg_record = NULL; + } } + seq->pg_record = update_cache.pg_record; + // key sequence and flow order seq->fo_start_idx = -1; if(NULL != seq->rg_record) { // It should exist in the SAM/BAM Header - seq->ks = sam_header_record_get(seq->rg_record, "KS"); - seq->fo = sam_header_record_get(seq->rg_record, "FO"); - + if(!use_cache){ + seq->ks = sam_header_record_get(seq->rg_record, "KS"); + seq->fo = sam_header_record_get(seq->rg_record, "FO"); + update_cache.ks = seq->ks; + update_cache.fo = seq->fo; + } + else{ + seq->ks = update_cache.ks; + seq->fo = update_cache.fo; + } // flow order index start if(NULL != seq->ks && NULL != seq->fo && TMAP_SEQ_TYPE_SFF == seq->type) { // only if it is an SFF // in addition, remove key sequence and trimming diff --git a/Analysis/TMAP/src/seq/tmap_seq.h b/Analysis/TMAP/src/seq/tmap_seq.h index 21e0e5c9..d3b65b40 100644 --- a/Analysis/TMAP/src/seq/tmap_seq.h +++ b/Analysis/TMAP/src/seq/tmap_seq.h @@ -27,6 +27,14 @@ enum { /*! */ + +typedef struct { + char *rg_id; + const char *ks; + const char *fo; + const sam_header_record_t *rg_record; + const sam_header_record_t *pg_record; +}seq_update_cache_t; typedef struct { int8_t type; /*!< the type associated with this structure */ union { diff --git a/Analysis/TMAP/src/sw/lib/AffineSWOptimization.cpp b/Analysis/TMAP/src/sw/lib/AffineSWOptimization.cpp index 4e65930c..1af30b6e 100644 --- a/Analysis/TMAP/src/sw/lib/AffineSWOptimization.cpp +++ b/Analysis/TMAP/src/sw/lib/AffineSWOptimization.cpp @@ -68,7 +68,7 @@ int AffineSWOptimization::process(const uint8_t *target, int32_t tlen, const uint8_t *query, int32_t qlen, int qsc, int qec, int mm, int mi, int o, int e, int dir, - int *opt, int *te, int *qe, int *n_best) { + int *opt, int *te, int *qe, int *n_best, int* fitflag) { int i; // resize b.resize(tlen); @@ -79,13 +79,13 @@ int AffineSWOptimization::process(const uint8_t *target, int32_t tlen, #ifdef AFFINESWOPTIMIZATION_USE_HASH // try the hash if(!hash->process(b, a, qsc, qec, mm, mi, o, e, dir, opt, te, qe, n_best)) { - s->process(b, a, qsc, qec, mm, mi, o, e, dir, opt, te, qe, n_best); + s->process(b, a, qsc, qec, mm, mi, o, e, dir, opt, te, qe, n_best, fitflag); // add to the hash - hash->add(b, a, qsc, qec, mm, mi, o, e, dir, opt, te, qe, n_best); + hash->add(b, a, qsc, qec, mm, mi, o, e, dir, opt, te, qe, n_best, fitflag); } return (*opt); #else - return s->process(b, a, qsc, qec, mm, mi, o, e, dir, opt, te, qe, n_best); + return s->process(b, a, qsc, qec, mm, mi, o, e, dir, opt, te, qe, n_best, fitflag); #endif } diff --git a/Analysis/TMAP/src/sw/lib/AffineSWOptimization.h b/Analysis/TMAP/src/sw/lib/AffineSWOptimization.h index 27ddd62a..5978c7a5 100644 --- a/Analysis/TMAP/src/sw/lib/AffineSWOptimization.h +++ b/Analysis/TMAP/src/sw/lib/AffineSWOptimization.h @@ -23,7 +23,7 @@ class AffineSWOptimization { const uint8_t *query, int32_t qlen, int qsc, int qec, int mm, int mi, int o, int e, int dir, - int *opt, int *te, int *qe, int *n_best); + int *opt, int *te, int *qe, int *n_best, int* fitflag); ~AffineSWOptimization(); diff --git a/Analysis/TMAP/src/sw/lib/AffineSWOptimizationHash.cpp b/Analysis/TMAP/src/sw/lib/AffineSWOptimizationHash.cpp index 120c5443..e7754045 100644 --- a/Analysis/TMAP/src/sw/lib/AffineSWOptimizationHash.cpp +++ b/Analysis/TMAP/src/sw/lib/AffineSWOptimizationHash.cpp @@ -79,7 +79,7 @@ static uint64_t hashDNA(const string &s) { bool AffineSWOptimizationHash::process(const string &b, const string &a, int _qsc, int _qec, int mm, int mi, int o, int e, int dir, - int *opt, int *te, int *qe, int *n_best) + int *opt, int *te, int *qe, int *n_best, int* fitflag) { int i; if(_qsc != qsc || _qec != qec || 0 != a.compare(query)) { // reset the hash? @@ -102,6 +102,7 @@ bool AffineSWOptimizationHash::process(const string &b, const string &a, int _qs (*te) = hash[htpos].te; (*qe) = hash[htpos].qe; (*n_best) = hash[htpos].n_best; + if (fitflag) (*fitflag) = hash[htpos].fitflag; return true; } } @@ -110,7 +111,7 @@ bool AffineSWOptimizationHash::process(const string &b, const string &a, int _qs void AffineSWOptimizationHash::add(const string &b, const string &a, int _qsc, int _qec, int mm, int mi, int o, int e, int dir, - int *opt, int *te, int *qe, int *n_best) + int *opt, int *te, int *qe, int *n_best, int* fitflag) { uint32_t hh = hashDNA(b); int htpos = hh % size; @@ -120,6 +121,7 @@ void AffineSWOptimizationHash::add(const string &b, const string &a, int _qsc, i hash[htpos].te = (*te); hash[htpos].qe = (*qe); hash[htpos].n_best = (*n_best); + hash[htpos].fitflag = (fitflag != NULL) ? (*fitflag) : 0; hash[htpos].dir = dir; hash[htpos].b = b; } diff --git a/Analysis/TMAP/src/sw/lib/AffineSWOptimizationHash.h b/Analysis/TMAP/src/sw/lib/AffineSWOptimizationHash.h index a1171aba..419f70fe 100644 --- a/Analysis/TMAP/src/sw/lib/AffineSWOptimizationHash.h +++ b/Analysis/TMAP/src/sw/lib/AffineSWOptimizationHash.h @@ -20,6 +20,7 @@ typedef struct { int te; int qe; int n_best; + int fitflag; } hash_t; class AffineSWOptimizationHash { @@ -28,11 +29,11 @@ class AffineSWOptimizationHash { bool process(const string &b, const string &a, int qsc, int qec, int mm, int mi, int o, int e, int dir, - int *opt, int *te, int *qe, int *n_best); + int *opt, int *te, int *qe, int *n_best, int* fitflag); void add(const string &b, const string &a, int _qsc, int _qec, int mm, int mi, int o, int e, int dir, - int *opt, int *te, int *qe, int *n_best); + int *opt, int *te, int *qe, int *n_best, int* fitflag); ~AffineSWOptimizationHash(); private: diff --git a/Analysis/TMAP/src/sw/lib/AffineSWOptimizationWrapper.cpp b/Analysis/TMAP/src/sw/lib/AffineSWOptimizationWrapper.cpp index 7018772e..9664973d 100644 --- a/Analysis/TMAP/src/sw/lib/AffineSWOptimizationWrapper.cpp +++ b/Analysis/TMAP/src/sw/lib/AffineSWOptimizationWrapper.cpp @@ -21,7 +21,7 @@ tmap_vsw_wrapper_process(tmap_vsw_wrapper_t *v, const uint8_t *query, int32_t qlen, int mm, int mi, int o, int e, int dir, int qsc, int qec, - int *opt, int *te, int *qe, int *n_best) + int *opt, int *te, int *qe, int *n_best, int* fitflag) { /* fprintf(stderr, "query=%d qlen=%d target=%d tlen=%d\n", @@ -47,7 +47,7 @@ tmap_vsw_wrapper_process(tmap_vsw_wrapper_t *v, -1, -1, -1, -1); */ - return v->process(target, tlen, query, qlen, qsc, qec, mm, mi, o, e, dir, opt, te, qe, n_best); + return v->process(target, tlen, query, qlen, qsc, qec, mm, mi, o, e, dir, opt, te, qe, n_best, fitflag); } void diff --git a/Analysis/TMAP/src/sw/lib/AffineSWOptimizationWrapper.h b/Analysis/TMAP/src/sw/lib/AffineSWOptimizationWrapper.h index 6e04feb3..cd590884 100644 --- a/Analysis/TMAP/src/sw/lib/AffineSWOptimizationWrapper.h +++ b/Analysis/TMAP/src/sw/lib/AffineSWOptimizationWrapper.h @@ -21,7 +21,7 @@ extern "C" { const uint8_t *query, int32_t qlen, int32_t mm, int32_t mi, int32_t o, int32_t e, int32_t dir, int32_t qsc, int32_t qec, - int32_t *opt, int32_t *target_end, int32_t *query_start, int32_t *n_best); + int32_t *opt, int32_t *target_end, int32_t *query_start, int32_t *n_best, int* fitflag); void tmap_vsw_wrapper_destroy(tmap_vsw_wrapper_t *v); diff --git a/Analysis/TMAP/src/sw/lib/Solution.h b/Analysis/TMAP/src/sw/lib/Solution.h index 10d9f1d0..8ad72fe4 100644 --- a/Analysis/TMAP/src/sw/lib/Solution.h +++ b/Analysis/TMAP/src/sw/lib/Solution.h @@ -17,7 +17,7 @@ class Solution { virtual int process(const string& b, const string& a, int qsc, int qec, int mm, int mi, int o, int e, int dir, - int *opt, int *te, int *qe, int *n_best) = 0; + int *opt, int *te, int *qe, int *n_best, int* fitflag) = 0; virtual ~Solution(); diff --git a/Analysis/TMAP/src/sw/lib/Solution1.cpp b/Analysis/TMAP/src/sw/lib/Solution1.cpp index ea735af1..3bf2914e 100644 --- a/Analysis/TMAP/src/sw/lib/Solution1.cpp +++ b/Analysis/TMAP/src/sw/lib/Solution1.cpp @@ -59,7 +59,7 @@ Solution1::~Solution1() { int Solution1::process(const string& b, const string& a, int qsc, int qec, int mm, int mi, int o, int e, int dir, - int *_opt, int *_te, int *_qe, int *_n_best) { + int *_opt, int *_te, int *_qe, int *_n_best, int* fitflag) { int i, score; int n = b.size(), m = a.size(); int16_t query_end, target_end; diff --git a/Analysis/TMAP/src/sw/lib/Solution1.h b/Analysis/TMAP/src/sw/lib/Solution1.h index c9630727..a753cc3e 100644 --- a/Analysis/TMAP/src/sw/lib/Solution1.h +++ b/Analysis/TMAP/src/sw/lib/Solution1.h @@ -22,7 +22,7 @@ class Solution1 : public Solution { virtual int process(const string& b, const string& a, int qsc, int qec, int mm, int mi, int o, int e, int dir, - int *opt, int *te, int *qe, int *n_best); + int *opt, int *te, int *qe, int *n_best, int* fitflag); int32_t query_cmp(string q, int n, uint8_t *query, int32_t query_len); private: diff --git a/Analysis/TMAP/src/sw/lib/Solution10.cpp b/Analysis/TMAP/src/sw/lib/Solution10.cpp index f90a2274..6b74e7ee 100644 --- a/Analysis/TMAP/src/sw/lib/Solution10.cpp +++ b/Analysis/TMAP/src/sw/lib/Solution10.cpp @@ -60,7 +60,7 @@ void buildMatrix (int match, int mismatch) offset = (i << 2); for (int j = 0; j < 4; ++j) matrix[offset+j] = (j==i) ? match : mismatch; - } + } } typedef struct { @@ -1319,16 +1319,16 @@ Solution10::~Solution10() { // dir: direction (bool) int Solution10::process(const string& b, const string& a, int qsc, int qec, int mm, int mi, int o, int e, int dir, - int *opt, int *te, int *qe, int *n_best) { + int *opt, int *te, int *qe, int *n_best, int* fitflag) { int n = b.size(), m = a.size(); - int id = ((qsc << 1) | qec); + int id = ((qsc << 1) | qec); int i; - SwStripedData *swData=NULL; + SwStripedData *swData=NULL; - if (unlikely(flag)) { + if (unlikely(flag)) { gapOpen = -(o+e); gapExtend = -e; buildMatrix(mm,mi); diff --git a/Analysis/TMAP/src/sw/lib/Solution10.h b/Analysis/TMAP/src/sw/lib/Solution10.h index 405247f9..0c297465 100644 --- a/Analysis/TMAP/src/sw/lib/Solution10.h +++ b/Analysis/TMAP/src/sw/lib/Solution10.h @@ -19,7 +19,7 @@ class Solution10 : public Solution { virtual int process(const string& b, const string& a, int qsc, int qec, int mm, int mi, int o, int e, int dir, - int *opt, int *te, int *qe, int *n_best); + int *opt, int *te, int *qe, int *n_best, int* fitflag); private: }; diff --git a/Analysis/TMAP/src/sw/lib/Solution2.cpp b/Analysis/TMAP/src/sw/lib/Solution2.cpp index c871db8c..9d9c6c98 100644 --- a/Analysis/TMAP/src/sw/lib/Solution2.cpp +++ b/Analysis/TMAP/src/sw/lib/Solution2.cpp @@ -4,6 +4,7 @@ #include #include "../../util/tmap_alloc.h" #include "Solution2.h" +#include // Ivan's Solution @@ -11,59 +12,109 @@ using namespace std; #define max(a, b) ((a)>(b)?a:b) -void Solution2::resize(int n) +typedef struct Sol2_CacheEntry{ + int m; + int n; + Sol2_CacheEntry *next; +}Sol2_CacheEntry_t; +static Sol2_CacheEntry_t *Sol2_cachePtr=NULL; +pthread_mutex_t cacheMutex=PTHREAD_MUTEX_INITIALIZER; + +static void FreeCachePtr(Sol2_CacheEntry_t *entry, int m, int n) +{ + pthread_mutex_lock(&cacheMutex); + entry->m=m; + entry->n=n; + entry->next=Sol2_cachePtr; + Sol2_cachePtr=entry; + pthread_mutex_unlock(&cacheMutex); +} + +static void *findCachePtr(int m, int n) +{ + void *rc=NULL; + pthread_mutex_lock(&cacheMutex); + Sol2_CacheEntry_t *entry=Sol2_cachePtr; + Sol2_CacheEntry_t *prevEntry=NULL; + while(entry){ + if(entry->m >= m && entry->n >= n){ + rc=entry; + if(prevEntry) + prevEntry->next=entry->next; + else + Sol2_cachePtr=entry->next; + break; + } + prevEntry=entry; + entry=entry->next; + } + pthread_mutex_unlock(&cacheMutex); + return rc; +} + +void Solution2::resize(int m, int n) { + _n = n; + _m = m; + if(n <= _alloc_n && m <= _alloc_m) return; + int i; - if(n <= mem) return; - M = (int**)tmap_realloc(M, sizeof(int*) * n, "M"); - H = (int**)tmap_realloc(H, sizeof(int*) * n, "H"); - V = (int**)tmap_realloc(V, sizeof(int*) * n, "V"); - for(i=0;i int Solution9Reference::process(string b, string a, int qsc, int qec, int mm, int mi, int o, int e, int dir, - int *_opt, int *_te, int *_qe, int *_n_best) { + int *_opt, int *_te, int *_qe, int *_n_best, int* fitflag) { int n = b.size(), m = a.size(); int id = -1; diff --git a/Analysis/TMAP/src/sw/lib/Solution9.h b/Analysis/TMAP/src/sw/lib/Solution9.h index c1ddacc0..206a3ed8 100644 --- a/Analysis/TMAP/src/sw/lib/Solution9.h +++ b/Analysis/TMAP/src/sw/lib/Solution9.h @@ -22,7 +22,7 @@ class Solution9Reference { int V[MAX_DIM][MAX_DIM]; int process(string b, string a, int qsc, int qec, int mm, int mi, int o, int e, int dir, - int *opt, int *te, int *qe, int *n_best); + int *opt, int *te, int *qe, int *n_best, int* fitflag); }; class Solution9 : public Solution { diff --git a/Analysis/TMAP/src/sw/tmap_vsw.c b/Analysis/TMAP/src/sw/tmap_vsw.c index 97e13bbd..958c5b8f 100644 --- a/Analysis/TMAP/src/sw/tmap_vsw.c +++ b/Analysis/TMAP/src/sw/tmap_vsw.c @@ -28,6 +28,7 @@ #include #include #include +#include #include #include "../util/tmap_alloc.h" #include "../util/tmap_error.h" @@ -37,34 +38,49 @@ #include "tmap_vsw.h" tmap_vsw_t* -tmap_vsw_init(const uint8_t *query, int32_t qlen, +tmap_vsw_init (const uint8_t *query, int32_t qlen, int32_t query_start_clip, int32_t query_end_clip, int32_t type, + int32_t fallback_type, tmap_vsw_opt_t *opt) { - tmap_vsw_t *vsw = NULL; - vsw = tmap_calloc(1, sizeof(tmap_vsw_t), "vsw"); - vsw->type = type; - vsw->query_start_clip = query_start_clip; - vsw->query_end_clip = query_end_clip; - vsw->opt = opt; - vsw->algorithm = tmap_vsw_wrapper_init(type); - vsw->algorithm_default = tmap_vsw_wrapper_init(1); - return vsw; + tmap_vsw_t *vsw = NULL; + vsw = tmap_calloc (1, sizeof (tmap_vsw_t), "vsw"); + vsw->type = type; + vsw->fallback_type = fallback_type; + vsw->query_start_clip = query_start_clip; + vsw->query_end_clip = query_end_clip; + vsw->opt = opt; + vsw->algorithm = tmap_vsw_wrapper_init (type); + vsw->algorithm_fallback = tmap_vsw_wrapper_init (fallback_type); + vsw->algorithm_default = tmap_vsw_wrapper_init (VSW_DEFAULT_METHOD); + return vsw; +} + +void tmap_vsw_set_params (tmap_vsw_t* vsw, + int32_t query_start_clip, + int32_t query_end_clip, + tmap_vsw_opt_t* opt ) +{ + vsw->query_start_clip = query_start_clip; + vsw->query_end_clip = query_end_clip; + *(vsw->opt) = *opt; } void -tmap_vsw_destroy(tmap_vsw_t *vsw) +tmap_vsw_destroy (tmap_vsw_t *vsw) { - if(NULL == vsw) return; - tmap_vsw_wrapper_destroy(vsw->algorithm); - tmap_vsw_wrapper_destroy(vsw->algorithm_default); - free(vsw); + if (NULL == vsw) + return; + tmap_vsw_wrapper_destroy (vsw->algorithm); + tmap_vsw_wrapper_destroy (vsw->algorithm_fallback); + tmap_vsw_wrapper_destroy (vsw->algorithm_default); + free (vsw); } #ifdef TMAP_VSW_DEBUG_CMP static void -tmap_vsw_process_compare(tmap_vsw_t *vsw, +tmap_vsw_process_compare (tmap_vsw_t *vsw, const uint8_t *query, int32_t qlen, uint8_t *target, int32_t tlen, tmap_vsw_result_t *result, @@ -78,8 +94,9 @@ tmap_vsw_process_compare(tmap_vsw_t *vsw, query_end_type1 = target_end_type1 = n_best_type1 = score_type1 = 0; // baseline - if(0 == cmp_non_vsw) { - tmap_vsw_wrapper_process(vsw->algorithm_default, + if (0 == cmp_non_vsw) + { + tmap_vsw_wrapper_process (vsw->algorithm_default, target, tlen, query, qlen, vsw->opt->score_match, @@ -90,27 +107,28 @@ tmap_vsw_process_compare(tmap_vsw_t *vsw, vsw->query_start_clip, vsw->query_end_clip, &score_type0, &target_end_type0, &query_end_type0, &n_best_type0); } - else { + else + { tmap_sw_param_t ap; - tmap_sw_path_t path[1024]; + tmap_sw_path_t path [1024]; int32_t path_len; - int32_t i, matrix[25]; + int32_t i, matrix [25]; ap.matrix=matrix; - for(i=0;i<25;i++) { - ap.matrix[i] = -(vsw->opt)->pen_mm; + for (i=0;i<25;i++) { + ap.matrix [i] = -(vsw->opt)->pen_mm; } - for(i=0;i<4;i++) { - ap.matrix[i*5+i] = vsw->opt->score_match; + for (i=0;i<4;i++) { + ap.matrix [i * 5 + i] = vsw->opt->score_match; } ap.gap_open = vsw->opt->pen_gapo; ap.gap_ext = vsw->opt->pen_gape; ap.gap_end = vsw->opt->pen_gape; ap.row = 5; - score_type0 = tmap_sw_clipping_core((uint8_t*)target, tlen, (uint8_t*)query, qlen, &ap, + score_type0 = tmap_sw_clipping_core ((uint8_t*)target, tlen, (uint8_t*)query, qlen, &ap, vsw->query_start_clip, vsw->query_end_clip, path, &path_len, dir); } // current - tmap_vsw_wrapper_process(vsw->algorithm, + tmap_vsw_wrapper_process (vsw->algorithm, target, tlen, query, qlen, vsw->opt->score_match, @@ -121,75 +139,81 @@ tmap_vsw_process_compare(tmap_vsw_t *vsw, vsw->query_start_clip, vsw->query_end_clip, &score_type1, &target_end_type1, &query_end_type1, &n_best_type1); - if(0 != cmp_non_vsw) { + if (0 != cmp_non_vsw) + { n_best_type0 = n_best_type1; target_end_type0 = target_end_type1; query_end_type0 = query_end_type1; } - if(tlen <= target_end_type0) tmap_bug(); - if(qlen <= query_end_type0) tmap_bug(); + if (tlen <= target_end_type0) tmap_bug (); + if (qlen <= query_end_type0) tmap_bug (); /* - if(tlen <= target_end_type1) tmap_bug(); - if(qlen <= query_end_type1) tmap_bug(); + if (tlen <= target_end_type1) tmap_bug (); + if (qlen <= query_end_type1) tmap_bug (); */ - if(score_type0 != score_type1 + if (score_type0 != score_type1 || target_end_type0 != target_end_type1 || query_end_type0 != query_end_type1 - || n_best_type0 != n_best_type1) { + || n_best_type0 != n_best_type1) + { int32_t i; - fprintf(stderr, "in %s dir=%d\n", __func__, dir); - fprintf(stderr, "query_start_clip=%d\n", vsw->query_start_clip); - fprintf(stderr, "query_end_clip=%d\n", vsw->query_end_clip); - fprintf(stderr, "qlen=%d tlen=%d\n", qlen, tlen); - for(i=0;iquery_start_clip); + fprintf (stderr, "query_end_clip=%d\n", vsw->query_end_clip); + fprintf (stderr, "qlen=%d tlen=%d\n", qlen, tlen); + for (i=0;iopt)->pen_mm; + for (i=0;i<25;i++) { + ap.matrix [i] = -(vsw->opt)->pen_mm; } - for(i=0;i<4;i++) { - ap.matrix[i*5+i] = vsw->opt->score_match; + for (i=0;i<4;i++) { + ap.matrix [i * 5 + i] = vsw->opt->score_match; } ap.gap_open = vsw->opt->pen_gapo; ap.gap_ext = vsw->opt->pen_gape; ap.gap_end = vsw->opt->pen_gape; ap.row = 5; path_len = 0; - path = tmap_calloc(1024, sizeof(tmap_sw_path_t), "path"); - score = tmap_sw_clipping_core((uint8_t*)target, tlen, (uint8_t*)query, qlen, &ap, + path = tmap_calloc (1024, sizeof (tmap_sw_path_t), "path"); + score = tmap_sw_clipping_core ((uint8_t*)target, tlen, (uint8_t*)query, qlen, &ap, vsw->query_start_clip, vsw->query_end_clip, path, &path_len, dir); // print out the path - cigar = tmap_sw_path2cigar(path, path_len, &n_cigar); - fprintf(stderr, "tmap_sw_clipping_core score=%d\n", score); - for(i=0;i>4, "MIDNSHP"[cigar[i]&0xf]); + cigar = tmap_sw_path2cigar (path, path_len, &n_cigar); + fprintf (stderr, "tmap_sw_clipping_core score=%d\n", score); + for (i=0;i>4, "MIDNSHP"[cigar [i]&0xf]); } - fputc('\n', stderr); - free(path); - free(cigar); - } while(0); + fputc ('\n', stderr); + free (path); + free (cigar); + } while (0); // try the opposite direction // baseline - tmap_vsw_wrapper_process(vsw->algorithm_default, + tmap_vsw_wrapper_process (vsw->algorithm_default, target, tlen, query, qlen, vsw->opt->score_match, @@ -199,18 +223,18 @@ tmap_vsw_process_compare(tmap_vsw_t *vsw, 1-dir, vsw->query_start_clip, vsw->query_end_clip, &score_type0, &target_end_type0, &query_end_type0, &n_best_type0); - fprintf(stderr, "baseline opposite reverse tlen=%d qlen=%d score=[%d,%d] target_end=[%d,%d] query_end=[%d,%d] n_best=[%d,%d]\n", + fprintf (stderr, "baseline opposite reverse tlen=%d qlen=%d score=[%d,%d] target_end=[%d,%d] query_end=[%d,%d] n_best=[%d,%d]\n", tlen, qlen, score_type0, score_type1, target_end_type0, target_end_type1, query_end_type0, query_end_type1, n_best_type0, n_best_type1); // top coder - for(i=0;iquery_start_clip, vsw->query_end_clip, vsw->opt->score_match, -vsw->opt->pen_mm, @@ -218,229 +242,352 @@ tmap_vsw_process_compare(tmap_vsw_t *vsw, -vsw->opt->pen_gape, dir, -1, -1, -1, -1); - fprintf(stderr, "Error: algorithms produced different results!\n"); - exit(1); + fprintf (stderr, "Error: algorithms produced different results!\n"); + exit (1); } } #endif static int32_t -tmap_vsw_process(tmap_vsw_t *vsw, +tmap_vsw_process (tmap_vsw_t *vsw, const uint8_t *query, int32_t qlen, uint8_t *target, int32_t tlen, tmap_vsw_result_t *result, int32_t *overflow, int32_t score_thr, - int32_t is_rev, int32_t direction) + int32_t is_rev, int32_t direction, + uint32_t confirm_conflicts, + uint32_t fallback_failed, + uint32_t fallback_noniupac, + tmap_map_stats_t* stat) { - int32_t found_forward = 1, query_end, target_end, n_best, score = INT32_MIN; - // TODO: check potential overflow - // TODO: check that gap penalties will not result in an overflow - // TODO: check that the max/min alignment score do not result in an overflow + int32_t found_forward = 1, query_end, target_end, n_best, score = INT32_MIN, do_not_process = 0; + // TODO: check potential overflow + // TODO: check that gap penalties will not result in an overflow + // TODO: check that the max/min alignment score do not result in an overflow + int32_t vect_used = 1; + int32_t fit_error = 0; #ifdef TMAP_VSW_DEBUG - if(1 == is_rev) { - int i; - fprintf(stderr, "in %s is_rev=%d\n", __func__, is_rev); - fprintf(stderr, "query_start_clip=%d\n", vsw->query_start_clip); - fprintf(stderr, "query_end_clip=%d\n", vsw->query_end_clip); - fprintf(stderr, "qlen=%d tlen=%d\n", qlen, tlen); - for(i=0;iquery_start_clip); + fprintf (stderr, "query_end_clip=%d\n", vsw->query_end_clip); + fprintf (stderr, "qlen=%d tlen=%d\n", qlen, tlen); + for (i=0;i 3); + for (i = 0; i < tlen && !non_std_base; ++i) + non_std_base = (target [i] > 3); + } + if (stat && non_std_base && vsw->type == 4) + { + if (is_rev) + ++stat->nonstd_base_fallbacks_rev; + else + ++stat->nonstd_base_fallbacks_fwd; + } - if(tlen <= tmap_vsw_wrapper_get_max_tlen(vsw->algorithm) - && qlen <= tmap_vsw_wrapper_get_max_qlen(vsw->algorithm)) { - tmap_vsw_wrapper_process(vsw->algorithm, - target, tlen, - query, qlen, - vsw->opt->score_match, - -vsw->opt->pen_mm, - -vsw->opt->pen_gapo, - -vsw->opt->pen_gape, - direction, - vsw->query_start_clip, vsw->query_end_clip, - &score, &target_end, &query_end, &n_best); -#ifdef TMAP_VSW_DEBUG_CMP - tmap_vsw_process_compare(vsw, - query, qlen, - target, tlen, - result, - overflow, score_thr, direction); -#endif - } - else { // try the default - if(1 != vsw->type) { - tmap_vsw_wrapper_process(vsw->algorithm_default, - target, tlen, - query, qlen, - vsw->opt->score_match, - -vsw->opt->pen_mm, - -vsw->opt->pen_gapo, - -vsw->opt->pen_gape, - direction, - vsw->query_start_clip, vsw->query_end_clip, - &score, &target_end, &query_end, &n_best); - } - } - if(score < score_thr || 0 == n_best) { - query_end = target_end = -1; - n_best = 0; - score = INT32_MIN; - } - - if(0 == is_rev) { +#ifdef FORCE_VSW_4_NONSTD_BASE_ERROR_PROPAGATION // do not enable for production :) + non_std_base = 0; +#else + if (non_std_base && vsw->type == 4 && !fallback_noniupac) + do_not_process = 1; + // non_std_base = 0; // for now force vectorized processing with currently elected method. May need a way to specify different fallback method later +#endif - result->query_end = query_end; - result->target_end = target_end; - result->n_best = n_best; - result->score_fwd = score; + // update based on current problem + query_end = target_end = n_best = 0; + if (NULL != overflow) (*overflow) = 0; + int32_t alignment_ok = 0; - // check forward results - if(NULL != overflow && 1 == (*overflow)) { - found_forward = 0; - } - else if(result->score_fwd < score_thr) { - found_forward = 0; - } - else if((result->query_end == result->query_start || result->target_end == result->target_start) - && result->score_fwd <= 0) { - found_forward = 0; - } - else if(n_best <= 0) { - found_forward = 0; - } - else if(-1 == result->query_end) { - tmap_bug(); - } + if (!do_not_process) + { + if (tlen <= tmap_vsw_wrapper_get_max_tlen (vsw->algorithm) + && qlen <= tmap_vsw_wrapper_get_max_qlen (vsw->algorithm) + && !(non_std_base && vsw->type == 4)) // DVK: TopCoder4 does not handle non-standard bases properly + { + ++ stat->vect_sw_calls; + vect_used = 1; + tmap_vsw_wrapper_process (vsw->algorithm, + target, tlen, + query, qlen, + vsw->opt->score_match, + -vsw->opt->pen_mm, + -vsw->opt->pen_gapo, + -vsw->opt->pen_gape, + direction, + vsw->query_start_clip, vsw->query_end_clip, + &score, &target_end, &query_end, &n_best, &fit_error); + #ifdef TMAP_VSW_DEBUG_CMP + tmap_vsw_process_compare (vsw, + query, qlen, + target, tlen, + result, + overflow, score_thr, direction); + #endif + if (fit_error) + { + alignment_ok = 0; + ++ stat->vswfails; + } + else + alignment_ok = 1; + } + if (!alignment_ok && (fallback_failed || non_std_base)) // try fallback + { + if (vsw->fallback_type != vsw->type + && tlen <= tmap_vsw_wrapper_get_max_tlen (vsw->algorithm_fallback) + && qlen <= tmap_vsw_wrapper_get_max_qlen (vsw->algorithm_fallback) + && !(non_std_base && vsw->fallback_type == 4)) + { + ++ stat->fallback_vsw_calls; + fit_error = 0; + vect_used = 1; + tmap_vsw_wrapper_process (vsw->algorithm_fallback, + target, tlen, + query, qlen, + vsw->opt->score_match, + -vsw->opt->pen_mm, + -vsw->opt->pen_gapo, + -vsw->opt->pen_gape, + direction, + vsw->query_start_clip, vsw->query_end_clip, + &score, &target_end, &query_end, &n_best, &fit_error); + if (fit_error) + { + alignment_ok = 0; + ++ stat->vswfails; + } + else + alignment_ok = 1; + } + } + if (!alignment_ok && fallback_failed) + { // try the default + if (vsw->type != VSW_DEFAULT_METHOD && vsw->fallback_type != VSW_DEFAULT_METHOD) + { + ++ stat->fallback_sw_calls; + fit_error = 0; + vect_used = 0; + tmap_vsw_wrapper_process (vsw->algorithm_default, + target, tlen, + query, qlen, + vsw->opt->score_match, + -vsw->opt->pen_mm, + -vsw->opt->pen_gapo, + -vsw->opt->pen_gape, + direction, + vsw->query_start_clip, vsw->query_end_clip, + &score, &target_end, &query_end, &n_best, &fit_error); + if (fit_error) + alignment_ok = 0; // irrelevant with current default SW implementation + else + alignment_ok = 1; + } + } + } - // return if we found no legal/good forward results - if(0 == found_forward) { - result->query_end = result->query_start = 0; - result->target_end = result->target_start = 0; - result->score_fwd = result->score_rev = INT16_MIN; - result->n_best = 0; - return INT32_MIN; - } + if (!alignment_ok || score < score_thr || 0 == n_best) + { + query_end = target_end = -1; + n_best = 0; + score = INT32_MIN; + } + if (!alignment_ok && !do_not_process) + ++stat->totswfails; + + if (0 == is_rev) + { + + result->query_end = query_end; + result->target_end = target_end; + result->n_best = n_best; + result->score_fwd = score; - result->query_start = result->target_start = 0; - result->score_rev = INT16_MIN; + // check forward results + if (!alignment_ok + || result->score_fwd < score_thr + || ((result->query_end == result->query_start || result->target_end == result->target_start) && result->score_fwd <= 0) + || n_best <= 0) + { + // return if we found no legal/good forward results + result->query_end = result->query_start = 0; + result->target_end = result->target_start = 0; + result->score_fwd = result->score_rev = INT16_MIN; + result->n_best = 0; + return INT32_MIN; + } + else if (-1 == result->query_end) + { + tmap_bug (); + } + + result->query_start = result->target_start = 0; + result->score_rev = INT16_MIN; #ifdef TMAP_VSW_DEBUG - fprintf(stderr, "result->score_fwd=%d result->score_rev=%d\n", - result->score_fwd, result->score_rev); - fprintf(stderr, "{?-%d] {?-%d}\n", - result->query_end, - result->target_end); + fprintf (stderr, "result->score_fwd=%d result->score_rev=%d\n", + result->score_fwd, result->score_rev); + fprintf (stderr, "{?-%d] {?-%d}\n", + result->query_end, + result->target_end); #endif - return result->score_fwd; - } - else { - - result->query_start = qlen - query_end - 1; - result->target_start = tlen - target_end - 1; - result->n_best = n_best; - result->score_rev = score; + return result->score_fwd; + } + else + { + result->query_start = qlen - query_end - 1; + result->target_start = tlen - target_end - 1; + result->n_best = n_best; + result->score_rev = score; #ifdef TMAP_VSW_DEBUG - fprintf(stderr, "is_rev=%d result->score_fwd=%d result->score_rev=%d\n", - is_rev, result->score_fwd, result->score_rev); + fprintf (stderr, "is_rev=%d result->score_fwd=%d result->score_rev=%d\n", + is_rev, result->score_fwd, result->score_rev); #endif - // check reverse results - if(NULL != overflow && 1 == (*overflow)) { - result->query_end = result->query_start = 0; - result->target_end = result->target_start = 0; - result->score_fwd = result->score_rev = INT16_MIN; - result->n_best = 0; - return INT32_MIN; - } - else if(result->score_fwd != result->score_rev) { // something went wrong... FIXME - // use the default - if(1 != vsw->type) { - tmap_vsw_wrapper_process(vsw->algorithm_default, - target, tlen, - query, qlen, - vsw->opt->score_match, - -vsw->opt->pen_mm, - -vsw->opt->pen_gapo, - -vsw->opt->pen_gape, - direction, - vsw->query_start_clip, vsw->query_end_clip, - &score, &target_end, &query_end, &n_best); - result->query_start = qlen - query_end - 1; - result->target_start = tlen - target_end - 1; - result->n_best = n_best; - result->score_rev = score; - if(result->score_fwd != result->score_rev) { // something went wrong... again... - // ignore - result->query_end = result->query_start = 0; - result->target_end = result->target_start = 0; - result->score_fwd = result->score_rev = INT16_MIN; - result->n_best = 0; - return INT32_MIN; - } - else { - return score; - } - } - // Bug! - fprintf(stderr, "{%d-%d} {%d-%d}\n", - result->query_start, result->query_end, - result->target_start, result->target_end); - fprintf(stderr, "result->score_fwd=%d result->score_rev=%d\n", - result->score_fwd, result->score_rev); - fprintf(stderr, "score=%d\n", score); - tmap_sw_param_t ap; - int32_t i, matrix[25]; - ap.matrix=matrix; - for(i=0;i<25;i++) { - ap.matrix[i] = -(vsw->opt)->pen_mm; - } - for(i=0;i<4;i++) { - ap.matrix[i*5+i] = vsw->opt->score_match; - } - ap.gap_open = vsw->opt->pen_gapo; ap.gap_ext = vsw->opt->pen_gape; - ap.gap_end = vsw->opt->pen_gape; - ap.row = 5; - score = tmap_sw_clipping_core((uint8_t*)target, tlen, (uint8_t*)query, qlen, &ap, + // check reverse results + if (!alignment_ok) + { + result->query_end = result->query_start = 0; + result->target_end = result->target_start = 0; + result->score_fwd = result->score_rev = INT16_MIN; + result->n_best = 0; + return INT32_MIN; + } + else if (result->score_fwd != result->score_rev) + { // something went wrong... FIXME + // re-process both with the default, warn the user if initial score could not be confirmed + // use the default + if (stat) + { + if (vect_used) + ++stat->vswfails; + ++stat->totswfails; + } + if (vsw->type != VSW_DEFAULT_METHOD && fallback_failed) + { + int32_t def_vsw_score = INT_MIN; + stat->fallback_sw_calls ++; + tmap_vsw_wrapper_process (vsw->algorithm_default, + target, tlen, + query, qlen, + vsw->opt->score_match, + -vsw->opt->pen_mm, + -vsw->opt->pen_gapo, + -vsw->opt->pen_gape, + direction, vsw->query_start_clip, vsw->query_end_clip, - NULL, NULL, direction); - fprintf(stderr, "score=%d\n", score); - tmap_bug(); - } + &def_vsw_score, &target_end, &query_end, &n_best, overflow); - return result->score_fwd; - } + // DVK: trust the default method, but optionally confirm with the non-vectorized SW + // LATER: (maybe) re-run forward algnment here to re-confirm score + uint32_t accept_correction = 1; + if (confirm_conflicts) + { + tmap_sw_param_t ap; + int32_t i, matrix [25]; + ap.matrix=matrix; + for ( i = 0; i < 25; ++i) + ap.matrix [i] = -(vsw->opt)->pen_mm; + for (i = 0; i < 4; ++i) + { + ap.matrix [i*5 + i] = vsw->opt->score_match; + } + ap.gap_open = vsw->opt->pen_gapo; + ap.gap_ext = vsw->opt->pen_gape; + ap.gap_end = vsw->opt->pen_gape; + ap.row = 5; + int32_t sw_score = tmap_sw_clipping_core ((uint8_t*)target, tlen, (uint8_t*)query, qlen, &ap, + vsw->query_start_clip, vsw->query_end_clip, + NULL, NULL, direction); + if (sw_score != def_vsw_score) + { + accept_correction = 0; + tmap_warning ("Unrecoverable internal error: VSW alignment score asymmetry. Forward score = %d, reverse score = %d, default (\"gold-standard\") VSW score = %d, non-vectorized score = %d.\nCandidate ignored, read may be unmapped or mapped improperly", result->score_fwd, result->score_rev, def_vsw_score, sw_score); + } + } + if (accept_correction) + { + // tmap_warning ("Correctable internal error: VSW alignment score assymetry. Forward score = %d, reverse score = %d,\n default (\"gold-standard\") VSW score = %d. Non-vectorized method matches reverse result; using confirmed score", result->score_fwd, result->score_rev, def_vsw_score); + if (stat) + ++stat->asymmetric_scores_corrected; + result->query_start = qlen - query_end - 1; + result->target_start = tlen - target_end - 1; + result->n_best = n_best; + result->score_rev = def_vsw_score; + result->score_fwd = def_vsw_score; + return score; + } + } + else + tmap_warning ("Unrecoverable internal error: VSW alignment score asymmetry in default method (#%d). Forward score = %d, reverse score = %d\nCandidate ignored, read may be unmapped or mapped improperly", result->score_fwd, result->score_rev); + // ignore candidate with conflict (warning already issued) + if (stat) + { + ++stat->asymmetric_scores_failed; + ++stat->totswfails; + } + result->query_end = result->query_start = 0; + result->target_end = result->target_start = 0; + result->score_fwd = result->score_rev = INT16_MIN; + result->n_best = 0; + return INT32_MIN; + } + else + { + if (stat) + ++stat->symmetric_scores; + } + return result->score_fwd; + } } int32_t -tmap_vsw_process_fwd(tmap_vsw_t *vsw, +tmap_vsw_process_fwd (tmap_vsw_t *vsw, const uint8_t *query, int32_t qlen, uint8_t *target, int32_t tlen, tmap_vsw_result_t *result, - int32_t *overflow, int32_t score_thr, int32_t direction) + int32_t *overflow, int32_t score_thr, int32_t direction, + uint32_t confirm_conflicts, + uint32_t fallback_failed, + uint32_t fallback_noniupac, + tmap_map_stats_t* stat) { - return tmap_vsw_process(vsw, query, qlen, target, tlen, result, overflow, score_thr, 0, direction); + return tmap_vsw_process (vsw, query, qlen, target, tlen, result, overflow, score_thr, 0, direction, confirm_conflicts, fallback_failed, fallback_noniupac, stat); } int32_t -tmap_vsw_process_rev(tmap_vsw_t *vsw, +tmap_vsw_process_rev (tmap_vsw_t *vsw, const uint8_t *query, int32_t qlen, uint8_t *target, int32_t tlen, tmap_vsw_result_t *result, - int32_t *overflow, int32_t score_thr, int32_t direction) + int32_t *overflow, int32_t score_thr, int32_t direction, + uint32_t confirm_conflicts, + uint32_t fallback_failed, + uint32_t fallback_noniupac, + tmap_map_stats_t* stat) { - return tmap_vsw_process(vsw, query, qlen, target, tlen, result, overflow, score_thr, 1, direction); + return tmap_vsw_process (vsw, query, qlen, target, tlen, result, overflow, score_thr, 1, direction, confirm_conflicts, fallback_failed, fallback_noniupac, stat); } diff --git a/Analysis/TMAP/src/sw/tmap_vsw.h b/Analysis/TMAP/src/sw/tmap_vsw.h index cd5d49fc..239c72dd 100644 --- a/Analysis/TMAP/src/sw/tmap_vsw.h +++ b/Analysis/TMAP/src/sw/tmap_vsw.h @@ -35,19 +35,26 @@ #include #include "tmap_vsw_definitions.h" #include "lib/AffineSWOptimizationWrapper.h" +#include "../map/util/tmap_map_stats.h" #ifdef __cplusplus extern "C" { #endif + +#define VSW_DEFAULT_METHOD 2 // this is a non-vectorized implementation + /*! Used to run the underlying vectorized smith waterman (VSW) types */ -typedef struct { +typedef struct __tmap_vsw_t +{ int32_t type; /*!< the vectorized smith waterman type */ + int32_t fallback_type; /*!< the vectorized smith waterman type of fallback algorithm */ tmap_vsw_wrapper_t *algorithm; /*!< the main VSW algorithm */ - tmap_vsw_wrapper_t *algorithm_default; /*!< the VSW algorithm to test if the main algorithm fails */ + tmap_vsw_wrapper_t *algorithm_fallback; /*!< the fallback VSW algorithm */ + tmap_vsw_wrapper_t *algorithm_default; /*!< the VSW algorithm to use if the main/fallback algorithms fail */ int32_t query_start_clip; /*!< 1 if we are to clip the start of the query, 0 otherwise */ int32_t query_end_clip; /*!< 1 if we are to clip the end of the query, 0 otherwise */ tmap_vsw_opt_t *opt; /*!< the alignment parameters */ @@ -63,16 +70,22 @@ typedef struct { @return the query sequence in vectorized form */ tmap_vsw_t* -tmap_vsw_init(const uint8_t *query, int32_t qlen, +tmap_vsw_init (const uint8_t *query, int32_t qlen, int32_t query_start_clip, int32_t query_end_clip, int32_t type, + int32_t fallback_type, tmap_vsw_opt_t *opt); +void tmap_vsw_set_params (tmap_vsw_t* vsw, + int32_t query_start_clip, + int32_t query_end_clip, + tmap_vsw_opt_t* opt); + /*! @param vsw the structure to destroy */ void -tmap_vsw_destroy(tmap_vsw_t *vsw); +tmap_vsw_destroy (tmap_vsw_t *vsw); /*! Performs alignment in the sequencing direction. This will update query_end and target_end @@ -92,12 +105,17 @@ tmap_vsw_destroy(tmap_vsw_t *vsw); cases, if there are still several possibilities, choose the one with the largest value of target_end among them). */ + int32_t -tmap_vsw_process_fwd(tmap_vsw_t *vsw, +tmap_vsw_process_fwd (tmap_vsw_t *vsw, const uint8_t *query, int32_t qlen, uint8_t *target, int32_t tlen, tmap_vsw_result_t *result, - int32_t *overflow, int32_t score_thr, int32_t direction); + int32_t *overflow, int32_t score_thr, int32_t direction, + uint32_t confirm_conflicts, + uint32_t fallback_failed, + uint32_t fallback_noniupac, + tmap_map_stats_t* stat); /*! Performs alignment in the reverse of the sequencing direction. This will update query_start @@ -117,12 +135,17 @@ tmap_vsw_process_fwd(tmap_vsw_t *vsw, cases, if there are still several possibilities, choose the one with the largest value of target_end among them). */ + int32_t -tmap_vsw_process_rev(tmap_vsw_t *vsw, +tmap_vsw_process_rev (tmap_vsw_t *vsw, const uint8_t *query, int32_t qlen, uint8_t *target, int32_t tlen, tmap_vsw_result_t *result, - int32_t *overflow, int32_t score_thr, int32_t direction); + int32_t *overflow, int32_t score_thr, int32_t direction, + uint32_t confirm_conflicts, + uint32_t fallback_failed, + uint32_t fallback_noniupac, + tmap_map_stats_t* stat); #ifdef __cplusplus } diff --git a/Analysis/TMAP/src/sw/tmap_vsw_bm.c b/Analysis/TMAP/src/sw/tmap_vsw_bm.c index da865929..dfdb8bf3 100644 --- a/Analysis/TMAP/src/sw/tmap_vsw_bm.c +++ b/Analysis/TMAP/src/sw/tmap_vsw_bm.c @@ -79,7 +79,7 @@ tmap_vsw_bm_core(int32_t seq_len, int32_t tlen, int32_t n_iter, tmp_sam.result.target_start = tmp_sam.result.target_end = 0; // run the vsw tmap_vsw_process_fwd(vsw, seq, seq_len, target, tlen, - &tmp_sam.result, &overflow, opt->score_thr, 0); + &tmp_sam.result, &overflow, opt->score_thr, 0, 1, 1, 1, NULL); } else { tmap_sw_clipping_core(seq, seq_len, target, tlen, diff --git a/Analysis/TMAP/src/util/tmap_bsearch.c b/Analysis/TMAP/src/util/tmap_bsearch.c index 8c47fc39..535fc4a4 100644 --- a/Analysis/TMAP/src/util/tmap_bsearch.c +++ b/Analysis/TMAP/src/util/tmap_bsearch.c @@ -1,5 +1,6 @@ /* Copyright (C) 2020 Ion Torrent Systems, Inc. All Rights Reserved */ #include "tmap_bsearch.h" +#include "tmap_error.h" // binary search for sorted arrays. Handles omitted keys // passed in 'lt' function should compare the key pointed to by the first argument to the data element pointed to by the second argument, in this order @@ -9,10 +10,10 @@ // can be improved to handle 'lucky strikes' if check for the equality in some form is available, or if no restriction on the comparison order is given -// (DK) WARNING! The implementation below is flowed! the search does not end (enters infinite loop) when searching for the value that is equal to 0 element in the array! -// +// (DK) WARNING! The implementation below is flawed! the search does not end (enters infinite loop) when searching for the value that is equal to 0 element in the array! +// (DK) A key greater then first and less then second element also makes a problem. -const void* tmap_binary_search (const void* key, const void* data, size_t num_elem, size_t elem_size, int (*lt) (const void* key, const void* elem)) +const void* tmap_binary_search_bad (const void* key, const void* data, size_t num_elem, size_t elem_size, int (*lt) (const void* key, const void* elem)) { size_t lower_idx = 0; // lower boundary of the narrowed zone size_t upper_idx = num_elem; // upper boundary of the narrowed zone @@ -30,8 +31,55 @@ const void* tmap_binary_search (const void* key, const void* data, size_t num_el return data + (lower_idx * elem_size); } +// DK this should fix the problem in the above code +// DK 12/3/2020 Tested and debugged the fix by creating comprehensive (all-cases) TestSuite case. Ok now. -const void* tmap_binary_search_nokey (const void* data, size_t num_elem, size_t elem_size, int (*above) (const void* elem)) +const void* tmap_binary_search_fixed (const void* key, const void* data, size_t num_elem, size_t elem_size, int (*lt) (const void* key, const void* elem)) +{ + size_t lower_idx = 0; // lower boundary of the narrowed zone + size_t upper_idx = num_elem; // upper boundary of the narrowed zone + size_t mid_idx; + + while (lower_idx < upper_idx) + { + + mid_idx = (lower_idx + upper_idx) >> 1; + if (lt (key, data + (mid_idx * elem_size))) // key lower then mid + upper_idx = mid_idx; + else // key greater or equal to mid. + { + if (lower_idx == mid_idx) // DK: in this case, greater and equal should be treated differently: equal - return lower, greater - return lower + 1 (upper in this case) + { + if (lt (data + (lower_idx * elem_size), key)) // mid == low is lower then key. Position of the next element is to be returned + ++lower_idx; + break; + } + else + lower_idx = mid_idx; + } + } + return data + (lower_idx * elem_size); +} + +const void* tmap_binary_search_nokey_bad (const void* data, size_t num_elem, size_t elem_size, int (*above) (const void* elem)) +{ + size_t lower_idx = 0; // lower boundary of the narrowed zone + size_t upper_idx = num_elem; // upper boundary of the narrowed zone + size_t mid_idx; + + while (lower_idx < upper_idx) + { + + mid_idx = (lower_idx + upper_idx) >> 1; + if (above (data + (mid_idx * elem_size))) // key lower then mid + upper_idx = mid_idx; + else // key greater or equal to mid + lower_idx = mid_idx; + } + return data + (lower_idx * elem_size); +} + +const void* tmap_binary_search_nokey_no_fix_possible (const void* data, size_t num_elem, size_t elem_size, int (*above) (const void* elem)) { size_t lower_idx = 0; // lower boundary of the narrowed zone size_t upper_idx = num_elem; // upper boundary of the narrowed zone @@ -44,11 +92,30 @@ const void* tmap_binary_search_nokey (const void* data, size_t num_elem, size_t if (above (data + (mid_idx * elem_size))) // key lower then mid upper_idx = mid_idx; else // key greater or equal to mid + { + if (lower_idx == mid_idx) // DK: search point is at or above lower_idx but below lower_idx + 1. + // if it is at the lower_idx, the lower_idx should be returned + // if it is above, the lower_idx+1 should be returned + // if only 'above' function is provided, there is no way to distinguish these cases + // match check is needed. This is a fundamental flaw in this algorithm design. + // Verdict: Not fixable without changing call signature. + { + ++lower_idx; + break; + } lower_idx = mid_idx; + } } return data + (lower_idx * elem_size); } +const void* tmap_binary_search_nokey (const void* data, size_t num_elem, size_t elem_size, int (*above) (const void* elem)) +{ + tmap_failure ("Internal error- the function tmap_binary_search_nokey is called which has no correct implementation"); + return NULL; +} + + // the above functions can be improved to handle 'lucky strikes' if check for the equality in some form is available, or if no restriction on the comparison order is given int lt_uint (const void* k, const void* e) diff --git a/Analysis/TMAP/src/util/tmap_bsearch.h b/Analysis/TMAP/src/util/tmap_bsearch.h index 59578b5e..40d65eb6 100644 --- a/Analysis/TMAP/src/util/tmap_bsearch.h +++ b/Analysis/TMAP/src/util/tmap_bsearch.h @@ -11,11 +11,14 @@ extern "C" #endif // binary search for sorted arrays. Handles omitted keys -// passed in 'lt' function should compare the key pointed to by the first argument to the data element pointed to by the second argument, in this order -// returns the pointer to the first key that is not lower than the passed one. +// passed in 'lt' function should be symmetric with respect to key and data pointers: (the bsearch would call it as lt (*key, *data) as well as lt (*data, *key)) +// returns the pointer to the first data element that is not lower than the passed key (could be equal to the key). +// if there is no such entries in the passed array, returns a pointer to the upper array boudary (one position above the last element in the array, == (data + num_elem)) // for multiple occurences returns pointer to the lowest occurence // performance is always ln(N), no worst/best case difference (each search on the array of given size takes same number of steps) -const void* tmap_binary_search (const void* key, const void* data, size_t num_elem, size_t elem_size, int (*lt) (const void* key, const void* elem)); +const void* tmap_binary_search_fixed (const void* key, const void* data, size_t num_elem, size_t elem_size, int (*lt) (const void* key, const void* elem)); + +#define tmap_binary_search tmap_binary_search_fixed // 'keyless' variant of the binary search // the passed in 'above' function should return 1 when the data element pointed by the argument is above the desired position, 0 otherwise diff --git a/Analysis/TMAP/src/util/tmap_definitions.c b/Analysis/TMAP/src/util/tmap_definitions.c index 6d43e212..f4ef45a4 100644 --- a/Analysis/TMAP/src/util/tmap_definitions.c +++ b/Analysis/TMAP/src/util/tmap_definitions.c @@ -682,7 +682,7 @@ tmap_detect_cpus() if (sysctl(mib, 2, &ncpu, &len, 0, 0) < 0 || len != sizeof(ncpu)) ncpu = 1; #elif defined(_SC_NPROCESSORS_ONLN) - ncpu = sysconf(_SC_NPROCESSORS_ONLN); + ncpu = sysconf(_SC_NPROCESSORS_ONLN)/2; #elif defined(WIN32) SYSTEM_INFO si; GetSystemInfo(&si); diff --git a/Analysis/TMAP/src/util/tmap_error.h b/Analysis/TMAP/src/util/tmap_error.h index f2ba367c..62eeef30 100644 --- a/Analysis/TMAP/src/util/tmap_error.h +++ b/Analysis/TMAP/src/util/tmap_error.h @@ -46,7 +46,7 @@ enum { ReadFileError, /*!< could not read from a file */ WriteFileError, /*!< could not write from a file */ EndOfFile, /*!< reached the end-of-file prematurely */ - ThreadError, /*!< error starting/joining threads */ + ThreadError, /*!< error starting/joining threads or mantaining sync control structure */ SigInt, /*!< SIGINT signal caught */ SharedMemoryGet, /*!< could not get the shared memory */ SharedMemoryAttach, /*!< could not attach the shared memory */ diff --git a/Analysis/TMAP/src/util/tmap_histo.c b/Analysis/TMAP/src/util/tmap_histo.c index 61ac65fe..e485fe34 100644 --- a/Analysis/TMAP/src/util/tmap_histo.c +++ b/Analysis/TMAP/src/util/tmap_histo.c @@ -45,12 +45,51 @@ int int64_cmp (const void* i1, const void* i2) else return 1; } +int double_cmp (const void* i1, const void* i2) +{ + if (*(double *) i1 < *(double *) i2) return -1; + else if (*(double *) i1 == *(double *) i2) return 0; + else return 1; +} + +// #define USE_TMAP_HISTO_LOCAL_BSEARCH +#if defined (USE_TMAP_HISTO_LOCAL_BSEARCH) +typedef int (*compar_fn_t) (const void *, const void *); + +void* local_bsearch (const void *key, const void *base, size_t nmemb, size_t size, compar_fn_t compar) +{ + size_t l, u, idx; + const void *p; + int comparison; + + l = 0; + u = nmemb; + while (l < u) + { + idx = (l + u) / 2; + p = (void *) (((const char *) base) + (idx * size)); + comparison = (*compar) (key, p); + if (comparison < 0) + u = idx; + else if (comparison > 0) + l = idx + 1; + else + return (void *) p; + } + + return (void *) (((const char *) base) + (l * size));; +} +#endif + void add_to_hist64i (uint64_t* hist, size_t bin_cnt, int64_t* bin_lower_bounds, int64_t value) { // find the bin: do linear search to save on recurrent calls (and on implementation, as bsearch does not fit :) // DK: tmap_binary_search is flawed (enters infine loop when searching for a value equal to first element in the array) - // const int64_t* bound = tmap_binary_search (&value, bin_lower_bounds, bin_cnt, sizeof (int64_t), lt_int); - const int64_t* bound = bsearch (&value, bin_lower_bounds, bin_cnt, sizeof (int64_t), int64_cmp); + // DK: 12/3/2020: Fixed tmap_binary_search + + const int64_t* bound = tmap_binary_search (&value, bin_lower_bounds, bin_cnt, sizeof (int64_t), lt_int); + // const int64_t* bound = bsearch (&value, bin_lower_bounds, bin_cnt, sizeof (int64_t), int64_cmp); + // const int64_t* bound = (const int64_t*) binary_search (&value, bin_lower_bounds, bin_cnt, sizeof (int64_t), int64_cmp); // get bin index size_t idx = bound - bin_lower_bounds; // increment histogram bin value @@ -61,6 +100,7 @@ void add_to_hist64d (uint64_t* hist, size_t bin_cnt, double* bin_lower_bounds, d { // find the bin: do linear search to save on recurrent calls (and on implementation, as bsearch does not fit :) const double* bound = tmap_binary_search (&value, bin_lower_bounds, bin_cnt, sizeof (double), lt_double); + // const double* bound = (const double*) local_bsearch (&value, bin_lower_bounds, bin_cnt, sizeof (double), double_cmp); // get bin index size_t idx = bound - bin_lower_bounds; // increment bin value diff --git a/Analysis/VariantCaller/Bookkeeping/VcfFormat.cpp b/Analysis/VariantCaller/Bookkeeping/VcfFormat.cpp index 7b78a84d..da23fa21 100644 --- a/Analysis/VariantCaller/Bookkeeping/VcfFormat.cpp +++ b/Analysis/VariantCaller/Bookkeeping/VcfFormat.cpp @@ -166,7 +166,7 @@ string getVCFHeader(const ExtendParameters *parameters, ReferenceReader& ref_rea << "##INFO=" << endl; } if (parameters->my_controls.report_ppa){ - headerss << "##INFO=" << endl; + headerss << "##INFO=" << endl; } if (parameters->my_controls.disable_filters){ headerss << "##INFO=" << endl diff --git a/Analysis/VariantCaller/EnsembleEval/StackEngine.cpp b/Analysis/VariantCaller/EnsembleEval/StackEngine.cpp index 0fcef529..ce8b098c 100644 --- a/Analysis/VariantCaller/EnsembleEval/StackEngine.cpp +++ b/Analysis/VariantCaller/EnsembleEval/StackEngine.cpp @@ -205,11 +205,34 @@ void HypothesisStack::AllocateFrequencyStarts(int num_hyp_no_null, vector fake_hs_alleles; fake_hs_alleles.reserve(num_hyp_no_null - 1); + // Find best alt allele from AO + int best_i_alt = -1; + int best_ao = 0; + // Find AO + map >::const_iterator ao_it = variant->info.find("AO"); + if (ao_it != variant->info.end() and ao_it->second.size() == variant->alt.size()){ + for (int i_alt = 0; i_alt < (int) ao_it->second.size(); ++i_alt){ + if (ao_it->second.at(i_alt) == "."){ + best_i_alt = -1; + break; + } + int ao = stoi(ao_it->second.at(i_alt)); + if (ao > best_ao){ + best_ao = ao; + best_i_alt = i_alt; + } + } + } + // try pure frequencies for the alleles if(try_alternatives){ // try pure frequencies for alt alleles for(int i_hyp = 1; i_hyp < num_hyp_no_null; ++i_hyp){ int i_alt = i_hyp - 1; + // Pure frequency for the best alt allele only. + if (i_alt != best_i_alt and best_i_alt >= 0){ + continue; + } if (allele_identity_vector[i_alt].status.isFakeHsAllele){ // I don't want to try the pure freq for a fake hs allele/ fake_hs_alleles.push_back(i_hyp); diff --git a/Analysis/VariantCaller/HandleVariant.cpp b/Analysis/VariantCaller/HandleVariant.cpp index eacde178..87481046 100644 --- a/Analysis/VariantCaller/HandleVariant.cpp +++ b/Analysis/VariantCaller/HandleVariant.cpp @@ -89,8 +89,9 @@ void OverrideMinVarCov(int fd_nonsnp_min_var_cov, vector& variant_specific_params) { assert(allele_identity_vector.size() + 1 == global_flow_disruptive_matrix.size()); - if (fd_nonsnp_min_var_cov < 1) + if (fd_nonsnp_min_var_cov < 1){ return; + } for (unsigned int i_alt = 0; i_alt < allele_identity_vector.size(); ++i_alt){ // Override min_var_coverage of the allele if all the following are satisfied diff --git a/Analysis/VariantCaller/tvcutils/prepare_hotspots.cpp b/Analysis/VariantCaller/tvcutils/prepare_hotspots.cpp index 62933853..ca1a8a69 100644 --- a/Analysis/VariantCaller/tvcutils/prepare_hotspots.cpp +++ b/Analysis/VariantCaller/tvcutils/prepare_hotspots.cpp @@ -694,6 +694,8 @@ int PrepareHotspots(int argc, const char *argv[]) // Process custom tags vector bstrand; vector hp_max_length; + vector oid; + vector omapalt; string raw_oid; string raw_omapalt; string raw_oalt; @@ -753,6 +755,10 @@ int PrepareHotspots(int argc, const char *argv[]) split(raw_bstrand, ',', bstrand); if (not raw_hp_max_length.empty()) split(raw_hp_max_length, ',', hp_max_length); + if (not raw_oid.empty()) + split(raw_oid, ',', oid); + if (not raw_omapalt.empty()) + split(raw_omapalt, ',', omapalt); } @@ -784,14 +790,19 @@ int PrepareHotspots(int argc, const char *argv[]) continue; } unsigned int allele_idx = 0; - for (char *sub_alt = strtok(current_alt,","); sub_alt; sub_alt = strtok(NULL,",")) { + // the below is wrong, since the alt list has to match to the omapalt to get the correct index. + if (oid.empty() or oid.size() != omapalt.size()) { + for (char *sub_alt = strtok(current_alt,","); sub_alt; sub_alt = strtok(NULL,",")) { Allele allele; allele.chr_idx = chr_idx; allele.ref = current_ref; allele.alt = sub_alt; allele.pos = strtol(current_start,NULL,10)-1; - allele.id = current_id; + if (allele_idx < oid.size()) + allele.id = oid[allele_idx]; + else + allele.id = current_id; if (allele.id == ".") allele.id = "hotspot"; @@ -818,7 +829,42 @@ int PrepareHotspots(int argc, const char *argv[]) line_status.back().opos = allele.opos; line_status.back().id = allele.id; allele_idx++; - } + } + } else { + for (allele_idx = 0; allele_idx < oid.size(); allele_idx++) { + Allele allele; + allele.chr_idx = chr_idx; + allele.ref = current_ref; + allele.alt = omapalt[allele_idx]; + allele.pos = strtol(current_start,NULL,10)-1; + allele.id = oid[allele_idx]; + if (allele.id == ".") + allele.id = "hotspot"; + + allele.filtered = false; + line_status.push_back(LineStatus(line_number)); + allele.line_status = &line_status.back(); + allele.opos = allele.pos; + allele.oref = allele.ref; + allele.oalt = allele.alt; + + if (allele_idx < bstrand.size()) { + if (bstrand[allele_idx] != ".") + allele.custom_tags["BSTRAND"] = bstrand[allele_idx]; + } + + if (allele_idx < hp_max_length.size()) { + if (hp_max_length[allele_idx] != ".") + allele.custom_tags["hp_max_length"] = hp_max_length[allele_idx]; + } + + alleles[allele.chr_idx].push_back(allele); + //line_status.back().allele = &alleles[allele.chr_idx].back(); + line_status.back().chr_idx = allele.chr_idx; + line_status.back().opos = allele.opos; + line_status.back().id = allele.id; + } //for + } // else } fclose(input); diff --git a/Analysis/VariantCaller/tvcutils/unify_vcf.cpp b/Analysis/VariantCaller/tvcutils/unify_vcf.cpp index 04b9d24e..d2eab72f 100644 --- a/Analysis/VariantCaller/tvcutils/unify_vcf.cpp +++ b/Analysis/VariantCaller/tvcutils/unify_vcf.cpp @@ -491,11 +491,24 @@ void VcfOrderedMerger::perform() { allele_subset.print_stats(); } +//static string get_gt(map > & sampleOutput) +string get_gt(vcf::Variant *v) +{ + if (v->samples.empty()) return "./."; + map > & sampleOutput = v->samples[v->sampleNames[0]]; + map >::const_iterator itg = sampleOutput.find("GT"); + if (itg == sampleOutput.end()) return "./."; + return itg->second[0]; +} + + static bool in_gt(vcf::Variant *v, int i, bool &alt_called) { alt_called = false; string gt_field; - stringstream gt(v->samples[v->sampleNames[0]]["GT"][0]); + //stringstream gt(v->samples[v->sampleNames[0]]["GT"][0]); + //stringstream gt(get_gt(v->samples[v->sampleNames[0]])); + stringstream gt(get_gt(v)); while (getline(gt, gt_field, '/')){ if (gt_field!="."){ int called_allele = std::stoi(gt_field); @@ -650,7 +663,8 @@ vcf::Variant* VcfOrderedMerger::merge_overlapping_variants() { vcf::Variant& novel_v = *novel_queue.current(); vcf::Variant& assembly_v = *assembly_queue.current(); - string gt = novel_queue.current()->samples[novel_queue.current()->sampleNames[0]]["GT"][0]; + //string gt = get_gt(novel_queue.current()->samples[novel_queue.current()->sampleNames[0]]); + string gt = get_gt(novel_queue.current()); if (false /*(gt == "./." || gt == "0/0"*/) { // Logging novel and indel merge cout << UNIFY_VARIANTS " Advanced merge of IndelAssembly variant " << assembly_queue.current()->sequenceName @@ -765,7 +779,9 @@ bool VcfOrderedMerger::find_match_new(vcf::Variant* merged_entry, vcf::Variant* if (left+*omapalti+right == ll+*omapalt+rr) { idx = omapalti-merged_entry->info["OMAPALT"].begin()+1; string gt_field; - stringstream gt(merged_entry->samples[merged_entry->sampleNames[0]]["GT"][0]); + //stringstream gt(merged_entry->samples[merged_entry->sampleNames[0]]["GT"][0]); + //stringstream gt(get_gt(merged_entry->samples[merged_entry->sampleNames[0]])); + stringstream gt(get_gt(merged_entry)); gt_v = 4; while (getline(gt, gt_field, '/')){ //if (pos == 7578381 and hotspot->position == 7578383) cerr << "gt_field=" << gt_field << endl; @@ -975,7 +991,8 @@ void VcfOrderedMerger::annotate_subset(vcf::Variant* variant) { // unpack called alleles -- First genotype then PPA set called_alts; - string gt_str = variant->samples[variant->sampleNames[0]]["GT"][0]; + //string gt_str = get_gt(variant->samples[variant->sampleNames[0]]); + string gt_str = get_gt(variant); genotype_to_set(called_alts, gt_str, '/'); map >::iterator it; diff --git a/Analysis/Wells/RawWells.cpp b/Analysis/Wells/RawWells.cpp index 7db68614..d2214d9d 100644 --- a/Analysis/Wells/RawWells.cpp +++ b/Analysis/Wells/RawWells.cpp @@ -283,8 +283,10 @@ RawWells::RawWells() { mSaveAsUShort = false; Init ("", "", 0,0,0); + mIs_copy=1; } + RawWells::RawWells ( const char *experimentPath, const char *rawWellsName, int rows, int cols ) { mSaveAsUShort = false; @@ -315,11 +317,13 @@ RawWells::~RawWells() { Close(); // JZ add for multithreading - CleanupHdf5(); + if(!mIs_copy) + CleanupHdf5(); } void RawWells::Init ( const char *experimentPath, const char *rawWellsName, int rows, int cols, int flows ) { + mIs_copy=0; mSaveCopies = false; mSaveRes = false; mConvertWithCopies = true; @@ -356,6 +360,59 @@ void RawWells::Init ( const char *experimentPath, const char *rawWellsName, int } +void RawWells::Init ( RawWells &rw) +{ + mIs_copy=1; + + mDirectory = rw.mDirectory; + mFileLeaf = rw.mFileLeaf; + mFilePath = rw.mFilePath; + mFlowOrder = rw.mFlowOrder; + mRows = rw.mRows; + mCols = rw.mCols; + mFlows = rw.mFlows; + mCurrentWell = rw.mCurrentWell; + WELL_NOT_LOADED = rw.WELL_NOT_LOADED; + WELL_NOT_SUBSET = rw.WELL_NOT_SUBSET; + mSaveCopies = rw.mSaveCopies; + mSaveRes = rw.mSaveRes; + mConvertWithCopies = rw.mConvertWithCopies; + //mInfo = rw.mInfo; + mRankData = rw.mRankData; + mStepSize = rw.mStepSize; + mCompression = rw.mCompression; + mHFile = rw.mHFile; + mWriteOnClose = rw.mWriteOnClose; + mRanks.copy(rw.mRanks); + mWells.copy(rw.mWells); + mResErr.copy(rw.mResErr); + mInfoKeys.copy(rw.mInfoKeys); + mInfoValues.copy(rw.mInfoValues); + mWellChunkSizeRow = rw.mWellChunkSizeRow; + mWellChunkSizeCol = rw.mWellChunkSizeCol; + mWellChunkSizeFlow = rw.mWellChunkSizeFlow; + mCurrentRegionRow = rw.mCurrentRegionRow; + mCurrentRegionCol = rw.mCurrentRegionCol; + mCurrentRow = rw.mCurrentRow; + mCurrentCol = rw.mCurrentCol; + mFirsttimeGetRegionData = rw.mFirsttimeGetRegionData; + mIsLegacy = rw.mIsLegacy; + mSaveAsUShort = rw.mSaveAsUShort; + mLower = rw.mLower; + mUpper = rw.mUpper; + + //WellData data; ///< For returning pointers to internal object, all memory owned internally + +// WellChunk mChunk; +// std::vector mIndexes; ///< Conversion of well index on chip to index in mFlowData below. +// std::vector mFlowData; ///< Big chunk of data... +// std::vector mResData; ///< residual error + + mWellsCopies.resize(mRows * mCols, 1.0); + mWellsCopies2.resize(mRows * mCols, 1.0); +} + + void RawWells::CreateEmpty ( int numFlows, const char *flowOrder, int rows, int cols ) { SetRows ( rows ); @@ -1438,6 +1495,7 @@ void RawWells::OpenWellsToRead() InitIndexes(); } + void RawWells::OpenResToRead() { mResErr.Close(); @@ -1740,8 +1798,11 @@ void RawWells::ReadWells() uint64_t localCount = 0; for ( size_t row = currentRowStart; row < currentRowEnd; row++ ) { + int32_t dbidxr=GetInternalIndex(row,currentColStart); + for ( size_t col = currentColStart; col < currentColEnd; col++ ) { + int dbidx=dbidxr+col-currentColStart; int idx = ToIndex ( col, row ); if ( mIndexes[idx] >= 0 ) { @@ -1755,7 +1816,7 @@ void RawWells::ReadWells() else val = -1.0; } - Set ( row, col, flow, val ); + WriteFlowgramWithIndex(flow,dbidx,val); } } localCount++; @@ -1969,6 +2030,12 @@ float RawWells::AtWithoutChecking ( size_t row, size_t col, size_t flow ) const return AtWithoutChecking ( ToIndex ( col,row ), flow ); } + +int32_t RawWells::GetInternalIndex(size_t row, size_t col) const +{ + return mIndexes[ToIndex ( col,row )]; +} + float RawWells::AtWithoutChecking ( size_t well, size_t flow ) const { uint64_t ii = ( uint64_t ) mIndexes[well] * mChunk.flowDepth + flow - mChunk.flowStart; @@ -2108,7 +2175,8 @@ void RawWells::CloseWithoutCleanupHdf5() void RawWells::Close() { CloseWithoutCleanupHdf5(); - CleanupHdf5(); + if(!mIs_copy) + CleanupHdf5(); } void RawWells::GetRegion ( int &rowStart, int &height, int &colStart, int &width ) diff --git a/Analysis/Wells/RawWells.h b/Analysis/Wells/RawWells.h index 169b30a9..14e5369f 100644 --- a/Analysis/Wells/RawWells.h +++ b/Analysis/Wells/RawWells.h @@ -71,6 +71,17 @@ class RWH5DataSet { bool mSaveAsUShort; float mLower; float mUpper; + + void copy(RWH5DataSet &other){ + mGroup=other.mGroup.c_str(); + mName=other.mName.c_str(); + mDataset=other.mDataset; + mDatatype=other.mDatatype; + mDataspace=other.mDataspace; + mSaveAsUShort=other.mSaveAsUShort; + mLower=other.mLower; + mUpper=other.mUpper; + }; }; @@ -269,6 +280,8 @@ class RawWells { /* Initialization and setup. */ void Init(const char *experimentPath, const char *rawWellsName, int rows, int col, int flows); + void Init ( RawWells &rw ); + void CreateEmpty(int numFlows, const char *flowOrder, int rows, int cols); void CreateEmpty(int numFlows, const char *flowOrder); void SetRegion(int rowStart, int height, int colStart, int width); @@ -319,6 +332,20 @@ class RawWells { float At(size_t well, size_t flow) const; float AtWithoutChecking(size_t row, size_t col, size_t flow) const; float AtWithoutChecking(size_t well, size_t flow) const; + inline float AtWithIndex(uint64_t index, size_t flow) const{ + return mFlowData[( uint64_t ) index * mChunk.flowDepth + flow - mChunk.flowStart]; + } + inline void AtFlowsWithIndex(uint64_t index, float *data) const + { + const float *tmp = &mFlowData[( uint64_t ) index * mChunk.flowDepth]; + int len= mChunk.flowDepth - mChunk.flowStart; + for(int flow=0; flow < len; flow++){ + data[flow]=tmp[flow]; + } + } + + + int32_t GetInternalIndex(size_t row, size_t col) const; float GetCopyCount(size_t row, size_t col) const; float GetCopyCount(size_t well) const; @@ -335,7 +362,9 @@ class RawWells { virtual void WriteFlowgram(size_t flow, size_t x, size_t y, float val, float copies); virtual void WriteFlowgram(size_t flow, size_t x, size_t y, float val, float copies, float resError); virtual void WriteFlowgramWithRes ( size_t flow, size_t x, size_t y, float val, float resError ); - + inline void WriteFlowgramWithIndex(size_t flow, int32_t index, float val){ + mFlowData[( uint64_t ) index * mChunk.flowDepth + flow - mChunk.flowStart] = val; + } void ResetCurrentWell() { mCurrentWell = 0; } void ResetCurrentRegionWell() { mCurrentRow = 0, mCurrentCol = 0, mFirsttimeGetRegionData = true, mCurrentRegionRow = 0, mCurrentRegionCol = 0; } @@ -461,7 +490,8 @@ class RawWells { size_t mStepSize; int mCompression; ///< What level of compression is being used. hid_t mHFile; ///< Id for hdf5 file operations. - + bool mIs_copy; + bool mWriteOnClose; ///< To support legacy api have a flag for writing when closing RWH5DataSet mRanks; ///< Ranks hdf5 dataset diff --git a/Analysis/Wells/WellsManager.cpp b/Analysis/Wells/WellsManager.cpp index 142abf2a..f5cb4d2f 100644 --- a/Analysis/Wells/WellsManager.cpp +++ b/Analysis/Wells/WellsManager.cpp @@ -2,13 +2,44 @@ #include "WellsManager.h" +#include "pthread.h" + + +WellsManager::WellsManager( WellsManager *rw) +: + keys_(rw->keys_), + chunk_size_row_(rw->chunk_size_row_), + chunk_size_col_(rw->chunk_size_col_), + chunk_size_flow_(rw->chunk_size_flow_), + do_norm_(rw->do_norm_), + compress_multi_taps_(rw->compress_multi_taps_), + chip_type_(rw->chip_type_), + num_flows_(rw->num_flows_), + verbose_(rw->verbose_), + ion_flow_order(rw->ion_flow_order), + read_class_map(rw->read_class_map) +{ + + raw_wells_.resize(rw->raw_wells_.size()); + for (unsigned int i=0; iraw_wells_.size(); ++i){ + raw_wells_.at(i).Init(rw->raw_wells_.at(i)); + } + if(do_norm_){ + wells_norm_.resize(raw_wells_.size()); + for (unsigned int i=0; i &wells_file_names, bool verbose) : chunk_size_row_(0), chunk_size_col_(0), chunk_size_flow_(0), do_norm_(false), compress_multi_taps_(true), chip_type_("unknown"), num_flows_(0), verbose_(verbose), - ion_flow_order(NULL), read_class_map(NULL) + norm_method_(""), ion_flow_order(NULL), read_class_map(NULL) { raw_wells_.resize(wells_file_names.size()); if (verbose) { @@ -96,11 +127,16 @@ void WellsManager::OpenForIncrementalRead() void WellsManager::LoadChunk(size_t rowStart, size_t rowHeight, size_t colStart, size_t colWidth, - size_t flowStart, size_t flowDepth) + size_t flowStart, size_t flowDepth, + pthread_mutex_t *mutex) { for (unsigned int i=0; i0 and ion_flow_order->nuc_at(flow-1)== ion_flow_order->nuc_at(flow)){ wells_measurements[flow] = 0.0; - wells_measurements[sig_idx] += raw_wells_[0].At(row,col,flow); + wells_measurements[sig_idx] += raw_wells_[0].AtWithIndex(idx,flow); } else { sig_idx = flow; - wells_measurements[flow] = raw_wells_[0].At(row,col,flow); + wells_measurements[flow] = raw_wells_[0].AtWithIndex(idx,flow); } } } - else //*/ + else { + int32_t idx=raw_wells_[0].GetInternalIndex(row,col); for (int flow = 0; flow < num_flows; ++flow) - wells_measurements[flow] = raw_wells_[0].At(row,col,flow); - + wells_measurements[flow] = raw_wells_[0].AtWithIndex(idx,flow); + } NaNcheck(row, col, num_flows, wells_measurements); } diff --git a/Analysis/Wells/WellsManager.h b/Analysis/Wells/WellsManager.h index e1b52d85..bae6f3b3 100644 --- a/Analysis/Wells/WellsManager.h +++ b/Analysis/Wells/WellsManager.h @@ -29,6 +29,7 @@ class WellsManager { string flow_order_; unsigned int num_flows_; bool verbose_; + string norm_method_; //unsigned int num_verbose_; public: @@ -37,17 +38,20 @@ class WellsManager { ReadClassMap const *read_class_map; WellsManager(const vector & wells_file_names, bool verbose); + WellsManager( WellsManager *rw); int NumWells() const { return raw_wells_.size(); }; void OpenForIncrementalRead(); + void Close(); void LoadChunk(size_t rowStart, size_t rowHeight, size_t colStart, size_t colWidth, - size_t flowStart, size_t flowDepth); + size_t flowStart, size_t flowDepth, + pthread_mutex_t *mutex=NULL); void SetWellsContext( ion::FlowOrder const *flow_order, diff --git a/Analysis/config/args_GX9v1_analysis.json b/Analysis/config/args_GX9v1_analysis.json new file mode 100644 index 00000000..a5b36901 --- /dev/null +++ b/Analysis/config/args_GX9v1_analysis.json @@ -0,0 +1,206 @@ +{ + "BkgModelControlOpts" : { + "bkg-dont-emphasize-by-compression" : 1, + "bkg-washout-flow-detection" : 6, + "bkg-washout-threshold" : 2.0, + "clonal-filter-bkgmodel" : true, + "clonal-filter-debug" : false, + "clonal-filter-use-last-iter-params" : true, + "filter-extreme-ppf-only" : false, + "max-iterations" : 30, + "mixed-first-flow" : 12, + "mixed-last-flow" : 72, + "mixed-model-option" : 0, + "mixed-stringency" : 0.50, + "n-unfiltered-lib" : 100000, + "nokey" : false, + "restart-region-params-file" : "", + "sigproc-regional-smoothing-alpha" : 1.0, + "sigproc-regional-smoothing-gamma" : 1.0, + "xtalk-correction" : false + }, + "DebugMe" : { + "bkg-dbg-trace" : [], + "bkg-debug-files" : false, + "bkg-debug-nsamples" : 9, + "bkg-debug-param" : 1, + "bkg-debug-region" : [ -1, -1 ], + "bkg-debug-trace-rcflow" : "", + "bkg-debug-trace-sse" : "", + "bkg-debug-trace-xyflow" : "", + "debug-bead-only" : true, + "region-vfrc-debug" : false + }, + "FlowContext" : { + "flow-order" : "", + "flowlimit" : -1, + "start-flow-plus-interval" : [ 0, 0 ] + }, + "GlobalDefaultsForBkgModel" : { + "barcode-spec-file" : "", + "bkg-dont-emphasize-by-compression" : false, + "bkg-well-xtalk-name" : "/opt/ion/config/xtalk.p2.2.1.settings.20140120.json", + "gopt" : "default", + "xtalk" : "disable" + }, + "GpuControlOpts" : { + "gpu-amp-guess" : 1, + "gpu-device-ids" : [], + "gpu-fitting-only" : true, + "gpu-flow-by-flow" : false, + "gpu-hybrid-fit-iter" : 3, + "gpu-multi-flow-fit" : 1, + "gpu-multi-flow-fit-blocksize" : 128, + "gpu-multi-flow-fit-l1config" : -1, + "gpu-num-history-flows" : 10, + "gpu-num-streams" : 2, + "gpu-partial-deriv-blocksize" : 128, + "gpu-partial-deriv-l1config" : -1, + "gpu-single-flow-fit" : 1, + "gpu-single-flow-fit-blocksize" : -1, + "gpu-single-flow-fit-l1config" : -1, + "gpu-single-flow-fit-type" : 3, + "gpu-switch-to-flow-by-flow-at" : 20, + "gpu-use-all-devices" : false, + "gpu-verbose" : false, + "gpuworkload" : 1.0, + "post-fit-handshake-worker" : true + }, + "ImageControlOpts" : { + "acqPrefix" : "acq_", + "col-doubles-xtalk-correct" : false, + "col-flicker-correct" : true, + "col-flicker-correct-aggressive" : true, + "col-flicker-correct-verbose" : false, + "corr-noise-correct" : true, + "dat-postfix" : "dat", + "flowtimeoffset" : 1000, + "fluid-potential-correct" : false, + "fluid-potential-threshold" : 1.0, + "frames" : -1, + "hilowfilter" : false, + "ignore-checksum-errors" : false, + "ignore-checksum-errors-1frame" : 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"ObsoleteOpts" : { + "forcenn" : 0, + "nuc-correct" : 0, + "use-pinned" : false + }, + "SignalProcessingBlockControl" : { + "bkg-bfmask-update" : false, + "numcputhreads" : 0, + "restart-check" : true, + "restart-from" : "", + "restart-next" : "", + "sigproc-compute-flow" : "", + "wells-compression" : 0, + "wells-save-flow" : 60, + "wells-save-freq" : -1 + }, + "SpatialContext" : { + "analysis-region" : [], + "cropped" : [], + "cropped-region-origin" : [], + "region-size" : [ 216, 224 ] + }, + "SystemContext" : { + "dat-source-directory" : "", + "explog-path" : "", + "local-wells-file" : false, + "no-subdir" : true, + "output-dir" : "", + "region-list" : [], + "stack-dump-file" : "", + "well-stat-file" : "", + "wells-convert-high" : 28.0, + "wells-convert-low" : -5.0, + "wells-convert-with-copies" : true, + "wells-format" : "hdf5", + "wells-save-as-ushort" : true, + "wells-save-number-copies" : true, + "wells-save-queue-size" : 0 + }, + "ThumbnailControl" : { + 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a/Analysis/config/gopt_GX9v1.param.json b/Analysis/config/gopt_GX9v1.param.json new file mode 100644 index 00000000..2691b214 --- /dev/null +++ b/Analysis/config/gopt_GX9v1.param.json @@ -0,0 +1,65 @@ +{ + "metadata": { + "compatible_chip_type": "GX9v1", + "created": "2015-05-14 11:25:51.416860", + "optimizable params": "km_const(1-4), krate(6-9), d_coeff(11-14), sigma_mult(16-19), t_mid_nuc_delay(21-24), sens(25), tau_R_m(26), tau_R_o(27), emphasis(28-35), emp_amplitude(36), emp_width(37), clonal_call_scale(38-42), tau_E(43), min_tauB/max_tauB/mid_tauB(44/45/46)", + "source": "gopt", + "version": 1 + }, + "parameters": { + "clonal_call_scale": [ + 0.56925, + 0.0396, + 0.0525, + 0.234, + 0.76275 + ], + "d_coeff": [ + 115.814957, + 137.319839, + 164.406784, + 136.495712 + ], + "emp_amplitude": 10.41, + "emp_width": 5.863, + "emphasis": [ + 3.500887, + 1.423262, + 0.85275, + 0.686812, + 11.354063, + 0.426375, + 0.16335, + 30.405375 + ], + "km_const": [ + 22.251457, + 24.723841, + 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1.43371 2 5 0.144355 -0.8098 9758 9 +1.02577 1.43371 1 5 0.144355 -0.8098 4290 9 +1.02577 1.43371 0 3 0.537133 -0.837831 52103 9 +1.02577 0.24279 4 2 0.537133 0 1068 9 +0.026834 1.43371 2 5 0.144355 -0.760692 16266 9 +1.02577 0.152455 4 4 0.537133 0 1069 9 +0.011011 1.43371 0 5 0.537133 -0.864334 1389 9 +0.021285 1.43371 8 5 0.120239 0 9913 9 +0.011524 1.43371 0 5 0.537133 -0.8098 4518 9 +0.015706 1.43371 0 5 0.537133 -0.886424 1035 9 +1.02577 1.43371 3 1 0.537133 -0.8098 3550 9 +0.026834 1.43371 1 5 0.120239 0 4486 9 +1.02577 1.43371 8 4 0.144355 -0.760692 8311 9 +0.015706 1.43371 0 5 0.537133 -0.873493 2324 9 +0.014132 1.43371 0 4 0.537133 -0.837831 3598 9 +0.021285 0.24279 1 4 0.537133 0 1012 9 +0.026834 0.24279 0 4 0.537133 0 1018 9 +0.017996 1.43371 0 4 0.537133 -0.864334 2365 9 +0.021285 1.43371 0 4 0.537133 -0.88069 2993 8 +0.012997 1.43371 0 4 0.537133 -0.8098 1100 8 +0.021285 1.43371 0 4 0.537133 -0.873493 1084 8 +0.017996 1.43371 0 4 0.537133 -0.853228 1808 8 +0.014132 1.43371 3 1 0.537133 0 1276 8 +0.026834 1.43371 1 3 0.537133 -0.897588 2603 8 +1.02577 1.43371 0 4 0.120239 0 1285 8 +0.026834 1.43371 0 3 0.537133 -0.8098 7220 8 +0.012997 1.43371 0 5 0.537133 -0.8098 1329 8 +1.02577 1.43371 3 1 0.537133 0 49550 8 +1.02577 0.186669 3 5 0.537133 -0.760692 1003 8 +1.02577 1.43371 1 2 0.537133 -0.897588 2126 8 +1.02577 1.43371 1 3 0.537133 -0.853228 96831 8 +0.026834 1.43371 2 3 0.537133 -0.890871 1080 8 +0.026834 1.43371 0 4 0.537133 -0.894537 1226 8 +0.021285 1.43371 0 4 0.537133 -0.837831 7300 8 +0.026834 1.43371 0 4 0.537133 -0.837831 11563 8 +1.02577 1.43371 1 4 0.120239 0 4219 8 +0.017996 1.43371 1 4 0.537133 -0.853228 1070 8 +0.015706 1.43371 0 3 0.537133 -0.760692 6294 8 +1.02577 0.24279 1 5 0.105575 0 1272 8 +0.015706 1.43371 0 4 0.537133 -0.8098 2012 8 +0.014132 1.43371 0 5 0.537133 -0.8098 1032 8 +1.02577 0.24279 3 4 0.144355 0 2222 8 +1.02577 1.43371 1 3 0.537133 -0.837831 32114 8 +0.021285 1.43371 1 4 0.537133 -0.837831 1223 9 +0.026834 1.43371 1 3 0.537133 -0.8098 22041 8 +0.017996 1.43371 8 5 0.144355 0 13042 8 +1.02577 1.43371 2 3 0.120239 0 1458 8 +0.026834 1.43371 1 4 0.537133 -0.853228 1253 8 +1.02577 0.186669 3 4 0.537133 0 1213 8 +0.021285 1.43371 0 4 0.537133 -0.8098 4342 8 +0.015706 1.43371 0 5 0.537133 -0.8098 1397 8 +1.02577 0.24279 3 3 0.537133 0 1197 8 +0.017996 1.43371 0 3 0.537133 -0.760692 3258 8 +1.02577 1.43371 1 2 0.537133 -0.8098 14817 8 +0.021285 1.43371 8 5 0.144355 0 7124 8 +0.017996 1.43371 0 5 0.537133 -0.853228 1896 8 +0.012178 1.43371 0 4 0.537133 -0.760692 1361 8 +0.017996 1.43371 0 5 0.537133 -0.8098 1250 8 +1.02577 1.43371 0 3 0.537133 -0.8098 11598 8 +0.017996 1.43371 1 3 0.537133 -0.760692 10071 8 +0.021285 1.43371 1 2 0.537133 -0.760692 5713 8 +0.026834 0.127708 1 7 0.537133 -0.760692 1043 8 +0.026834 1.43371 2 4 0.144355 0 13640 8 +1.02577 1.43371 3 5 0.120239 0 1591 8 +1.02577 1.43371 0 4 0.537133 -0.837831 24154 8 +0.026834 1.43371 1 2 0.537133 -0.760692 9858 8 +0.021285 1.43371 1 3 0.537133 -0.760692 6368 8 +1.02577 0.24279 0 5 0.537133 -0.760692 1073 8 +0.014132 1.43371 1 4 0.537133 -0.760692 1814 8 +1.02577 1.43371 2 3 0.537133 -0.837831 19608 8 +0.017996 1.43371 3 4 0.537133 -0.8098 1640 8 +0.026834 1.43371 2 3 0.537133 -0.8098 2609 8 +0.021285 1.43371 0 5 0.537133 -0.873493 1569 8 +1.02577 1.43371 1 3 0.537133 -0.8098 3435 8 +0.026834 0.24279 0 6 0.537133 -0.853228 1336 8 +1.02577 1.43371 1 2 0.537133 -0.760692 16476 8 +0.014132 1.43371 0 5 0.537133 -0.760692 1108 8 +0.021285 1.43371 3 3 0.537133 -0.760692 3938 7 +0.026834 1.43371 8 4 0.537133 -0.837831 1087 7 +1.02577 0.24279 1 4 0.537133 0 2953 7 +0.011524 1.43371 0 3 0.537133 0 1250 7 +1.02577 1.43371 2 3 0.537133 -0.8098 4385 7 +1.02577 1.43371 4 1 0.537133 0 10914 7 +0.026834 1.43371 0 4 0.537133 -0.8098 3659 7 +1.02577 1.43371 1 4 0.537133 -0.853228 3619 7 +0.021285 1.43371 1 2 0.537133 0 16923 7 +1.02577 1.43371 2 2 0.144355 0 12276 7 +0.021285 1.43371 0 5 0.537133 -0.837831 1893 7 +0.012178 1.43371 1 3 0.537133 0 1039 7 +1.02577 1.43371 0 6 0.144355 -0.8098 1321 7 +0.021285 1.43371 3 5 0.537133 -0.8098 2462 7 +1.02577 1.43371 3 4 0.144355 0 6674 7 +1.02577 1.43371 1 4 0.537133 -0.837831 1192 7 +0.021285 0.24279 8 6 0.537133 -0.760692 1112 7 +0.026834 0.24279 3 5 0.537133 0 2249 7 +1.02577 1.43371 1 7 0.105575 -0.760692 1040 7 +0.012997 1.43371 2 3 0.537133 0 1845 7 +0.015706 1.43371 0 3 0.537133 0 2975 7 +0.026834 1.43371 3 3 0.537133 -0.760692 14137 7 +0.026834 1.43371 1 2 0.537133 0 12181 7 +0.015706 1.43371 0 4 0.537133 -0.760692 1091 7 +1.02577 1.43371 3 5 0.144355 0 1635 7 +1.02577 1.43371 2 2 0.537133 -0.760692 5985 7 +0.015706 1.43371 4 3 0.537133 0 2885 7 +0.017996 1.43371 2 4 0.537133 -0.760692 2260 7 +1.02577 1.43371 1 2 0.537133 0 19396 7 +0.011524 1.43371 2 5 0.537133 0 1465 7 +1.02577 1.43371 0 4 0.537133 -0.8098 5227 7 +0.021285 1.43371 2 2 0.537133 0 5080 7 +1.02577 1.43371 1 4 0.537133 -0.8098 1920 7 +0.026834 1.43371 3 5 0.537133 -0.8098 7155 7 +1.02577 1.43371 4 3 0.537133 -0.760692 18961 7 +1.02577 1.43371 5 1 0.537133 0 1785 7 +0.021285 0.186669 8 7 0.537133 0 1034 7 +1.02577 0.24279 2 7 0.144355 -0.8098 1005 7 +0.026834 1.43371 2 2 0.537133 0 6456 7 +0.017996 1.43371 3 3 0.537133 0 4914 7 +0.021285 1.43371 4 4 0.537133 -0.760692 3283 7 +0.011524 1.43371 2 7 0.537133 -0.760692 1181 6 +0.012997 1.43371 2 5 0.537133 0 1473 6 +0.021285 1.43371 2 3 0.537133 0 7514 6 +1.02577 1.43371 2 2 0.537133 0 12631 6 +1.02577 0.152455 0 6 0.537133 0 1230 6 +0.026834 1.43371 3 2 0.537133 0 2405 6 +0.026834 1.43371 3 4 0.537133 -0.760692 4841 6 +0.026834 0.24279 0 7 0.537133 -0.760692 1160 6 +1.02577 1.43371 0 5 0.537133 -0.837831 8750 6 +0.017996 1.43371 0 5 0.537133 -0.760692 1178 6 +1.02577 1.43371 3 2 0.537133 0 4021 6 +1.02577 1.43371 8 5 0.537133 -0.837831 2366 6 +1.02577 1.43371 4 2 0.537133 0 1398 6 +1.02577 1.43371 0 5 0.537133 -0.8098 1927 6 +0.014132 1.43371 0 5 0.537133 0 1006 6 +0.026834 1.43371 4 3 0.537133 0 12275 6 +1.02577 0.24279 3 5 0.537133 0 2124 6 +0.012997 1.43371 0 7 0.537133 -0.760692 1040 6 +0.026834 1.43371 2 7 0.144355 0 1037 6 +0.021285 1.43371 4 5 0.537133 -0.760692 1375 6 +0.015706 1.43371 4 5 0.537133 0 2167 6 +1.02577 1.43371 4 4 0.537133 -0.760692 6694 6 +0.017996 1.43371 0 4 0.537133 0 1662 6 +0.015706 1.43371 8 7 0.537133 -0.837831 1273 6 +1.02577 0.24279 8 6 0.537133 -0.8098 1229 5 +0.021285 0.24279 1 9 0.144355 -0.8098 1038 5 +1.02577 1.43371 6 3 0.537133 0 19553 5 +0.017996 1.43371 0 7 0.537133 -0.837831 1010 5 +0.017996 1.43371 2 5 0.537133 0 1420 5 +0.021285 1.43371 0 4 0.537133 0 2478 5 +0.026834 1.43371 0 5 0.537133 -0.760692 1383 5 +1.02577 1.43371 2 7 0.120239 0 1160 5 +1.02577 1.43371 2 5 0.537133 -0.760692 3104 5 +0.026834 1.43371 1 4 0.537133 0 5806 5 +0.021285 1.43371 6 5 0.537133 0 1512 5 +0.026834 1.43371 1 5 0.537133 0 1661 5 +1.02577 0.24279 8 7 0.537133 -0.760692 1125 5 +0.015706 1.43371 0 6 0.537133 0 1079 5 +1.02577 1.43371 7 4 0.537133 0 8102 5 +0.021285 1.43371 1 7 0.537133 -0.837831 1668 5 +0.021285 0.24279 2 8 0.537133 0 1013 5 +0.021285 1.43371 2 6 0.537133 -0.760692 1420 5 +0.026834 1.43371 1 7 0.537133 -0.8098 3090 4 +1.02577 1.43371 7 5 0.537133 0 2701 4 +1.02577 1.43371 1 8 0.144355 -0.760692 1048 4 +1.02577 1.43371 0 7 0.537133 -0.837831 3445 4 +0.021285 1.43371 8 7 0.537133 0 1231 4 +1.02577 0.24279 2 7 0.537133 0 1321 4 +1.02577 1.43371 8 7 0.537133 -0.8098 1703 4 +1.02577 1.43371 8 6 0.537133 -0.760692 1220 4 +0.017996 1.43371 1 9 0.537133 0 1080 4 +1.02577 1.43371 2 7 0.537133 0 2087 4 +1.02577 0.24279 8 9 0.537133 -0.760692 1032 4 +1.02577 1.43371 8 8 0.537133 -0.760692 1025 3 +1.02577 1.43371 3 9 0.537133 0 1370 3 +1.02577 1.43371 3 10 0.537133 0 1458 3 diff --git a/Analysis/config/phredTable.GX9v1.Recal.h5 b/Analysis/config/phredTable.GX9v1.Recal.h5 new file mode 100644 index 00000000..87fe4760 Binary files /dev/null and b/Analysis/config/phredTable.GX9v1.Recal.h5 differ diff --git a/Analysis/config/phredTable.GX9v1.h5 b/Analysis/config/phredTable.GX9v1.h5 new file mode 100644 index 00000000..76f4ecd6 Binary files /dev/null and b/Analysis/config/phredTable.GX9v1.h5 differ diff --git a/Analysis/crop/lbTest.cpp b/Analysis/crop/lbTest.cpp new file mode 100644 index 00000000..c6464862 --- /dev/null +++ b/Analysis/crop/lbTest.cpp @@ -0,0 +1,241 @@ +/* Copyright (C) 2010 Ion Torrent Systems, Inc. All Rights Reserved */ +#include +#include +#include +#include +#include +#include +#include +#include + +#ifdef __linux__ +#include +#endif +#ifdef __APPLE__ +#include +#include +#endif +#include +#include +#include "ByteSwapUtils.h" +#include "datahdr.h" +#include "LinuxCompat.h" +// #include "Raw2Wells.h" +#include "Image.h" +#include "crop/Acq.h" +#include "IonVersion.h" +#include "Utils.h" + + + + +void usage (char *name ) +{ + fprintf ( stdout, "%s - Utility to investigate using less bits to transmit data.\n",name ); + fprintf ( stdout, "options:\n" ); + fprintf ( stdout, "\n" ); + fprintf ( stdout, "usage:\n" ); + fprintf ( stdout, " %s \n",name ); + fprintf ( stdout, "\n" ); + exit ( 1 ); +} + +void MaskBits(RawImage *img, int bits) +{ + short mask=(1<image; + int limit=img->frameStride*img->frames; + for(int idx=0;idxframes;frm++){ + uint64_t avg=0; + short *imgPtr=&img->image[frm*img->frameStride]; + for(int idx=0;idxframeStride;idx++){ + avg += imgPtr[idx]; + } + avgTrace[frm]=avg/(uint64_t)img->frameStride; + } + for(int frm=1;frmframes;frm++){ + avgTrace[frm]-=avgTrace[0]; + } + avgTrace[0]=0; + + printf("Avg Trc %s:\n ",fname); + for(int frm=0;frmframes;frm++){ + //avgTrace[frm] = (avgTrace[frm] * 15) / 10; + printf(" %03d",avgTrace[frm]); + } + printf("\n"); +} + +void modAvgTrace(RawImage *img, unsigned short *avg, int sub) +{ + for(int frm=0;frmframes;frm++){ + short *imgPtr=&img->image[frm*img->frameStride]; + short subVal=avg[frm]; + for(int idx=0;idxframeStride;idx++){ + if(sub) + imgPtr[idx] -= subVal; + else + imgPtr[idx] += subVal; + } + } +} + +void PrintHistogram(Image *mimg, char *fname,const char *txt) +{ + RawImage *img = mimg->raw; +#define NUMBINS 16 + uint64_t bins[NUMBINS]={0}; + + for(int frm=1;frmframes;frm++){ + short *imgPtr=&img->image[frm*img->frameStride]; + short *pimgPtr=&img->image[(frm-1)*img->frameStride]; + for(int idx=0;idxframeStride;idx++){ + short val = imgPtr[idx]-pimgPtr[idx]; + if(val <0) + val=-val; + for(int bit=15;bit >=0;bit--){ + if((1<cols,img->rows); + + +} + +void ZeroFirstFrame(RawImage *img) +{ + for(int idx=0;idxframeStride;idx++){ + short *imgPtr=&img->image[idx]; + short subVal=imgPtr[0]; + for(int frm=1;frmframes;frm++){ + imgPtr[frm*img->frameStride] -= subVal-32; + } + imgPtr[0]=32; + } +} + + + +int main ( int argc, char *argv[] ) +{ + //int cropx = 624, cropy = 125, cropw = 100, croph = 100; + int cropx = 0, cropy = 0, cropw = 0, croph = 0; + int i,x,y,idx; + char srcFile[1024],dstFile[1024]; + char *srcDir; + unsigned short avgTrace[105]; + unsigned short avgTrace1[105]; + Image loader_extraG, loader_src, loader_dst; + bool allocate = true; + RawImage *src_extraG,*src_raw,*dst_raw; + struct timeval tv; + double startT; + double stopT; + + if ( argc < 2 ) { + usage ( argv[0]); + } + + srcDir = argv[1]; + + sprintf(srcFile,"%s/extraG_0000.dat",srcDir); + sprintf(dstFile,"%s/op",srcDir); + mkdir(dstFile,0644); + + gettimeofday ( &tv, NULL ); + startT = ( double ) tv.tv_sec + ( ( double ) tv.tv_usec/1000000 ); + + if(!loader_extraG.LoadRaw ( srcFile, 0, allocate, false, false )) + { + printf("failed to load file %s\n",srcFile); + return -1; + } + gettimeofday ( &tv, NULL ); + stopT = ( double ) tv.tv_sec + ( ( double ) tv.tv_usec/1000000 ); + printf ( "Converted: %s in %0.2lf sec\n", srcFile,stopT - startT ); + fflush ( stdout ); + src_extraG = loader_extraG.raw; + + // determine the average trace + getAvgTrace(src_extraG,avgTrace,srcFile); + + + for(int fnum=0;fnum<4;fnum++){ + sprintf(srcFile,"%s/acq_000%d.dat",srcDir,fnum); + + gettimeofday ( &tv, NULL ); + startT = ( double ) tv.tv_sec + ( ( double ) tv.tv_usec/1000000 ); + + if(!loader_src.LoadRaw ( srcFile, 0, allocate, false, false )) + { + printf("failed to load file %s\n",srcFile); + return -1; + } + gettimeofday ( &tv, NULL ); + stopT = ( double ) tv.tv_sec + ( ( double ) tv.tv_usec/1000000 ); + printf ( "Converted: %s in %0.2lf sec\n", srcFile,stopT - startT ); + fflush ( stdout ); + src_raw = loader_src.raw; + + sprintf(dstFile,"%s/op/acq_000%d.dat_orig",srcDir,fnum); + PrintHistogram(&loader_src,dstFile,""); + getAvgTrace(src_raw,avgTrace1,srcFile); + printf("Sub Avg Trc :\n "); + for(int frm=0;frmframes;frm++){ + //avgTrace[frm] = (avgTrace[frm] * 15) / 10; + printf(" %03d",(avgTrace[frm] * 15) / 10); + } + printf("\n"); + + + // subtract extraG trace + modAvgTrace(src_raw, avgTrace, 1); + + sprintf(dstFile,"%s/op/acq_000%d.dat_subt",srcDir,fnum); + PrintHistogram(&loader_src,dstFile,""); + + //ZeroFirstFrame(src_raw); + + // mask off upper bits.. + MaskBits(src_raw,8); + + // determine the histogram of differences + sprintf(dstFile,"%s/op/acq_000%d.dat_mask",srcDir,fnum); + PrintHistogram(&loader_src,dstFile,""); + + // try to re-construct the traces.. + // add extraG trace + + // save re-constructed traces + } + return 0; +} + + diff --git a/Analysis/ionstats/ionstats_alignment.h b/Analysis/ionstats/ionstats_alignment.h index 68be516d..cc737b72 100644 --- a/Analysis/ionstats/ionstats_alignment.h +++ b/Analysis/ionstats/ionstats_alignment.h @@ -39,7 +39,7 @@ #define DEFAULT_DEBUG_ERROR_FLOW -1 #define DEFAULT_DEBUG_ALIGNED_FLOW -1 #define DEFAULT_DEBUG_POSITIVE_REF_FLOW -1 -#define DEFAULT_N_THREADS 5 +#define DEFAULT_N_THREADS 0 #define DEFAULT_THREADS_SHARE_MEMORY "false" using namespace std; diff --git a/Analysis/validate_reference.pl b/Analysis/validate_reference.pl index 52b056fe..7638311b 100755 --- a/Analysis/validate_reference.pl +++ b/Analysis/validate_reference.pl @@ -103,7 +103,7 @@ sub error my $origname = $name; if ($name=~s/^[\s\*\=]+//g) {error("Sequence name '$origname' starts with a white space, or an asterisk or equal sign at line $line !\n",4);} # if ($name=~s/\:/_/g) {error("Sequence name '$origname' contains a colon at line $line, which should be replaced by an underscore to avoid breaking samtools mpileup!\n",14)} - if ($name=~/[^\w\.\-\+\s\|\,\:]/) {error("Sequence name '$name' contains a non-alphanumeric character at line $line !\n",13)} + if ($name=~s/[^\w\.\-\+\s\|\,\:]/_/g) {error("Sequence name '$origname' contains a non-alphanumeric character at line $line !\n",13)} $emptyline = ''; } else diff --git a/Analysis/version b/Analysis/version index ba71ac5a..1241b4e9 100644 --- a/Analysis/version +++ b/Analysis/version @@ -1,4 +1,4 @@ # Version for target of current development cycle MAJOR=5 -MINOR=16 +MINOR=18 RELEASE=6 diff --git a/LICENSE.txt b/LICENSE.txt index 9edf73b6..8fb701c1 100644 --- a/LICENSE.txt +++ b/LICENSE.txt @@ -1,12 +1,13 @@ -Torrent Suite Software Version 5.8 +This end-user license agreement contains 4 separate and distinct licenses: (1) Torrent Suite(TM) Software Version 5.18 Open Source License (pgs. 1-32), (2) Service & Support Telemetry Module Software Version 2.0.1 End User License Agreement (pgs. 32 - 47), (3) Ion Chef(TM) Instrument Software Version 5.18 License Agreement (pgs. 47 - 182), and (4) Ion GeneStudio(TM) S5 V5.18 License Agreement (pgs. 182 - 236). + +(1) Torrent Suite(TM) Software Version 5.18 ===================================================================== -Torrent Suite(tm) Software v5.8: This software provides for the analysis and storage of data received from the Ion Personal Genome Machine(tm) Sequencer, -the Ion Proton(tm) Sequencer, the Ion GeneStudio S5 Sequencer or the Ion GeneStudio S5 XL Sequencer, -the Ion GeneStudio S5 Prime or the Ion GeneStudio S5 Pro. +Torrent Suite(TM) Software v5.18: This software provides for the analysis and storage of data received from the Ion Personal Genome Machine(TM) (PGM(TM)) Sequencer, the Ion Proton(TM) Sequencer, the Ion S5TM Sequencer, the Ion S5TM XL Sequencer, or the Ion GeneStudio(TM) S5 Prime. +The Ion Chef(TM) System provides automated, high-throughput template preparation and chip loading for use with an Ion Personal Genome Machine(TM) PGM(TM) Sequencer, Ion Proton(TM) Sequencer, Ion S5(TM) Sequencer, Ion S5(TM) XL Sequencer, or the Ion GeneStudio(TM) S5 Prime. -November 30, 2017 +May 26th, 2022 -Copyright (C) 2017 Life Technologies Corporation +Copyright (C) 2011 - 2022 Life Technologies Corporation All Rights Reserved. This program is free software; you can redistribute it and/or modify it @@ -23,12 +24,13 @@ with this program (see Section 2 below); if not, write to the Free Software Foun 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. You can also find the GPL version 2 on the GNU web site: https://www.gnu.org/licenses/gpl-2.0.html - -1. Third Party Software Notices and Licenses ===================================================================== - + 1. Third Party Software Notices and Licenses +===================================================================== + This software uses third party software components from several sources. Portions of these software components are copyrighted and licensed by their respective owners as indicated below. Various licenses require distribution of source code or if a link is used to point the end-user to a source-code repository, and the source code is not available at such site, the distributor must, for a time determined by license, offer to provide source code. In such cases, please contact your Life Technologies representative. As well, various licenses require that the end-user receive a copy of the license or certain notices. Such licenses and notices may be found below. In order to use this software, the end-user must abide by the terms and conditions of these third party licenses. + Armadillo ------------------------------------------------------------- @@ -37,622 +39,238 @@ Apache License Version 2.0, January 2004 http://www.apache.org/licenses/ -TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION - -1. Definitions. - - "License" shall mean the terms and conditions for use, reproduction, - and distribution as defined by Sections 1 through 9 of this document. - - "Licensor" shall mean the copyright owner or entity authorized by - the copyright owner that is granting the License. - - "Legal Entity" shall mean the union of the acting entity and all - other entities that control, are controlled by, or are under common - control with that entity. For the purposes of this definition, - "control" means (i) the power, direct or indirect, to cause the - direction or management of such entity, whether by contract or - otherwise, or (ii) ownership of fifty percent (50%) or more of the - outstanding shares, or (iii) beneficial ownership of such entity. - - "You" (or "Your") shall mean an individual or Legal Entity - exercising permissions granted by this License. - - "Source" form shall mean the preferred form for making modifications, - including but not limited to software source code, documentation - source, and configuration files. - - "Object" form shall mean any form resulting from mechanical - transformation or translation of a Source form, including but - not limited to compiled object code, generated documentation, - and conversions to other media types. - - "Work" shall mean the work of authorship, whether in Source or - Object form, made available under the License, as indicated by a - copyright notice that is included in or attached to the work - (an example is provided in the Appendix below). - - "Derivative Works" shall mean any work, whether in Source or Object - form, that is based on (or derived from) the Work and for which the - editorial revisions, annotations, elaborations, or other modifications - represent, as a whole, an original work of authorship. For the purposes - of this License, Derivative Works shall not include works that remain - separable from, or merely link (or bind by name) to the interfaces of, - the Work and Derivative Works thereof. - - "Contribution" shall mean any work of authorship, including - the original version of the Work and any modifications or additions - to that Work or Derivative Works thereof, that is intentionally - submitted to Licensor for inclusion in the Work by the copyright owner - or by an individual or Legal Entity authorized to submit on behalf of - the copyright owner. For the purposes of this definition, "submitted" - means any form of electronic, verbal, or written communication sent - to the Licensor or its representatives, including but not limited to - communication on electronic mailing lists, source code control systems, - and issue tracking systems that are managed by, or on behalf of, the - Licensor for the purpose of discussing and improving the Work, but - excluding communication that is conspicuously marked or otherwise - designated in writing by the copyright owner as "Not a Contribution." - - "Contributor" shall mean Licensor and any individual or Legal Entity - on behalf of whom a Contribution has been received by Licensor and - subsequently incorporated within the Work. - -2. Grant of Copyright License. Subject to the terms and conditions of - this License, each Contributor hereby grants to You a perpetual, - worldwide, non-exclusive, no-charge, royalty-free, irrevocable - copyright license to reproduce, prepare Derivative Works of, - publicly display, publicly perform, sublicense, and distribute the - Work and such Derivative Works in Source or Object form. - -3. Grant of Patent License. Subject to the terms and conditions of - this License, each Contributor hereby grants to You a perpetual, - worldwide, non-exclusive, no-charge, royalty-free, irrevocable - (except as stated in this section) patent license to make, have made, - use, offer to sell, sell, import, and otherwise transfer the Work, - where such license applies only to those patent claims licensable - by such Contributor that are necessarily infringed by their - Contribution(s) alone or by combination of their Contribution(s) - with the Work to which such Contribution(s) was submitted. If You - institute patent litigation against any entity (including a - cross-claim or counterclaim in a lawsuit) alleging that the Work - or a Contribution incorporated within the Work constitutes direct - or contributory patent infringement, then any patent licenses - granted to You under this License for that Work shall terminate - as of the date such litigation is filed. - -4. Redistribution. You may reproduce and distribute copies of the - Work or Derivative Works thereof in any medium, with or without - modifications, and in Source or Object form, provided that You - meet the following conditions: - - (a) You must give any other recipients of the Work or - Derivative Works a copy of this License; and - - (b) You must cause any modified files to carry prominent notices - stating that You changed the files; and - - (c) You must retain, in the Source form of any Derivative Works - that You distribute, all copyright, patent, trademark, and - attribution notices from the Source form of the Work, - excluding those notices that do not pertain to any part of - the Derivative Works; and - - (d) If the Work includes a "NOTICE" text file as part of its - distribution, then any Derivative Works that You distribute must - include a readable copy of the attribution notices contained - within such NOTICE file, excluding those notices that do not - pertain to any part of the Derivative Works, in at least one - of the following places: within a NOTICE text file distributed - as part of the Derivative Works; within the Source form or - documentation, if provided along with the Derivative Works; or, - within a display generated by the Derivative Works, if and - wherever such third-party notices normally appear. The contents - of the NOTICE file are for informational purposes only and - do not modify the License. You may add Your own attribution - notices within Derivative Works that You distribute, alongside - or as an addendum to the NOTICE text from the Work, provided - that such additional attribution notices cannot be construed - as modifying the License. - - You may add Your own copyright statement to Your modifications and - may provide additional or different license terms and conditions - for use, reproduction, or distribution of Your modifications, or - for any such Derivative Works as a whole, provided Your use, - reproduction, and distribution of the Work otherwise complies with - the conditions stated in this License. - -5. Submission of Contributions. Unless You explicitly state otherwise, - any Contribution intentionally submitted for inclusion in the Work - by You to the Licensor shall be under the terms and conditions of - this License, without any additional terms or conditions. - Notwithstanding the above, nothing herein shall supersede or modify - the terms of any separate license agreement you may have executed - with Licensor regarding such Contributions. - -6. Trademarks. This License does not grant permission to use the trade - names, trademarks, service marks, or product names of the Licensor, - except as required for reasonable and customary use in describing the - origin of the Work and reproducing the content of the NOTICE file. - -7. Disclaimer of Warranty. Unless required by applicable law or - agreed to in writing, Licensor provides the Work (and each - Contributor provides its Contributions) on an "AS IS" BASIS, - WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or - implied, including, without limitation, any warranties or conditions - of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A - PARTICULAR PURPOSE. You are solely responsible for determining the - appropriateness of using or redistributing the Work and assume any - risks associated with Your exercise of permissions under this License. - -8. Limitation of Liability. In no event and under no legal theory, - whether in tort (including negligence), contract, or otherwise, - unless required by applicable law (such as deliberate and grossly - negligent acts) or agreed to in writing, shall any Contributor be - liable to You for damages, including any direct, indirect, special, - incidental, or consequential damages of any character arising as a - result of this License or out of the use or inability to use the - Work (including but not limited to damages for loss of goodwill, - work stoppage, computer failure or malfunction, or any and all - other commercial damages or losses), even if such Contributor - has been advised of the possibility of such damages. - -9. Accepting Warranty or Additional Liability. While redistributing - the Work or Derivative Works thereof, You may choose to offer, - and charge a fee for, acceptance of support, warranty, indemnity, - or other liability obligations and/or rights consistent with this - License. However, in accepting such obligations, You may act only - on Your own behalf and on Your sole responsibility, not on behalf - of any other Contributor, and only if You agree to indemnify, - defend, and hold each Contributor harmless for any liability - incurred by, or claims asserted against, such Contributor by reason - of your accepting any such warranty or additional liability. - - -END OF TERMS AND CONDITIONS - -APPENDIX: How to apply the Apache License to your work. - -To apply the Apache License to your work, attach the following -boilerplate notice, with the fields enclosed by brackets "[]" -replaced with your own identifying information. (Don't include -the brackets!) The text should be enclosed in the appropriate -comment syntax for the file format. We also recommend that a -file or class name and description of purpose be included on the -same "printed page" as the copyright notice for easier -identification within third-party archives. - -Copyright [yyyy] [name of copyright owner] - -Licensed under the Apache License, Version 2.0 (the "License"); -you may not use this file except in compliance with the License. -You may obtain a copy of the License at - -http://www.apache.org/licenses/LICENSE-2.0 - -Unless required by applicable law or agreed to in writing, software -distributed under the License is distributed on an "AS IS" BASIS, -WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -See the License for the specific language governing permissions and -limitations under the License. - - -Mozilla Public License Version 2.0 -------------------------------------------------------------- - -1. Definitions -------------------------------------------------------------- - -1.1. "Contributor" - means each individual or legal entity that creates, contributes to - the creation of, or owns Covered Software. -1.2. "Contributor Version" - means the combination of the Contributions of others (if any) used - by a Contributor and that particular Contributor's Contribution. - -1.3. "Contribution" - means Covered Software of a particular Contributor. - -1.4. "Covered Software" - means Source Code Form to which the initial Contributor has attached - the notice in Exhibit A, the Executable Form of such Source Code - Form, and Modifications of such Source Code Form, in each case - including portions thereof. - -1.5. "Incompatible With Secondary Licenses" - means - - (a) that the initial Contributor has attached the notice described - in Exhibit B to the Covered Software; or - - (b) that the Covered Software was made available under the terms of - version 1.1 or earlier of the License, but not also under the - terms of a Secondary License. - -1.6. "Executable Form" - means any form of the work other than Source Code Form. - -1.7. "Larger Work" - means a work that combines Covered Software with other material, in - a separate file or files, that is not Covered Software. - -1.8. "License" - means this document. - -1.9. "Licensable" - means having the right to grant, to the maximum extent possible, - whether at the time of the initial grant or subsequently, any and - all of the rights conveyed by this License. - -1.10. "Modifications" - means any of the following: - - (a) any file in Source Code Form that results from an addition to, - deletion from, or modification of the contents of Covered - Software; or - - (b) any new file in Source Code Form that contains any Covered - Software. - -1.11. "Patent Claims" of a Contributor - means any patent claim(s), including without limitation, method, - process, and apparatus claims, in any patent Licensable by such - Contributor that would be infringed, but for the grant of the - License, by the making, using, selling, offering for sale, having - made, import, or transfer of either its Contributions or its - Contributor Version. - -1.12. "Secondary License" - means either the GNU General Public License, Version 2.0, the GNU - Lesser General Public License, Version 2.1, the GNU Affero General - Public License, Version 3.0, or any later versions of those - licenses. - -1.13. "Source Code Form" - means the form of the work preferred for making modifications. - -1.14. "You" (or "Your") - means an individual or a legal entity exercising rights under this - License. For legal entities, "You" includes any entity that - controls, is controlled by, or is under common control with You. For - purposes of this definition, "control" means (a) the power, direct - or indirect, to cause the direction or management of such entity, - whether by contract or otherwise, or (b) ownership of more than - fifty percent (50%) of the outstanding shares or beneficial - ownership of such entity. - -2. License Grants and Conditions -------------------------------------------------------------- - -2.1. Grants - -Each Contributor hereby grants You a world-wide, royalty-free, -non-exclusive license: - -(a) under intellectual property rights (other than patent or trademark) - Licensable by such Contributor to use, reproduce, make available, - modify, display, perform, distribute, and otherwise exploit its - Contributions, either on an unmodified basis, with Modifications, or - as part of a Larger Work; and - -(b) under Patent Claims of such Contributor to make, use, sell, offer - for sale, have made, import, and otherwise transfer either its - Contributions or its Contributor Version. - -2.2. Effective Date - -The licenses granted in Section 2.1 with respect to any Contribution -become effective for each Contribution on the date the Contributor first -distributes such Contribution. - -2.3. Limitations on Grant Scope - -The licenses granted in this Section 2 are the only rights granted under -this License. No additional rights or licenses will be implied from the -distribution or licensing of Covered Software under this License. -Notwithstanding Section 2.1(b) above, no patent license is granted by a -Contributor: - -(a) for any code that a Contributor has removed from Covered Software; - or - -(b) for infringements caused by: (i) Your and any other third party's - modifications of Covered Software, or (ii) the combination of its - Contributions with other software (except as part of its Contributor - Version); or - -(c) under Patent Claims infringed by Covered Software in the absence of - its Contributions. - -This License does not grant any rights in the trademarks, service marks, -or logos of any Contributor (except as may be necessary to comply with -the notice requirements in Section 3.4). - -2.4. Subsequent Licenses - -No Contributor makes additional grants as a result of Your choice to -distribute the Covered Software under a subsequent version of this -License (see Section 10.2) or under the terms of a Secondary License (if -permitted under the terms of Section 3.3). - -2.5. Representation - -Each Contributor represents that the Contributor believes its -Contributions are its original creation(s) or it has sufficient rights -to grant the rights to its Contributions conveyed by this License. - -2.6. Fair Use - -This License is not intended to limit any rights You have under -applicable copyright doctrines of fair use, fair dealing, or other -equivalents. - -2.7. Conditions - -Sections 3.1, 3.2, 3.3, and 3.4 are conditions of the licenses granted -in Section 2.1. - -3. Responsibilities -------------------------------------------------------------- - -3.1. Distribution of Source Form - -All distribution of Covered Software in Source Code Form, including any -Modifications that You create or to which You contribute, must be under -the terms of this License. You must inform recipients that the Source -Code Form of the Covered Software is governed by the terms of this -License, and how they can obtain a copy of this License. You may not -attempt to alter or restrict the recipients' rights in the Source Code -Form. - -3.2. Distribution of Executable Form - -If You distribute Covered Software in Executable Form then: - -(a) such Covered Software must also be made available in Source Code - Form, as described in Section 3.1, and You must inform recipients of - the Executable Form how they can obtain a copy of such Source Code - Form by reasonable means in a timely manner, at a charge no more - than the cost of distribution to the recipient; and - -(b) You may distribute such Executable Form under the terms of this - License, or sublicense it under different terms, provided that the - license for the Executable Form does not attempt to limit or alter - the recipients' rights in the Source Code Form under this License. - -3.3. Distribution of a Larger Work - -You may create and distribute a Larger Work under terms of Your choice, -provided that You also comply with the requirements of this License for -the Covered Software. If the Larger Work is a combination of Covered -Software with a work governed by one or more Secondary Licenses, and the -Covered Software is not Incompatible With Secondary Licenses, this -License permits You to additionally distribute such Covered Software -under the terms of such Secondary License(s), so that the recipient of -the Larger Work may, at their option, further distribute the Covered -Software under the terms of either this License or such Secondary -License(s). - -3.4. Notices - -You may not remove or alter the substance of any license notices -(including copyright notices, patent notices, disclaimers of warranty, -or limitations of liability) contained within the Source Code Form of -the Covered Software, except that You may alter any license notices to -the extent required to remedy known factual inaccuracies. - -3.5. Application of Additional Terms - -You may choose to offer, and to charge a fee for, warranty, support, -indemnity or liability obligations to one or more recipients of Covered -Software. However, You may do so only on Your own behalf, and not on -behalf of any Contributor. You must make it absolutely clear that any -such warranty, support, indemnity, or liability obligation is offered by -You alone, and You hereby agree to indemnify every Contributor for any -liability incurred by such Contributor as a result of warranty, support, -indemnity or liability terms You offer. You may include additional -disclaimers of warranty and limitations of liability specific to any -jurisdiction. - -4. Inability to Comply Due to Statute or Regulation ---------------------------------------------------- - -If it is impossible for You to comply with any of the terms of this -License with respect to some or all of the Covered Software due to -statute, judicial order, or regulation then You must: (a) comply with -the terms of this License to the maximum extent possible; and (b) -describe the limitations and the code they affect. Such description must -be placed in a text file included with all distributions of the Covered -Software under this License. Except to the extent prohibited by statute -or regulation, such description must be sufficiently detailed for a -recipient of ordinary skill to be able to understand it. - -5. Termination -------------------------------------------------------------- - -5.1. The rights granted under this License will terminate automatically -if You fail to comply with any of its terms. However, if You become -compliant, then the rights granted under this License from a particular -Contributor are reinstated (a) provisionally, unless and until such -Contributor explicitly and finally terminates Your grants, and (b) on an -ongoing basis, if such Contributor fails to notify You of the -non-compliance by some reasonable means prior to 60 days after You have -come back into compliance. Moreover, Your grants from a particular -Contributor are reinstated on an ongoing basis if such Contributor -notifies You of the non-compliance by some reasonable means, this is the -first time You have received notice of non-compliance with this License -from such Contributor, and You become compliant prior to 30 days after -Your receipt of the notice. - -5.2. If You initiate litigation against any entity by asserting a patent -infringement claim (excluding declaratory judgment actions, -counter-claims, and cross-claims) alleging that a Contributor Version -directly or indirectly infringes any patent, then the rights granted to -You by any and all Contributors for the Covered Software under Section -2.1 of this License shall terminate. - -5.3. In the event of termination under Sections 5.1 or 5.2 above, all -end user license agreements (excluding distributors and resellers) which -have been validly granted by You or Your distributors under this License -prior to termination shall survive termination. - - - -6. Disclaimer of Warranty -------------------------------------------------------------- - -Covered Software is provided under this License on an "as is" basis, without -warranty of any kind, either expressed, implied, or statutory, including, -without limitation, warranties that the Covered Software is free of defects, -merchantable, fit for a particular purpose or non-infringing. The entire risk -as to the quality and performance of the Covered Software is with You. Should -any Covered Software prove defective in any respect, You (not any Contributor) -assume the cost of any necessary servicing, repair, or correction. This -disclaimer of warranty constitutes an essential part of this License. No use of -any Covered Software is authorized under this License except under this -disclaimer. - - -7. Limitation of Liability -------------------------------------------------------------- - -Under no circumstances and under no legal theory, whether tort (including -negligence), contract, or otherwise, shall any Contributor, or anyone who -distributes Covered Software as permitted above, be liable to You for any -direct, indirect, special, incidental, or consequential damages of any -character including, without limitation, damages for lost profits, loss of -goodwill, work stoppage, computer failure or malfunction, or any and all other -commercial damages or losses, even if such party shall have been informed of -the possibility of such damages. This limitation of liability shall not apply -to liability for death or personal injury resulting from such party's -negligence to the extent applicable law prohibits such limitation. Some -jurisdictions do not allow the exclusion or limitation of incidental or -consequential damages, so this exclusion and limitation may not apply to You. - - -8. Litigation -------------------------------------------------------------- - -Any litigation relating to this License may be brought only in the -courts of a jurisdiction where the defendant maintains its principal -place of business and such litigation shall be governed by laws of that -jurisdiction, without reference to its conflict-of-law provisions. -Nothing in this Section shall prevent a party's ability to bring -cross-claims or counter-claims. - -9. Miscellaneous -------------------------------------------------------------- - -This License represents the complete agreement concerning the subject -matter hereof. If any provision of this License is held to be -unenforceable, such provision shall be reformed only to the extent -necessary to make it enforceable. Any law or regulation which provides -that the language of a contract shall be construed against the drafter -shall not be used to construe this License against a Contributor. - -10. Versions of the License -------------------------------------------------------------- - -10.1. New Versions - -Mozilla Foundation is the license steward. Except as provided in Section -10.3, no one other than the license steward has the right to modify or -publish new versions of this License. Each version will be given a -distinguishing version number. - -10.2. Effect of New Versions - -You may distribute the Covered Software under the terms of the version -of the License under which You originally received the Covered Software, -or under the terms of any subsequent version published by the license -steward. - -10.3. Modified Versions - -If you create software not governed by this License, and you want to -create a new license for such software, you may create and use a -modified version of this License if you rename the license and remove -any references to the name of the license steward (except to note that -such modified license differs from this License). - -10.4. Distributing Source Code Form that is Incompatible With Secondary -Licenses - -If You choose to distribute Source Code Form that is Incompatible With -Secondary Licenses under the terms of this version of the License, the -notice described in Exhibit B of this License must be attached. - -Exhibit A - Source Code Form License Notice -------------------------------------------------------------- - -This Source Code Form is subject to the terms of the Mozilla Public -License, v. 2.0. If a copy of the MPL was not distributed with this -file, You can obtain one at http://mozilla.org/MPL/2.0/. - -If it is not possible or desirable to put the notice in a particular -file, then You may include the notice in a location (such as a LICENSE -file in a relevant directory) where a recipient would be likely to look -for such a notice. - -You may add additional accurate notices of copyright ownership. - -Exhibit B - "Incompatible With Secondary Licenses" Notice -------------------------------------------------------------- - -This Source Code Form is "Incompatible With Secondary Licenses", as -defined by the Mozilla Public License, v. 2.0. - + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. Definitions. + + "License" shall mean the terms and conditions for use, reproduction, + and distribution as defined by Sections 1 through 9 of this document. + + "Licensor" shall mean the copyright owner or entity authorized by + the copyright owner that is granting the License. + + "Legal Entity" shall mean the union of the acting entity and all + other entities that control, are controlled by, or are under common + control with that entity. For the purposes of this definition, + "control" means (i) the power, direct or indirect, to cause the + direction or management of such entity, whether by contract or + otherwise, or (ii) ownership of fifty percent (50%) or more of the + outstanding shares, or (iii) beneficial ownership of such entity. + + "You" (or "Your") shall mean an individual or Legal Entity + exercising permissions granted by this License. + + "Source" form shall mean the preferred form for making modifications, + including but not limited to software source code, documentation + source, and configuration files. + + "Object" form shall mean any form resulting from mechanical + transformation or translation of a Source form, including but + not limited to compiled object code, generated documentation, + and conversions to other media types. + + "Work" shall mean the work of authorship, whether in Source or + Object form, made available under the License, as indicated by a + copyright notice that is included in or attached to the work + (an example is provided in the Appendix below). + + "Derivative Works" shall mean any work, whether in Source or Object + form, that is based on (or derived from) the Work and for which the + editorial revisions, annotations, elaborations, or other modifications + represent, as a whole, an original work of authorship. For the purposes + of this License, Derivative Works shall not include works that remain + separable from, or merely link (or bind by name) to the interfaces of, + the Work and Derivative Works thereof. + + "Contribution" shall mean any work of authorship, including + the original version of the Work and any modifications or additions + to that Work or Derivative Works thereof, that is intentionally + submitted to Licensor for inclusion in the Work by the copyright owner + or by an individual or Legal Entity authorized to submit on behalf of + the copyright owner. For the purposes of this definition, "submitted" + means any form of electronic, verbal, or written communication sent + to the Licensor or its representatives, including but not limited to + communication on electronic mailing lists, source code control systems, + and issue tracking systems that are managed by, or on behalf of, the + Licensor for the purpose of discussing and improving the Work, but + excluding communication that is conspicuously marked or otherwise + designated in writing by the copyright owner as "Not a Contribution." + + "Contributor" shall mean Licensor and any individual or Legal Entity + on behalf of whom a Contribution has been received by Licensor and + subsequently incorporated within the Work. + + 2. Grant of Copyright License. Subject to the terms and conditions of + this License, each Contributor hereby grants to You a perpetual, + worldwide, non-exclusive, no-charge, royalty-free, irrevocable + copyright license to reproduce, prepare Derivative Works of, + publicly display, publicly perform, sublicense, and distribute the + Work and such Derivative Works in Source or Object form. + + 3. Grant of Patent License. Subject to the terms and conditions of + this License, each Contributor hereby grants to You a perpetual, + worldwide, non-exclusive, no-charge, royalty-free, irrevocable + (except as stated in this section) patent license to make, have made, + use, offer to sell, sell, import, and otherwise transfer the Work, + where such license applies only to those patent claims licensable + by such Contributor that are necessarily infringed by their + Contribution(s) alone or by combination of their Contribution(s) + with the Work to which such Contribution(s) was submitted. If You + institute patent litigation against any entity (including a + cross-claim or counterclaim in a lawsuit) alleging that the Work + or a Contribution incorporated within the Work constitutes direct + or contributory patent infringement, then any patent licenses + granted to You under this License for that Work shall terminate + as of the date such litigation is filed. + + 4. Redistribution. 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In the event either party provides Feedback to the other party, the party receiving the Feedback may use any Feedback that the other party voluntarily provides to improve the (i) SOFTWARE or other related NVIDIA technologies, respectively for the benefit of NVIDIA; or (ii) Licensee's product or other related Licensee technologies, respectively for the benefit of Licensee. Accordingly, if either party provides Feedback to the other party, both parties agree that the other party and its respective licensees may freely use, reproduce, license, distribute, and otherwise commercialize the Feedback in the (i) SOFTWARE or other related technologies; or (ii) Licensee's products or other related technologies, respectively, without the payment of any royalties or fees. - - 1.7.1.2. Residual Rights Licensee agrees that NVIDIA shall be free to use any general knowledge, skills and experience, (including, but not limited to, ideas, concepts, know-how, or techniques) ("Residuals"), contained in the (i) Feedback provided by Licensee to NVIDIA; (ii) Licensee's products shared or disclosed to NVIDIA in connection with the Feedback; or (c) Licensee's confidential information voluntarily provided to NVIDIA in connection with the Feedback, which are retained in the memories of NVIDIA's employees, agents, or contractors who have had access to such Residuals. Subject to the terms and conditions of this Agreement, NVIDIA's employees, agents, or contractors shall not be prevented from using Residuals as part of such employee's, agent's or contractor's general knowledge, skills, experience, talent, and/or expertise. NVIDIA shall not have any obligation to limit or restrict the assignment of such employees, agents or contractors or to pay royalties for any work resulting from the use of Residuals. - 1.7.1.3. Disclaimer of Warranty FEEDBACK FROM EITHER PARTY IS PROVIDED FOR THE OTHER PARTY'S USE "AS IS" AND BOTH PARTIES DISCLAIM ALL WARRANTIES, EXPRESS, IMPLIED AND STATUTORY INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR NONINFRINGEMENT. BOTH PARTIES DO NOT REPRESENT OR WARRANT THAT THE FEEDBACK WILL MEET THE OTHER PARTY'S REQUIREMENTS OR THAT THE OPERATION OR IMPLEMENTATION OF THE FEEDBACK WILL BE UNINTERRUPTED OR ERROR-FREE. - 1.7.1.4. No Liability for Consequential Damages TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL EITHER PARTY OR ITS SUPPLIERS BE LIABLE FOR ANY SPECIAL, INCIDENTAL, INDIRECT, OR CONSEQUENTIAL DAMAGES WHATSOEVER (INCLUDING, WITHOUT LIMITATION, DAMAGES FOR LOSS OF BUSINESS PROFITS, BUSINESS INTERRUPTION, LOSS OF BUSINESS INFORMATION, OR ANY OTHER PECUNIARY LOSS) ARISING OUT OF THE USE OF OR INABILITY TO USE THE FEEDBACK, EVEN IF THE OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. +## Django +Copyright (C) Django Software Foundation and individual contributors. - 1.7.2. Freedom of Action Licensee agrees that this Agreement is nonexclusive and NVIDIA may currently or in the future be developing software, other technology or confidential information internally, or receiving confidential information from other parties that maybe similar to the Feedback and Licensee's confidential information (as provided in Section 1.7.1.2 above), which may be provided to NVIDIA in connection with Feedback by Licensee. Accordingly, Licensee agrees that nothing in this Agreement will be construed as a representation or inference that NVIDIA will not develop, design, manufacture, acquire, market products, or have products developed, designed, manufactured, acquired, or marketed for NVIDIA, that compete with the Licensee's products or confidential information. +All rights reserved. - 1.7.3. No Implied Licenses Under no circumstances should anything in this Agreement be construed as NVIDIA granting by implication, estoppel or otherwise, (i) a license to any NVIDIA product or technology other than the SOFTWARE; or (ii) any additional license rights for the SOFTWARE other than the licenses expressly granted in this Agreement. If any provision of this Agreement is inconsistent with, or cannot be fully enforced under, the law, such provision will be construed as limited to the extent necessary to be consistent with and fully enforceable under the law. This Agreement is the final, complete and exclusive agreement between the parties relating to the subject matter hereof, and supersedes all prior or contemporaneous understandings and agreements relating to such subject matter, whether oral or written. This Agreement may only be modified in writing signed by an authorized officer of NVIDIA. Licensee agrees that it will not ship, transfer or export the SOFTWARE into any country, or use the SOFTWARE in any manner, prohibited by the United States Bureau of Industry and Security or any export laws, restrictions or regulations. The parties agree that the following sections of the Agreement will survive the termination of the License: Section 1.2.1.4, Section 1.4, Section 1.5, Section 1.6, and Section 1.7. -1.8. Attachment A Redistributable Software In connection with Section 1.2.1.1 of this Agreement, the following files may be redistributed with software applications developed by Licensee, including certain variations of these files that have version number or architecture specific information NVIDIA CUDA Toolkit License Agreement www.nvidia.com End User License Agreements (EULA) DR-06739-001_v01_v8.0 | 9 embedded in the file name - as an example only, for release version 6.0 of the 64-bit Windows software, the file cudart64_60.dll is redistributable. -Component : CUDA Runtime Windows : cudart.dll, cudart_static.lib, cudadevrt.lib Mac OSX : libcudart.dylib, libcudart_static.a, libcudadevrt.a Linux : libcudart.so, libcudart_static.a, libcudadevrt.a Android : libcudart.so, libcudart_static.a, libcudadevrt.a Component : CUDA FFT Library Windows : cufft.dll, cufftw.dll Mac OSX : libcufft.dylib, libcufft_static.a, libcufftw.dylib, libcufftw_static.a Linux : libcufft.so, libcufft_static.a, libcufftw.so, libcufftw_static.a Android : libcufft.so, libcufft_static.a, libcufftw.so, libcufftw_static.a Component : CUDA BLAS Library Windows : cublas.dll, cublas_device.lib Mac OSX : libcublas.dylib, libcublas_static.a, libcublas_device.a Linux : libcublas.so, libcublas_static.a, libcublas_device.a Android : libcublas.so, libcublas_static.a, libcublas_device.a Component : NVIDIA "Drop-in" BLAS Library Windows : nvblas.dll Mac OSX : libnvblas.dylib Linux : libnvblas.so Component : CUDA Sparse Matrix Library Windows : cusparse.dll Mac OSX : libcusparse.dylib, libcusparse_static.a Linux : libcusparse.so, libcusparse_static.a Android : libcusparse.so, libcusparse_static.a Component : CUDA Linear Solver Library Windows : cusolver.dll Mac OSX : libcusolver.dylib, libcusolver_static.a Linux : libcusolver.so, libcusolver_static.a Android : libcusolver.so, libcusolver_static.a Component : CUDA Random Number Generation Library Windows : curand.dll Mac OSX : libcurand.dylib, libcurand_static.a Linux : libcurand.so, libcurand_static.a Android : libcurand.so, libcurand_static.a Component : NVIDIA Performance Primitives Library Windows : nppc.dll, nppi.dll, npps.dll Mac OSX : libnppc.dylib, libnppi.dylib, libnpps.dylib, libnppc_static.a, libnpps_static.a, libnppi_static.a Linux : libnppc.so, libnppi.so, libnpps.so, libnppc_static.a, libnpps_static.a, libnppi_static.a Android : libnppc.so, libnppi.so, libnpps.so, libnppc_static.a, libnpps_static.a, libnppi_static.a Component : Internal common library required for statically linking to cuBLAS, cuSPARSE, cuFFT, cuRAND and NPP Mac OSX : libculibos.a Linux : libculibos.a Component : NVIDIA Runtime Compilation Library Windows : nvrtc.dll, nvrtc-builtins.dll Mac OSX : libnvrtc.dylib, libnvrtc-builtins.dylib Linux : libnvrtc.so, libnvrtc-builtins.so Component : NVIDIA Optimizing Compiler Library Windows : nvvm.dll Mac OSX : libnvvm.dylib Linux : libnvvm.so Component : NVIDIA Common Device Math Functions Library Windows : libdevice.compute_20.bc, libdevice.compute_30.bc, libdevice.compute_35.bc Mac OSX : libdevice.compute_20.bc, libdevice.compute_30.bc, libdevice.compute_35.bc Linux : libdevice.compute_20.bc, libdevice.compute_30.bc, libdevice.compute_35.bc Component : CUDA Occupancy Calculation Header Library All : cuda_occupancy.h Component : Profiling Tools Interface Library Windows : cupti.dll Mac OSX : libcupti.dylib Linux : libcupti.so - -1.9. Attachment B Additional Licensing Obligations The following third party components included in the SOFTWARE are licensed to Licensee pursuant to the following terms and conditions: - - -1. Licensee's use of the GDB third party component is subject to the terms and conditions of GNU GPL v3: This product includes copyrighted third-party software licensed under the terms of the GNU General Public License v3 ("GPL v3"). All third-party software packages are copyright by their respective authors. GPL v3 terms and conditions are hereby incorporated into the Agreement by this reference: http://www.gnu.org/licenses/gpl.txt Consistent with these licensing requirements, the software listed below is provided under the terms of the specified open source software licenses. To obtain source code for software provided under licenses that require redistribution of source code, including the GNU General Public License (GPL) and GNU Lesser General Public License (LGPL), contact oss-requests@nvidia.com. This offer is valid for a period of three (3) years from the date of the distribution of this product by NVIDIA CORPORATION. Component License CUDA-GDB GPL v3 - -2. Licensee represents and warrants that any and all third party licensing and/or royalty payment obligations in connection with Licensee's use of the H.264 video codecs are solely the responsibility of Licensee. - -3. Licensee's use of the Thrust library is subject to the terms and conditions of the Apache License Version 2.0. All third-party software packages are copyright by their respective authors. Apache License Version 2.0 terms and conditions are hereby incorporated into the Agreement by this reference. http://www.apache.org/licenses/ LICENSE-2.0.html. In addition, Licensee acknowledges the following notice: Thrust includes source code from the Boost Iterator, Tuple, System, and Random Number libraries. Boost Software License - Version 1.0 - August 17th, 2003 . . . . Permission is hereby granted, free of charge, to any person or organization obtaining a copy of the software and accompanying documentation covered by this license (the "Software") to use, reproduce, display, distribute, execute, and transmit the Software, and to prepare derivative works of the Software, and to permit third-parties to whom the Software is furnished to do so, all subject to the following: The copyright notices in the Software and this entire statement, including the above license grant, this restriction and the following disclaimer, must be included in all copies of the Software, in whole or in part, and all derivative works of the Software, unless such copies or derivative works are solely in the form of machine-executable object code generated by a source language processor. 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You may not convey a covered + work if you are a party to an arrangement with a third party that is in the business of + distributing software, under which you make payment to the third party based on the + extent of your activity of conveying the work, and under which the third party grants, to + any of the parties who would receive the covered work from you, a discriminatory patent + license (a) in connection with copies of the covered work conveyed by you (or copies + made from those copies), or (b) primarily for and in connection with specific products or + compilations that contain the covered work, unless you entered into that arrangement, or + that patent license was granted, prior to 28 March 2007. + Nothing in this License shall be construed as excluding or limiting any implied license or + other defenses to infringement that may otherwise be available to you under applicable + patent law. + 12. No Surrender of Others' Freedom. + If conditions are imposed on you (whether by court order, agreement or otherwise) that + contradict the conditions of this License, they do not excuse you from the conditions of + this License. If you cannot convey a covered work so as to satisfy simultaneously your + obligations under this License and any other pertinent obligations, then as a consequence + you may not convey it at all. For example, if you agree to terms that obligate you to + collect a royalty for further conveying from those to whom you convey the Program, the + only way you could satisfy both those terms and this License would be to refrain entirely + from conveying the Program. + 13. Use with the GNU Affero General Public License. + Notwithstanding any other provision of this License, you have permission to link or + combine any covered work with a work licensed under version 3 of the GNU Affero + General Public License into a single combined work, and to convey the resulting work. + The terms of this License will continue to apply to the part which is the covered work, but + the special requirements of the GNU Affero General Public License, section 13, + concerning interaction through a network will apply to the combination as such. + 14. Revised Versions of this License. + The Free Software Foundation may publish revised and/or new versions of the GNU + General Public License from time to time. Such new versions will be similar in spirit to the + present version, but may differ in detail to address new problems or concerns. + Each version is given a distinguishing version number. If the Program specifies that a + certain numbered version of the GNU General Public License "or any later version" + applies to it, you have the option of following the terms and conditions either of that + numbered version or of any later version published by the Free Software Foundation. If + the Program does not specify a version number of the GNU General Public License, you + may choose any version ever published by the Free Software Foundation. + If the Program specifies that a proxy can decide which future versions of the GNU + General Public License can be used, that proxy's public statement of acceptance of a + version permanently authorizes you to choose that version for the Program. + Later license versions may give you additional or different permissions. However, no + additional obligations are imposed on any author or copyright holder as a result of your + choosing to follow a later version. + 15. Disclaimer of Warranty. + THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT + PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN + WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE + THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER + EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR + PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF + THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, + YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR + CORRECTION. + 16. Limitation of Liability. + IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN + WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO + MODIFIES AND/OR CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE + LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, + INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE + OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO + LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES + SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM + TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR + OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH + DAMAGES. + 17. Interpretation of Sections 15 and 16. + If the disclaimer of warranty and limitation of liability provided above cannot be given + local legal effect according to their terms, reviewing courts shall apply local law that most + closely approximates an absolute waiver of all civil liability in connection with the + Program, unless a warranty or assumption of liability accompanies a copy of the Program + in return for a fee. -15. BECAUSE THE LIBRARY IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE LIBRARY, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE LIBRARY "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE LIBRARY IS WITH YOU. SHOULD THE LIBRARY PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. -16. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE LIBRARY AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE LIBRARY (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE LIBRARY TO OPERATE WITH ANY OTHER SOFTWARE), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. OEM Plupload -------------------------------------------------------------------------- -GNU General Public License + GNU General Public License Version 2, June 1991 -Copyright (C) 1989, 1991 Free Software Foundation, Inc., - -51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA + Copyright (C) 1989, 1991 Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA See Section 2 below for text of GPL v2.0 license. Font awesome -------------------------------------------------------------------------- The Font Awesome font is licensed under the SIL OFL 1.1: This Font Software is licensed under the SIL Open Font License, Version 1.1. - This license is copied below, and is also available with a FAQ at: http://scripts.sil.org/OFL ------------------------------------------------------------ + + SIL OPEN FONT LICENSE Version 1.1 - 26 February 2007 ----------------------------------------------------------- @@ -1556,95 +988,5245 @@ Font Awesome CSS, LESS, and Sass files are licensed under the MIT License: The MIT License -Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated -documentation files (the "Software"), to deal in the Software without restriction, including without limitation -the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, -and to permit persons to whom the Software is furnished to do so, subject to the following conditions: - +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. 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GNU General Public License version 2 (GPL v2) ===================================================================== GNU GENERAL PUBLIC LICENSE -Version 2, June 1991 -Copyright (C) 1989, 1991 Free Software Foundation, Inc. +Version 2, June 1991 + +Copyright (C) 1989, 1991 Free Software Foundation, Inc. 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. -Preamble +###Preamble The licenses for most software are designed to take away your freedom to share and change it. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change free software--to make sure the software is free for all its users. This General Public License applies to most of the Free Software Foundation's software and to any other program whose authors commit to using it. (Some other Free Software Foundation software is covered by the GNU Lesser General Public License instead.) You can apply it to your programs, too. - When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for this service if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs; and that you know you can do these things. - To protect your rights, we need to make restrictions that forbid anyone to deny you these rights or to ask you to surrender the rights. These restrictions translate to certain responsibilities for you if you distribute copies of the software, or if you modify it. - For example, if you distribute copies of such a program, whether gratis or for a fee, you must give the recipients all the rights that you have. You must make sure that they, too, receive or can get the source code. And you must show them these terms so they know their rights. - We protect your rights with two steps: (1) copyright the software, and (2) offer you this license which gives you legal permission to copy, distribute and/or modify the software. - Also, for each author's protection and ours, we want to make certain that everyone understands that there is no warranty for this free software. If the software is modified by someone else and passed on, we want its recipients to know that what they have is not the original, so that any problems introduced by others will not reflect on the original authors' reputations. - Finally, any free program is threatened constantly by software patents. We wish to avoid the danger that redistributors of a free program will individually obtain patent licenses, in effect making the program proprietary. To prevent this, we have made it clear that any patent must be licensed for everyone's free use or not licensed at all. - The precise terms and conditions for copying, distribution and modification follow. - TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION -------------------------------------------------------------- 0. This License applies to any program or other work which contains a notice placed by the copyright holder saying it may be distributed under the terms of this General Public License. The "Program", below, refers to any such program or work, and a "work based on the Program" means either the Program or any derivative work under copyright law: that is to say, a work containing the Program or a portion of it, either verbatim or with modifications and/or translated into another language. (Hereinafter, translation is included without limitation in the term "modification".) Each licensee is addressed as "you". Activities other than copying, distribution and modification are not covered by this License; they are outside its scope. The act of running the Program is not restricted, and the output from the Program is covered only if its contents constitute a work based on the Program (independent of having been made by running the Program). Whether that is true depends on what the Program does. - 1. You may copy and distribute verbatim copies of the Program's source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty; keep intact all the notices that refer to this License and to the absence of any warranty; and give any other recipients of the Program a copy of this License along with the Program. You may charge a fee for the physical act of transferring a copy, and you may at your option offer warranty protection in exchange for a fee. - 2. You may modify your copy or copies of the Program or any portion of it, thus forming a work based on the Program, and copy and distribute such modifications or work under the terms of Section 1 above, provided that you also meet all of these conditions: - - a) You must cause the modified files to carry prominent notices stating that you changed the files and the date of any change. - b) You must cause any work that you distribute or publish, that in whole or in part contains or is derived from the Program or any part thereof, to be licensed as a whole at no charge to all third parties under the terms of this License. - c) If the modified program normally reads commands interactively when run, you must cause it, when started running for such interactive use in the most ordinary way, to print or display an announcement including an appropriate copyright notice and a notice that there is no warranty (or else, saying that you provide a warranty) and that users may redistribute the program under these conditions, and telling the user how to view a copy of this License. (Exception: if the Program itself is interactive but does not normally print such an announcement, your work based on the Program is not required to print an announcement.) - - These requirements apply to the modified work as a whole. If identifiable sections of that work are not derived from the Program, and can be reasonably considered independent and separate works in themselves, then this License, and its terms, do not apply to those sections when you distribute them as separate works. But when you distribute the same sections as part of a whole which is a work based on the Program, the distribution of the whole must be on the terms of this License, whose permissions for other licensees extend to the entire whole, and thus to each and every part regardless of who wrote it. - - Thus, it is not the intent of this section to claim rights or contest your rights to work written entirely by you; rather, the intent is to exercise the right to control the distribution of derivative or collective works based on the Program. - - In addition, mere aggregation of another work not based on the Program with the Program (or with a work based on the Program) on a volume of a storage or distribution medium does not bring the other work under the scope of this License. - +a) You must cause the modified files to carry prominent notices stating that you changed the files and the date of any change. +b) You must cause any work that you distribute or publish, that in whole or in part contains or is derived from the Program or any part thereof, to be licensed as a whole at no charge to all third parties under the terms of this License. +c) If the modified program normally reads commands interactively when run, you must cause it, when started running for such interactive use in the most ordinary way, to print or display an announcement including an appropriate copyright notice and a notice that there is no warranty (or else, saying that you provide a warranty) and that users may redistribute the program under these conditions, and telling the user how to view a copy of this License. (Exception: if the Program itself is interactive but does not normally print such an announcement, your work based on the Program is not required to print an announcement.) +These requirements apply to the modified work as a whole. If identifiable sections of that work are not derived from the Program, and can be reasonably considered independent and separate works in themselves, then this License, and its terms, do not apply to those sections when you distribute them as separate works. But when you distribute the same sections as part of a whole which is a work based on the Program, the distribution of the whole must be on the terms of this License, whose permissions for other licensees extend to the entire whole, and thus to each and every part regardless of who wrote it. +Thus, it is not the intent of this section to claim rights or contest your rights to work written entirely by you; rather, the intent is to exercise the right to control the distribution of derivative or collective works based on the Program. +In addition, mere aggregation of another work not based on the Program with the Program (or with a work based on the Program) on a volume of a storage or distribution medium does not bring the other work under the scope of this License. 3. You may copy and distribute the Program (or a work based on it, under Section 2) in object code or executable form under the terms of Sections 1 and 2 above provided that you also do one of the following: - - a) Accompany it with the complete corresponding machine-readable source code, which must be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, - b) Accompany it with a written offer, valid for at least three years, to give any third party, for a charge no more than your cost of physically performing source distribution, a complete machine-readable copy of the corresponding source code, to be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, - c) Accompany it with the information you received as to the offer to distribute corresponding source code. (This alternative is allowed only for noncommercial distribution and only if you received the program in object code or executable form with such an offer, in accord with Subsection b above.) +a) Accompany it with the complete corresponding machine-readable source code, which must be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, +b) Accompany it with a written offer, valid for at least three years, to give any third party, for a charge no more than your cost of physically performing source distribution, a complete machine-readable copy of the corresponding source code, to be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, +c) Accompany it with the information you received as to the offer to distribute corresponding source code. (This alternative is allowed only for noncommercial distribution and only if you received the program in object code or executable form with such an offer, in accord with Subsection b above.) The source code for a work means the preferred form of the work for making modifications to it. For an executable work, complete source code means all the source code for all modules it contains, plus any associated interface definition files, plus the scripts used to control compilation and installation of the executable. However, as a special exception, the source code distributed need not include anything that is normally distributed (in either source or binary form) with the major components (compiler, kernel, and so on) of the operating system on which the executable runs, unless that component itself accompanies the executable. If distribution of executable or object code is made by offering access to copy from a designated place, then offering equivalent access to copy the source code from the same place counts as distribution of the source code, even though third parties are not compelled to copy the source along with the object code. - 4. You may not copy, modify, sublicense, or distribute the Program except as expressly provided under this License. Any attempt otherwise to copy, modify, sublicense or distribute the Program is void, and will automatically terminate your rights under this License. However, parties who have received copies, or rights, from you under this License will not have their licenses terminated so long as such parties remain in full compliance. - 5. You are not required to accept this License, since you have not signed it. However, nothing else grants you permission to modify or distribute the Program or its derivative works. These actions are prohibited by law if you do not accept this License. Therefore, by modifying or distributing the Program (or any work based on the Program), you indicate your acceptance of this License to do so, and all its terms and conditions for copying, distributing or modifying the Program or works based on it. - 6. Each time you redistribute the Program (or any work based on the Program), the recipient automatically receives a license from the original licensor to copy, distribute or modify the Program subject to these terms and conditions. You may not impose any further restrictions on the recipients' exercise of the rights granted herein. You are not responsible for enforcing compliance by third parties to this License. - 7. If, as a consequence of a court judgment or allegation of patent infringement or for any other reason (not limited to patent issues), conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot distribute so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not distribute the Program at all. For example, if a patent license would not permit royalty-free redistribution of the Program by all those who receive copies directly or indirectly through you, then the only way you could satisfy both it and this License would be to refrain entirely from distribution of the Program. If any portion of this section is held invalid or unenforceable under any particular circumstance, the balance of the section is intended to apply and the section as a whole is intended to apply in other circumstances. - - It is not the purpose of this section to induce you to infringe any patents or other property right claims or to contest validity of any such claims; this section has the sole purpose of protecting the integrity of the free software distribution system, which is implemented by public license practices. Many people have made generous contributions to the wide range of software distributed through that system in reliance on consistent application of that system; it is up to the author/donor to decide if he or she is willing to distribute software through any other system and a licensee cannot impose that choice. +It is not the purpose of this section to induce you to infringe any patents or other property right claims or to contest validity of any such claims; this section has the sole purpose of protecting the integrity of the free software distribution system, which is implemented by public license practices. Many people have made generous contributions to the wide range of software distributed through that system in reliance on consistent application of that system; it is up to the author/donor to decide if he or she is willing to distribute software through any other system and a licensee cannot impose that choice. This section is intended to make thoroughly clear what is believed to be a consequence of the rest of this License. - 8. If the distribution and/or use of the Program is restricted in certain countries either by patents or by copyrighted interfaces, the original copyright holder who places the Program under this License may add an explicit geographical distribution limitation excluding those countries, so that distribution is permitted only in or among countries not thus excluded. In such case, this License incorporates the limitation as if written in the body of this License. - 9. The Free Software Foundation may publish revised and/or new versions of the General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. Each version is given a distinguishing version number. If the Program specifies a version number of this License which applies to it and "any later version", you have the option of following the terms and conditions either of that version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of this License, you may choose any version ever published by the Free Software Foundation. - 10. If you wish to incorporate parts of the Program into other free programs whose distribution conditions are different, write to the author to ask for permission. For software which is copyrighted by the Free Software Foundation, write to the Free Software Foundation; we sometimes make exceptions for this. Our decision will be guided by the two goals of preserving the free status of all derivatives of our free software and of promoting the sharing and reuse of software generally. NO WARRANTY - 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. - 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. + +###End of (1) Torrent Suite(TM) Software Version 5.18 Open Source License + +**************************************************** + (2) BEGINS: +================================================================================ + +LIFE TECHNOLOGIES CORPORATION + +END USER LICENSE AGREEMENT +## FOR SERVICE & SUPPORT TELEMETRY MODULE SOFTWARE VERSION 2.0.1 + +NOTICE TO USER: PLEASE READ THIS DOCUMENT CAREFULLY. THIS IS THE CONTRACT BETWEEN YOU AND LIFE TECHNOLOGIES CORPORATION ("LIFE TECHNOLOGIES") REGARDING THIS SOFTWARE PRODUCT. THIS AGREEMENT CONTAINS WARRANTY AND LIABILITY DISCLAIMERS AND LIMITATIONS. YOUR INSTALLATION AND/OR USE OF THIS LIFE TECHNOLOGIES SOFTWARE IS SUBJECT TO THE TERMS AND CONDITIONS CONTAINED IN THIS END USER SOFTWARE LICENSE AGREEMENT, AND YOU WILL BE BOUND BY THESE TERMS AND CONDITIONS IF YOU INSTALL AND/OR USE THE SOFTWARE. +IF YOU DO NOT AGREE TO THESE TERMS AND CONDITIONS, YOU SHOULD PROMPTLY RETURN THIS SOFTWARE, TOGETHER WITH ALL PACKAGING, TO LIFE TECHNOLOGIES AND YOUR PURCHASE PRICE WILL BE REFUNDED. +This Life Technologies End User License Agreement accompanies a Life Technologies software product ("Software") and related explanatory materials ("Documentation"). The term "Software" also includes any upgrades, modified versions, updates, additions and copies of the Software licensed to you by Life Technologies. 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You shall not reverse assemble, decompile, discover the source code or otherwise reverse engineer the Software. +3. You shall not remove any proprietary, copyright, trade secret or warning legend from the Software or any Documentation. +4. You agree to comply fully with all export laws and restrictions and regulations of the United States or applicable foreign agencies or authorities. You agree that you will not export or reexport, directly or indirectly, the Software and the Documentation into any country prohibited by the United States Export Administration Act and the regulations thereunder or other applicable United States law. +5. You may not use the Software or Documentation for the benefit of any third party by means of an outsourcing or service bureau relationship or for any similar commercial time-sharing or third-party training use. +6. You agree to use Software, and data generated by Software, for the sole purpose of review and analysis of data generated by Life Technologies instruments. + +TRIAL + +If this license is granted on a trial basis, you are hereby notified that license management software may be included to automatically cause the Software to cease functioning at the end of the trial period (and in any case you agree to discontinue usage at the end of the trial period or at the express written request of Life Technologies). + +TERMINATION + +You may terminate this Agreement by discontinuing use of the Software, removing all copies from your computers and storage media, and returning the Software and Documentation, and all copies thereof, to Life Technologies. Life Technologies may terminate this Agreement if you fail to comply with all of its terms, in which case you agree to discontinue using the Software, remove all copies from your computers and storage media, and return the Software and Documentation, and all copies thereof, to Life Technologies. + +U.S. GOVERNMENT END USERS + +The Software is a "commercial item," as that term is defined in 48 C.F.R. 2.101 (Oct. 1995), consisting of "commercial computer software" and "commercial computer software documentation," as such terms are used in 48 C.F.R. 12.212 (Sept. 1995). Consistent with 48 C.F.R. 12.212 and 48 C.F.R. 227.7202-1 through 227.7202-4 (June 1995), all U.S. Government End Users acquire the Software with only those rights set forth herein. + +EUROPEAN UNION END USERS + +If this Software is used within a country of the European Union, nothing in this Agreement shall be construed as restricting any rights available under Directive 2009/24/EC of the European Parliament and of the Council of 23 April 2009 on the legal protection of computer programs. +YOU ACKNOWLEDGE THAT LIFE TECHNOLOGIES HAS NO CONTROL OVER THE SPECIFIC CONDITIONS UNDER WHICH YOU USE THE SOFTWARE. LICENSOR CANNOT AND DOES NOT WARRANT THE PERFORMANCE OF THE SOFTWARE OR ANY PARTICULAR RESULTS THAT MAY BE OBTAINED BY THE USE OF THE SOFTWARE. THE SOFTWARE DOES NOT REPLACE YOUR OBLIGATION TO EXERCISE YOUR INDEPENDENT JUDGMENT IN USING THE SOFTWARE. The warranties, if any, made by Life Technologies may be voided by abuse or misuse of the Software. +LIMITATION OF LIABILITY +IN NO EVENT SHALL LIFE TECHNOLOGIES OR ITS SUPPLIERS BE RESPONSIBLE OR LIABLE, WHETHER IN CONTRACT, TORT, WARRANTY OR UNDER ANY STATUTE (INCLUDING WITHOUT LIMITATION ANY TRADE PRACTICE, UNFAIR COMPETITION OR OTHER STATUTE OF SIMILAR IMPORT) OR ON ANY OTHER BASIS FOR DAMAGES ARISING FROM PERSONAL INJURY OR DEATH OR SPECIAL, INDIRECT, INCIDENTAL, MULTIPLE, PUNITIVE, OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE POSSESSION OR USE OF, OR THE INABILITY TO USE, THE SOFTWARE, THE GENERATED DATA OR DOCUMENTATION, EVEN IF LIFE TECHNOLOGIES IS ADVISED IN ADVANCE OF THE POSSIBILITY OF SUCH DAMAGES, INCLUDING WITHOUT LIMITATION DAMAGES OR EXPENSES ARISING FROM OR RELATED TO, OR ALLEGED TO HAVE ARISEN FROM OR BE RELATED TO, LOSS OF USE, LOSS OF DATA, DOWNTIME, OR FOR LOSS OF REVENUE, PROFITS, GOODWILL OR BUSINESS OR OTHER FINANCIAL LOSS. IN ANY CASE, THE ENTIRE LIABILITY OF LIFE TECHNOLOGIES AND ITS SUPPLIERS UNDER THIS LICENSE, OR ARISING OUT OF THE USE OF THE SOFTWARE OR DOCUMENTATION OR GENERATED DATA, SHALL NOT EXCEED, IN THE AGGREGATE, THE PURCHASE PRICE OF THE PRODUCT. +SOME STATES, COUNTRIES OR JURISDICTIONS LIMIT THE SCOPE OF OR PRECLUDE LIMITATIONS OR EXCLUSION OF REMEDIES OR DAMAGES, OR OF LIABILITY, SUCH AS LIABILITY FOR GROSS NEGLIGENCE OR WILLFUL MISCONDUCT, AS OR TO THE EXTENT SET FORTH ABOVE, OR DO NOT ALLOW IMPLIED WARRANTIES TO BE EXCLUDED. IN SUCH STATES, COUNTRIES OR JURISDICTIONS, THE LIMITATION OR EXCLUSION OF WARRANTIES, REMEDIES, DAMAGES OR LIABILITY SET FORTH ABOVE MAY NOT APPLY TO YOU. HOWEVER, ALTHOUGH THEY SHALL NOT APPLY TO THE EXTENT PROHIBITED BY LAW, THEY SHALL APPLY TO THE FULLEST EXTENT PERMITTED BY LAW. YOU MAY ALSO HAVE OTHER RIGHTS THAT VARY BY STATE, COUNTRY OR OTHER JURISDICTION. + +CONFIDENTIALITY + +You agree to protect Life Technologies Confidential Information with the same degree of care used to protect your own confidential information (but in no event less than a reasonable standard of care), and not to use or disclose any portion of such Confidential Information to third parties, except as expressly authorized in this Agreement. You acknowledge that the Software, including its content, structure, organization and design constitute proprietary and valuable trade secrets (and other intellectual property rights) of Life Technology and/or its licensors. The term "Confidential Information" means, collectively, non-public information that Life Technologies (and its licensors) provide and reasonably consider to be of a confidential, proprietary or trade secret nature, including but not limited to (i) the Software, and (ii) confidential elements of the Software and Life Technologies (and its licensors) technology and know-how, whether in tangible or intangible form, whether designated as confidential or not, and whether or not stored, compiled or memorialized physically, electronically, graphically, photographically, or in writing. Confidential Information does not include any information which you can demonstrate by credible evidence: (a) is, as of the time of its disclosure, or thereafter becomes part of the public domain through no fault of yours; (b) was rightfully known to you prior to the time of its disclosure, or to have been independently developed by you without use of Confidential Information; and/or (C) is subsequently learned from a third party not under a confidentiality obligation with respect to such Confidential Information. Confidential Information that is required to be disclosed by you pursuant to a duly authorized subpoena, court order, or government authority shall continue to be Confidential Information for all other purposes and you agree, prior to disclosing pursuant to a subpoena, court order, or government authority, to provide prompt written notice and assistance to Life Technologies prior to such disclosure, so that Life Technologies may seek a protective order or other appropriate remedy to protect against disclosure. + +SOFTWARE IMPROVEMENTS + +You acknowledge and agree that any ideas, enhancements, modifications, and the like disclosed by you to Life Technologies with respect to the Software ("Software Improvements and Feedback") will be the property of Life Technologies. You agree to assign, and hereby assign, all right, title, and interest worldwide in the Software Improvements and Feedback to Life Technologies and agree to assist Life Technologies, at Life Technologies' expense, in perfecting and enforcing Life Technologies rights thereto and ownership thereof. You acknowledge and agree that Life Technologies may use such Software Improvements and Feedback for its business purposes without restriction. + +GENERAL + +This Agreement shall be governed by laws of the State of California, exclusive of its conflict of laws provisions. This Agreement shall not be governed by the United Nations Convention on Contracts for the International Sale of Goods. This Agreement contains the complete agreement between the parties with respect to the subject matter hereof, and supersedes all prior or contemporaneous agreements or understandings, whether oral or written. If any provision of this Agreement is held by a court of competent jurisdiction to be contrary to law, that provision will be enforced to the maximum extent permissible and the remaining provisions of this Agreement will remain in full force and effect. The controlling language of this Agreement, and any proceedings relating to this Agreement, shall be English. You agree to bear any and all costs of translation, if necessary. The headings to the sections of this Agreement are used for convenience only and shall have no substantive meaning. All questions concerning this Agreement shall be directed to: Life Technologies Corporation, 5781 Van Allen Way, Carlsbad, CA 92008, Attention: Legal Department. +Unpublished rights reserved under the copyright laws of the United States. Life Technologies Corporation, 5781 Van Allen Way, Carlsbad, CA 92008. +Life Technologies is a trademark of Life Technologies Corporation or its subsidiaries in the U.S. and certain other countries. +All other trademarks are the sole property of their respective owners. + +July 15, 2020 + +Appendix 1 + +Life Technologies Corporation + +Third Party Copyright Notices and Licenses + SERVICE & SUPPORT TELEMETRY MODULE SOFTWARE VERSION 2.0.1 +This software uses third party software components from several sources. Portions of these software components are copyrighted and licensed by their respective owners as indicated below. Various licenses require distribution of source code or if a link is used to point the end-user to a source-code repository, and the source code is not available at such site, the distributor must, for a time determined by license, offer to provide source code. In such cases, please contact your Life Technologies representative. As well, various licenses require that the end-user receive a copy of the license or certain notices. Such licenses and notices may be found in this appendix. + +Asn1crypto Copyright (C) 2015-2018 Will Bond +Six Copyright (C) 2010-2018 Benjamin Peterson + + + +The MIT License + +Permission is hereby granted, free of charge, to any person obtaining a copy of + this software and associated documentation files (the "Software"), to deal in + the Software without restriction, including without limitation the rights to + use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies + of the Software, and to permit persons to whom the Software is furnished to do + so, subject to the following conditions: + + The above copyright notice and this permission notice shall be included in all + copies or substantial portions of the Software. + + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE + SOFTWARE. + +Boto3 + +Botocore + +Pelix + +S3transfer + +Apache License + +Version 2.0, January 2004 + +TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + +1. Definitions. +"License" shall mean the terms and conditions for use, reproduction, and distribution as defined by Sections 1 through 9 of this document. +"Licensor" shall mean the copyright owner or entity authorized by the copyright owner that is granting the License. +"Legal Entity" shall mean the union of the acting entity and all other entities that control, are controlled by, or are under common control with that entity. For the purposes of this definition, "control" means (i) the power, direct or indirect, to cause the direction or management of such entity, whether by contract or otherwise, or (ii) ownership of fifty percent (50%) or more of the outstanding shares, or (iii) beneficial ownership of such entity. +"You" (or "Your") shall mean an individual or Legal Entity exercising permissions granted by this License. +"Source" form shall mean the preferred form for making modifications, including but not limited to software source code, documentation source, and configuration files. +"Object" form shall mean any form resulting from mechanical transformation or translation of a Source form, including but not limited to compiled object code, generated documentation, and conversions to other media types. +"Work" shall mean the work of authorship, whether in Source or Object form, made available under the License, as indicated by a copyright notice that is included in or attached to the work (an example is provided in the Appendix below). +"Derivative Works" shall mean any work, whether in Source or Object form, that is based on (or derived from) the Work and for which the editorial revisions, annotations, elaborations, or other modifications represent, as a whole, an original work of authorship. For the purposes of this License, Derivative Works shall not include works that remain separable from, or merely link (or bind by name) to the interfaces of, the Work and Derivative Works thereof. +"Contribution" shall mean any work of authorship, including the original version of the Work and any modifications or additions to that Work or Derivative Works thereof, that is intentionally submitted to Licensor for inclusion in the Work by the copyright owner or by an individual or Legal Entity authorized to submit on behalf of the copyright owner. For the purposes of this definition, "submitted" means any form of electronic, verbal, or written communication sent to the Licensor or its representatives, including but not limited to communication on electronic mailing lists, source code control systems, and issue tracking systems that are managed by, or on behalf of, the Licensor for the purpose of discussing and improving the Work, but excluding communication that is conspicuously marked or otherwise designated in writing by the copyright owner as "Not a Contribution." +"Contributor" shall mean Licensor and any individual or Legal Entity on behalf of whom a Contribution has been received by Licensor and subsequently incorporated within the Work. +2. Grant of Copyright License. Subject to the terms and conditions of this License, each Contributor hereby grants to You a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable copyright license to reproduce, prepare Derivative Works of, publicly display, publicly perform, sublicense, and distribute the Work and such Derivative Works in Source or Object form. +3. Grant of Patent License. Subject to the terms and conditions of this License, each Contributor hereby grants to You a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable (except as stated in this section) patent license to make, have made, use, offer to sell, sell, import, and otherwise transfer the Work, where such license applies only to those patent claims licensable by such Contributor that are necessarily infringed by their Contribution(s) alone or by combination of their Contribution(s) with the Work to which such Contribution(s) was submitted. If You institute patent litigation against any entity (including a cross-claim or counterclaim in a lawsuit) alleging that the Work or a Contribution incorporated within the Work constitutes direct or contributory patent infringement, then any patent licenses granted to You under this License for that Work shall terminate as of the date such litigation is filed. +4. Redistribution. You may reproduce and distribute copies of the Work or Derivative Works thereof in any medium, with or without modifications, and in Source or Object form, provided that You meet the following conditions: +1. You must give any other recipients of the Work or Derivative Works a copy of this License; and +2. You must cause any modified files to carry prominent notices stating that You changed the files; and +3. You must retain, in the Source form of any Derivative Works that You distribute, all copyright, patent, trademark, and attribution notices from the Source form of the Work, excluding those notices that do not pertain to any part of the Derivative Works; and +4. If the Work includes a "NOTICE" text file as part of its distribution, then any Derivative Works that You distribute must include a readable copy of the attribution notices contained within such NOTICE file, excluding those notices that do not pertain to any part of the Derivative Works, in at least one of the following places: within a NOTICE text file distributed as part of the Derivative Works; within the Source form or documentation, if provided along with the Derivative Works; or, within a display generated by the Derivative Works, if and wherever such third-party notices normally appear. The contents of the NOTICE file are for informational purposes only and do not modify the License. You may add Your own attribution notices within Derivative Works that You distribute, alongside or as an addendum to the NOTICE text from the Work, provided that such additional attribution notices cannot be construed as modifying the License. +You may add Your own copyright statement to Your modifications and may provide additional or different license terms and conditions for use, reproduction, or distribution of Your modifications, or for any such Derivative Works as a whole, provided Your use, reproduction, and distribution of the Work otherwise complies with the conditions stated in this License. +5. Submission of Contributions. Unless You explicitly state otherwise, any Contribution intentionally submitted for inclusion in the Work by You to the Licensor shall be under the terms and conditions of this License, without any additional terms or conditions. Notwithstanding the above, nothing herein shall supersede or modify the terms of any separate license agreement you may have executed with Licensor regarding such Contributions. +6. Trademarks. This License does not grant permission to use the trade names, trademarks, service marks, or product names of the Licensor, except as required for reasonable and customary use in describing the origin of the Work and reproducing the content of the NOTICE file. +7. Disclaimer of Warranty. Unless required by applicable law or agreed to in writing, Licensor provides the Work (and each Contributor provides its Contributions) on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied, including, without limitation, any warranties or conditions of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A PARTICULAR PURPOSE. You are solely responsible for determining the appropriateness of using or redistributing the Work and assume any risks associated with Your exercise of permissions under this License. +8. Limitation of Liability. In no event and under no legal theory, whether in tort (including negligence), contract, or otherwise, unless required by applicable law (such as deliberate and grossly negligent acts) or agreed to in writing, shall any Contributor be liable to You for damages, including any direct, indirect, special, incidental, or consequential damages of any character arising as a result of this License or out of the use or inability to use the Work (including but not limited to damages for loss of goodwill, work stoppage, computer failure or malfunction, or any and all other commercial damages or losses), even if such Contributor has been advised of the possibility of such damages. +9. Accepting Warranty or Additional Liability. While redistributing the Work or Derivative Works thereof, You may choose to offer, and charge a fee for, acceptance of support, warranty, indemnity, or other liability obligations and/or rights consistent with this License. However, in accepting such obligations, You may act only on Your own behalf and on Your sole responsibility, not on behalf of any other Contributor, and only if You agree to indemnify, defend, and hold each Contributor harmless for any liability incurred by, or claims asserted against, such Contributor by reason of your accepting any such warranty or additional liability. + +Concurrent + +The Python Software Foundation License Version 2 + + 1. This LICENSE AGREEMENT is between the Python Software Foundation + ("PSF"), and the Individual or Organization ("Licensee") accessing and + otherwise using this software ("Python") in source or binary form and + its associated documentation. + + 2. Subject to the terms and conditions of this License Agreement, PSF + hereby grants Licensee a nonexclusive, royalty-free, world-wide + license to reproduce, analyze, test, perform and/or display publicly, + prepare derivative works, distribute, and otherwise use Python + alone or in any derivative version, provided, however, that PSF's + License Agreement and PSF's notice of copyright, i.e., "Copyright (C) + 2001, 2002, 2003, 2004, 2005, 2006 Python Software Foundation; All Rights + Reserved" are retained in Python alone or in any derivative version + prepared by Licensee. + + 3. In the event Licensee prepares a derivative work that is based on + or incorporates Python or any part thereof, and wants to make + the derivative work available to others as provided herein, then + Licensee hereby agrees to include in any such work a brief summary of + the changes made to Python. + + 4. PSF is making Python available to Licensee on an "AS IS" + basis. PSF MAKES NO REPRESENTATIONS OR WARRANTIES, EXPRESS OR + IMPLIED. BY WAY OF EXAMPLE, BUT NOT LIMITATION, PSF MAKES NO AND + DISCLAIMS ANY REPRESENTATION OR WARRANTY OF MERCHANTABILITY OR FITNESS + FOR ANY PARTICULAR PURPOSE OR THAT THE USE OF PYTHON WILL NOT + INFRINGE ANY THIRD PARTY RIGHTS. + + 5. PSF SHALL NOT BE LIABLE TO LICENSEE OR ANY OTHER USERS OF PYTHON + FOR ANY INCIDENTAL, SPECIAL, OR CONSEQUENTIAL DAMAGES OR LOSS AS + A RESULT OF MODIFYING, DISTRIBUTING, OR OTHERWISE USING PYTHON, + OR ANY DERIVATIVE THEREOF, EVEN IF ADVISED OF THE POSSIBILITY THEREOF. + + 6. This License Agreement will automatically terminate upon a material + breach of its terms and conditions. + + 7. Nothing in this License Agreement shall be deemed to create any + relationship of agency, partnership, or joint venture between PSF and + Licensee. This License Agreement does not grant permission to use PSF + trademarks or trade name in a trademark sense to endorse or promote + products or services of Licensee, or any third party. + + 8. By copying, installing or otherwise using Python, Licensee + agrees to be bound by the terms and conditions of this License + Agreement. + +Paho + +Eclipse Distribution License - v 1.0 + +Copyright (C) 2007, Eclipse Foundation, Inc. and its licensors. + +All rights reserved. + +Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: + +* Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. +* Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. +* Neither the name of the Eclipse Foundation, Inc. nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +AND + +Eclipse Public License - v 1.0 + +THE ACCOMPANYING PROGRAM IS PROVIDED UNDER THE TERMS OF THIS ECLIPSE PUBLIC LICENSE ("AGREEMENT"). ANY USE, REPRODUCTION OR DISTRIBUTION OF THE PROGRAM CONSTITUTES RECIPIENT'S ACCEPTANCE OF THIS AGREEMENT. + +1. DEFINITIONS + + + "Contribution" means: + + a) in the case of the initial Contributor, the initial code and documentation distributed under this Agreement, and + + b) in the case of each subsequent Contributor: + + i)changes to the Program, and + + ii)additions to the Program; + where such changes and/or additions to the Program originate from and are distributed by that particular Contributor. A Contribution 'originates' from a Contributor if it was added to the Program by such Contributor itself or anyone acting on such Contributor's behalf. Contributions do not include additions to the Program which: (i) are separate modules of software distributed in conjunction with the Program under their own license agreement, and (ii) are not derivative works of the Program. +"Contributor" means any person or entity that distributes the Program. +"Licensed Patents " mean patent claims licensable by a Contributor which are necessarily infringed by the use or sale of its Contribution alone or when combined with the Program. +"Program" means the Contributions distributed in accordance with this Agreement. +"Recipient" means anyone who receives the Program under this Agreement, including all Contributors. + +2. GRANT OF RIGHTS + + + a) Subject to the terms of this Agreement, each Contributor hereby grants Recipient a non-exclusive, worldwide, royalty-free copyright license to reproduce, prepare derivative works of, publicly display, publicly perform, distribute and sublicense the Contribution of such Contributor, if any, and such derivative works, in source code and object code form. + + b) Subject to the terms of this Agreement, each Contributor hereby grants Recipient a non-exclusive, worldwide, royalty-free patent license under Licensed Patents to make, use, sell, offer to sell, import and otherwise transfer the Contribution of such Contributor, if any, in source code and object code form. This patent license shall apply to the combination of the Contribution and the Program if, at the time the Contribution is added by the Contributor, such addition of the Contribution causes such combination to be covered by the Licensed Patents. The patent license shall not apply to any other combinations which include the Contribution. No hardware per se is licensed hereunder. + + c) Recipient understands that although each Contributor grants the licenses to its Contributions set forth herein, no assurances are provided by any Contributor that the Program does not infringe the patent or other intellectual property rights of any other entity. Each Contributor disclaims any liability to Recipient for claims brought by any other entity based on infringement of intellectual property rights or otherwise. As a condition to exercising the rights and licenses granted hereunder, each Recipient hereby assumes sole responsibility to secure any other intellectual property rights needed, if any. For example, if a third party patent license is required to allow Recipient to distribute the Program, it is Recipient's responsibility to acquire that license before distributing the Program. +d) Each Contributor represents that to its knowledge it has sufficient copyright rights in its Contribution, if any, to grant the copyright license set forth in this Agreement. + +3. REQUIREMENTS + + A Contributor may choose to distribute the Program in object code form under its own license agreement, provided that: + + a) it complies with the terms and conditions of this Agreement; and + + b) its license agreement: + + i) effectively disclaims on behalf of all Contributors all warranties and conditions, express and implied, including warranties or conditions of title and non-infringement, and implied warranties or conditions of merchantability and fitness for a particular purpose; + + ii) effectively excludes on behalf of all Contributors all liability for damages, including direct, indirect, special, incidental and consequential damages, such as lost profits; + + iii) states that any provisions which differ from this Agreement are offered by that Contributor alone and not by any other party; and + + iv) states that source code for the Program is available from such Contributor, and informs licensees how to obtain it in a reasonable manner on or through a medium customarily used for software exchange. +When the Program is made available in source code form: + + a) it must be made available under this Agreement; and + + b) a copy of this Agreement must be included with each copy of the Program. + Contributors may not remove or alter any copyright notices contained within the Program. + Each Contributor must identify itself as the originator of its Contribution, if any, in a manner that reasonably allows subsequent Recipients to identify the originator of the Contribution. + +4. COMMERCIAL DISTRIBUTION + + Commercial distributors of software may accept certain responsibilities with respect to end users, business partners and the like. While this license is intended to facilitate the commercial use of the Program, the Contributor who includes the Program in a commercial product offering should do so in a manner which does not create potential liability for other Contributors. Therefore, if a Contributor includes the Program in a commercial product offering, such Contributor ("Commercial Contributor") hereby agrees to defend and indemnify every other Contributor ("Indemnified Contributor") against any losses, damages and costs (collectively "Losses") arising from claims, lawsuits and other legal actions brought by a third party against the Indemnified Contributor to the extent caused by the acts or omissions of such Commercial Contributor in connection with its distribution of the Program in a commercial product offering. The obligations in this section do not apply to any claims or Losses relating to any actual or alleged intellectual property infringement. In order to qualify, an Indemnified Contributor must: a) promptly notify the Commercial Contributor in writing of such claim, and b) allow the Commercial Contributor to control, and cooperate with the Commercial Contributor in, the defense and any related settlement negotiations. The Indemnified Contributor may participate in any such claim at its own expense. + For example, a Contributor might include the Program in a commercial product offering, Product X. That Contributor is then a Commercial Contributor. If that Commercial Contributor then makes performance claims, or offers warranties related to Product X, those performance claims and warranties are such Commercial Contributor's responsibility alone. Under this section, the Commercial Contributor would have to defend claims against the other Contributors related to those performance claims and warranties, and if a court requires any other Contributor to pay any damages as a result, the Commercial Contributor must pay those damages. + +5. NO WARRANTY + + EXCEPT AS EXPRESSLY SET FORTH IN THIS AGREEMENT, THE PROGRAM IS PROVIDED ON AN "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, EITHER EXPRESS OR IMPLIED INCLUDING, WITHOUT LIMITATION, ANY WARRANTIES OR CONDITIONS OF TITLE, NON-INFRINGEMENT, MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. Each Recipient is solely responsible for determining the appropriateness of using and distributing the Program and assumes all risks associated with its exercise of rights under this Agreement , including but not limited to the risks and costs of program errors, compliance with applicable laws, damage to or loss of data, programs or equipment, and unavailability or interruption of operations. + +6. DISCLAIMER OF LIABILITY + + EXCEPT AS EXPRESSLY SET FORTH IN THIS AGREEMENT, NEITHER RECIPIENT NOR ANY CONTRIBUTORS SHALL HAVE ANY LIABILITY FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING WITHOUT LIMITATION LOST PROFITS), HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OR DISTRIBUTION OF THE PROGRAM OR THE EXERCISE OF ANY RIGHTS GRANTED HEREUNDER, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. + +7. GENERAL + + If any provision of this Agreement is invalid or unenforceable under applicable law, it shall not affect the validity or enforceability of the remainder of the terms of this Agreement, and without further action by the parties hereto, such provision shall be reformed to the minimum extent necessary to make such provision valid and enforceable. + + If Recipient institutes patent litigation against any entity (including a cross-claim or counterclaim in a lawsuit) alleging that the Program itself (excluding combinations of the Program with other software or hardware) infringes such Recipient's patent(s), then such Recipient's rights granted under Section 2(b) shall terminate as of the date such litigation is filed. + + All Recipient's rights under this Agreement shall terminate if it fails to comply with any of the material terms or conditions of this Agreement and does not cure such failure in a reasonable period of time after becoming aware of such noncompliance. If all Recipient's rights under this Agreement terminate, Recipient agrees to cease use and distribution of the Program as soon as reasonably practicable. However, Recipient's obligations under this Agreement and any licenses granted by Recipient relating to the Program shall continue and survive. +Everyone is permitted to copy and distribute copies of this Agreement, but in order to avoid inconsistency the Agreement is copyrighted and may only be modified in the following manner. The Agreement Steward reserves the right to publish new versions (including revisions) of this Agreement from time to time. No one other than the Agreement Steward has the right to modify this Agreement. The Eclipse Foundation is the initial Agreement Steward. The Eclipse Foundation may assign the responsibility to serve as the Agreement Steward to a suitable separate entity. Each new version of the Agreement will be given a distinguishing version number. The Program (including Contributions) may always be distributed subject to the version of the Agreement under which it was received. In addition, after a new version of the Agreement is published, Contributor may elect to distribute the Program (including its Contributions) under the new version. Except as expressly stated in Sections 2(a) and 2(b) above, Recipient receives no rights or licenses to the intellectual property of any Contributor under this Agreement, whether expressly, by implication, estoppel or otherwise. All rights in the Program not expressly granted under this Agreement are reserved. + + This Agreement is governed by the laws of the State of New York and the intellectual property laws of the United States of America. No party to this Agreement will bring a legal action under this Agreement more than one year after the cause of action arose. Each party waives its rights to a jury trial in any resulting litigation. + +## Docutils + + Public Domain Dedication + + The persons who have associated their work with this project (the "Dedicator": David Goodger and the many contributors to the Docutils project) hereby dedicate the entire copyright, less the exceptions listed below, in the work of authorship known as "Docutils" identified below (the "Work") to the public domain. + + The primary repository for the Work is the Internet World Wide Web site . The Work consists of the files within the "docutils" module of the Docutils project Subversion repository (Internet host docutils.svn.sourceforge.net, filesystem path /svnroot/docutils), whose Internet web interface is located at . Files dedicated to the public domain may be identified by the inclusion, near the beginning of each file, of a declaration of the form: + + Copyright: This document/module/DTD/stylesheet/file/etc. has been + placed in the public domain. + + Dedicator makes this dedication for the benefit of the public at large and to the detriment of Dedicator's heirs and successors. Dedicator intends this dedication to be an overt act of relinquishment in perpetuity of all present and future rights under copyright law, whether vested or contingent, in the Work. Dedicator understands that such relinquishment of all rights includes the relinquishment of all rights to enforce (by lawsuit or otherwise) those copyrights in the Work. + + Dedicator recognizes that, once placed in the public domain, the Work may be freely reproduced, distributed, transmitted, used, modified, built upon, or otherwise exploited by anyone for any purpose, commercial or non-commercial, and in any way, including by methods that have not yet been invented or conceived. + +## Dateutil + + Copyright (C) 2003-2011 - Gustavo Niemeyer + + Copyright (C) 2012-2014 - Tomi Pievilainen + + Copyright (C) 2014 - Yaron de Leeuw + + All rights reserved. + + Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + * Redistributions of source code must retain the above copyright notice, + this list of conditions and the following disclaimer. + * Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + * Neither the name of the copyright holder nor the names of its + contributors may be used to endorse or promote products derived from + this software without specific prior written permission. + + THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS +"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT +LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR +A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR +CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +## Enum + +Copyright (C) 2013, Ethan Furman. + +All rights reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions +are met: + + Redistributions of source code must retain the above + copyright notice, this list of conditions and the + following disclaimer. + + Redistributions in binary form must reproduce the above + copyright notice, this list of conditions and the following + disclaimer in the documentation and/or other materials + provided with the distribution. + + Neither the name Ethan Furman nor the names of any + contributors may be used to endorse or promote products + derived from this software without specific prior written + permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE +LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR +CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF +SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS +INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN +CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) +ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE +POSSIBILITY OF SUCH DAMAGE. + +## Jmespath + +Copyright (C) 2013 Amazon.com, Inc. or its affiliates. All Rights Reserved + +Permission is hereby granted, free of charge, to any person obtaining a +copy of this software and associated documentation files (the +"Software"), to deal in the Software without restriction, including +without limitation the rights to use, copy, modify, merge, publish, dis- +tribute, sublicense, and/or sell copies of the Software, and to permit +persons to whom the Software is furnished to do so, subject to the fol- +lowing conditions: + +The above copyright notice and this permission notice shall be included +in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS +OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABIL- +ITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT +SHALL THE AUTHOR BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, +WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS +IN THE SOFTWARE. + +## Oscrypto + +Copyright (C) 2015-2018 Will Bond + +Permission is hereby granted, free of charge, to any person obtaining a copy of +this software and associated documentation files (the "Software"), to deal in +the Software without restriction, including without limitation the rights to +use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies +of the Software, and to permit persons to whom the Software is furnished to do +so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. + +## Pubsub + +Copyright (C) since 2006, Oliver Schoenborn +All rights reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + +1. Redistributions of source code must retain the above copyright notice, this + list of conditions and the following disclaimer. +2. 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For example, if a patent +license would not permit royalty-free redistribution of the Library by all those who receive copies directly or indirectly through you, then the only way you could satisfy both it and this License would be to refrain entirely from distribution of the Library. + + + If any portion of this section is held invalid or unenforceable under any particular circumstance, the balance of the section is intended to apply, and the section as a whole is intended to apply in other circumstances. + + + It is not the purpose of this section to induce you to infringe any patents or other property right claims or to contest validity of any such claims; this section has the sole purpose of protecting the integrity of the free software distribution system which is implemented by public license practices. Many people have made generous contributions to the wide range of software distributed through that system in reliance on consistent application of that system; it is up to the author/donor to decide if he or she is willing +to distribute software through any other system and a licensee cannot impose that choice. + + + This section is intended to make thoroughly clear what is believed to be a consequence of the rest of this License. +12. If the distribution and/or use of the Library is restricted in certain countries either by patents or by copyrighted interfaces, the +original copyright holder who places the Library under this License may add an explicit geographical distribution limitation excluding those countries, +so that distribution is permitted only in or among countries not thus excluded. In such case, this License incorporates the limitation as if written in the body of this License. + + +13. The Free Software Foundation may publish revised and/or new versions of the Lesser General Public License from time to time. Such new versions will be similar in spirit to the present version, +but may differ in detail to address new problems or concerns. + + + Each version is given a distinguishing version number. If the Library specifies a version number of this License which applies to it and +"any later version", you have the option of following the terms and conditions either of that version or of any later version published by the Free Software Foundation. If the Library does not specify a +license version number, you may choose any version ever published by the Free Software Foundation. + +14. If you wish to incorporate parts of the Library into other free programs whose distribution conditions are incompatible with these, write to the author to ask for permission. For software which is copyrighted by the Free Software Foundation, write to the Free Software Foundation; we sometimes make exceptions for this. Our decision will be guided by the two goals of preserving the free status of all derivatives of our free software and of promoting the sharing and reuse of software generally. + + + NO WARRANTY + + +15. BECAUSE THE LIBRARY IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE LIBRARY, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE LIBRARY "AS IS" WITHOUT WARRANTY OF ANY +KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE LIBRARY IS WITH YOU. SHOULD THE LIBRARY PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. + + +16. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY +AND/OR REDISTRIBUTE THE LIBRARY AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE LIBRARY (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE LIBRARY TO OPERATE WITH ANY OTHER SOFTWARE), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. + + +END OF TERMS AND CONDITIONS + + + + +GPL v2 + +Linux Kernel + +https://www.kernel.org/doc/html/v4.18/process/license-rules.html#:~:text=The%20Linux%20Kernel% +20is%20provideddescribed%20in%20the%20COPYING%20file + + +GNU GENERAL PUBLIC LICENSE Version 2, June 1991 + + +Copyright (C) 1989, 1991 Free Software Foundation, Inc. +51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. + + +Preamble + + +The licenses for most software are designed to take away your freedom to share and change it. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change free software--to make sure the software is free for all its users. This General Public License applies to most of the Free Software +Foundation's software and to any other program whose authors commit to using it. (Some other Free Software Foundation software is covered by the GNU Library General Public License instead.) You can apply it to your programs, too. + + +When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for this service if you wish), that you receive source code or can get it +if you want it, that you can change the software or use pieces of it in new free programs; and that you know you can do these things. +To protect your rights, we need to make restrictions that forbid anyone to deny you these rights or to ask you to surrender the rights. These restrictions translate to certain responsibilities for you if you distribute copies of the software, or if you modify it. + + +For example, if you distribute copies of such a program, whether gratis or for a fee, you must give the recipients all the rights that +you have. You must make sure that they, too, receive or can get the source code. And you must show them these terms so they know their rights. + + +We protect your rights with two steps: (1) copyright the software, and (2) offer you this license which gives you legal permission to copy, distribute and/or modify the software. + + +Also, for each author's protection and ours, we want to make certain that everyone understands that there is no warranty for this free +software. If the software is modified by someone else and passed on, we want its recipients to know that what they have is not the original, so +that any problems introduced by others will not reflect on the original authors' reputations. + + +Finally, any free program is threatened constantly by software patents. We wish to avoid the danger that redistributors of a free program will individually obtain patent licenses, in effect making the program proprietary. To prevent this, we have made it clear that any patent must be licensed for everyone's free use or not licensed at all. + + +The precise terms and conditions for copying, distribution and modification follow. + +GNU GENERAL PUBLIC LICENSE +TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION + + +0. This License applies to any program or other work which contains a notice placed by the copyright holder saying it may be distributed under the terms of this General Public License. The "Program", below, refers to any such program or work, and a "work based on the Program" means either the Program or any derivative work under copyright law: that is to say, a work containing the Program or a portion of it, +either verbatim or with modifications and/or translated into another language. (Hereinafter, translation is included without limitation in the term "modification".) Each licensee is addressed as "you". +Activities other than copying, distribution and modification are not covered by this License; they are outside its scope. The act of +running the Program is not restricted, and the output from the Program is covered only if its contents constitute a work based on the +Program (independent of having been made by running the Program). Whether that is true depends on what the Program does. + + +1. You may copy and distribute verbatim copies of the Program's source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty; keep intact all the notices that refer to this License and to the absence of any warranty; and give any other recipients of the Program a copy of this License along with the Program. + + + You may charge a fee for the physical act of transferring a copy, and you may at your option offer warranty protection in exchange for a fee. + + +2. You may modify your copy or copies of the Program or any portion of it, thus forming a work based on the Program, and copy and +distribute such modifications or work under the terms of Section 1 above, provided that you also meet all of these conditions: + + + a) You must cause the modified files to carry prominent notices stating that you changed the files and the date of any change. + + + b) You must cause any work that you distribute or publish, that in whole or in part contains or is derived from the Program or any part thereof, to be licensed as a whole at no charge to all third parties under the terms of this License. + + + c) If the modified program normally reads commands interactively when run, you must cause it, when started running for such interactive use in the most ordinary way, to print or display an announcement including an appropriate copyright notice and a notice that there is no warranty (or else, saying that you provide +a warranty) and that users may redistribute the program under these conditions, and telling the user how to view a copy of this License. (Exception: if the Program itself is interactive but +does not normally print such an announcement, your work based on +the Program is not required to print an announcement.) + + + These requirements apply to the modified work as a whole. If identifiable sections of that work are not derived from the Program, +and can be reasonably considered independent and separate works in themselves, then this License, and its terms, do not apply to those sections when you distribute them as separate works. But when you distribute the same sections as part of a whole which is a work based on the Program, the distribution of the whole must be on the terms of this License, whose permissions for other licensees extend to the +entire whole, and thus to each and every part regardless of who wrote it. + + + Thus, it is not the intent of this section to claim rights or contest your rights to work written entirely by you; rather, the intent is to exercise the right to control the distribution of derivative or collective works based on the Program. + + + In addition, mere aggregation of another work not based on the Program with the Program (or with a work based on the Program) on a volume of a storage or distribution medium does not bring the other work under +the scope of this License. + + +3. You may copy and distribute the Program (or a work based on it, under Section 2) in object code or executable form under the terms of Sections 1 and 2 above provided that you also do one of the following: + + + a) Accompany it with the complete corresponding machine-readable source code, which must be distributed under the terms of Sections +1 and 2 above on a medium customarily used for software interchange; or, + + + b) Accompany it with a written offer, valid for at least three years, to give any third party, for a charge no more than your cost of physically performing source distribution, a complete machine-readable copy of the corresponding source code, to be +distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, + + + c) Accompany it with the information you received as to the offer to distribute corresponding source code. (This alternative is allowed only for noncommercial distribution and only if you received the program in object code or executable form with such an offer, in accord with Subsection b above.) + + + The source code for a work means the preferred form of the work for making modifications to it. For an executable work, complete source code means all the source code for all modules it contains, plus any associated interface definition files, plus the scripts used to +control compilation and installation of the executable. However, as a +special exception, the source code distributed need not include anything that is normally distributed (in either source or binary +form) with the major components (compiler, kernel, and so on) of the operating system on which the executable runs, unless that component itself accompanies the executable. + + + If distribution of executable or object code is made by offering access to copy from a designated place, then offering equivalent access to copy the source code from the same place counts as distribution of the source code, even though third parties are not compelled to copy the source along with the object code. + +4. You may not copy, modify, sublicense, or distribute the Program except as expressly provided under this License. Any attempt otherwise to copy, modify, sublicense or distribute the Program is void, and will automatically terminate your rights under this License. However, parties who have received copies, or rights, from you under this License will not have their licenses terminated so long as such parties remain in full compliance. + + +5. You are not required to accept this License, since you have not signed it. However, nothing else grants you permission to modify or distribute the Program or its derivative works. These actions are prohibited by law if you do not accept this License. Therefore, by modifying or distributing the Program (or any work based on the Program), you indicate your acceptance of this License to do so, and all its terms and conditions for copying, distributing or modifying +the Program or works based on it. + + +6. Each time you redistribute the Program (or any work based on the Program), the recipient automatically receives a license from the original licensor to copy, distribute or modify the Program subject to these terms and conditions. You may not impose any further restrictions on the recipients' exercise of the rights granted herein. +You are not responsible for enforcing compliance by third parties to this License. + + +7. If, as a consequence of a court judgment or allegation of patent infringement or for any other reason (not limited to patent issues), conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot distribute so as to satisfy simultaneously your obligations under this +License and any other pertinent obligations, then as a consequence you +may not distribute the Program at all. For example, if a patent +license would not permit royalty-free redistribution of the Program by all those who receive copies directly or indirectly through you, then the only way you could satisfy both it and this License would be to refrain entirely from distribution of the Program. + + + If any portion of this section is held invalid or unenforceable under any particular circumstance, the balance of the section is intended to apply and the section as a whole is intended to apply in other circumstances. + + + It is not the purpose of this section to induce you to infringe any patents or other property right claims or to contest validity of any such claims; this section has the sole purpose of protecting the integrity of the free software distribution system, which is implemented by public license practices. Many people have made generous contributions to the wide range of software distributed through that system in reliance on consistent application of that system; it is up to the author/donor to decide if he or she is willing +to distribute software through any other system and a licensee cannot impose that choice. + + + This section is intended to make thoroughly clear what is believed to be a consequence of the rest of this License. + +8. If the distribution and/or use of the Program is restricted in certain countries either by patents or by copyrighted interfaces, the original copyright holder who places the Program under this License may add an explicit geographical distribution limitation excluding those countries, so that distribution is permitted only in or among countries not thus excluded. In such case, this License incorporates the limitation as if written in the body of this License. + + +9. The Free Software Foundation may publish revised and/or new versions of the General Public License from time to time. Such new versions will +be similar in spirit to the present version, but may differ in detail to address new problems or concerns. + + + Each version is given a distinguishing version number. If the Program specifies a version number of this License which applies to it and "any later version", you have the option of following the terms and conditions either of that version or of any later version published by the Free +Software Foundation. If the Program does not specify a version number of +this License, you may choose any version ever published by the Free Software +Foundation. + + +10. If you wish to incorporate parts of the Program into other free programs whose distribution conditions are different, write to the author to ask for permission. For software which is copyrighted by the Free +Software Foundation, write to the Free Software Foundation; we sometimes make exceptions for this. Our decision will be guided by the two goals +of preserving the free status of all derivatives of our free software and of promoting the sharing and reuse of software generally. + + + NO WARRANTY + + +11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED +OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, +REPAIR OR CORRECTION. + + +12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, +INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING +OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY +YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER +PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. + + +END OF TERMS AND CONDITIONS + +Mozilla Public License, v. 2.0 + +DHCP + +Mozilla Public License +Version 2.0 + +1. Definitions + + 1.1. "Contributor" +means each individual or legal entity that creates, contributes to the creation of, or owns Covered +Software. + + + 1.2. "Contributor Version" +means the combination of the Contributions of others (if any) used by a Contributor and that particular +Contributor's Contribution. + + + 1.3. "Contribution" +means Covered Software of a particular Contributor. + + + 1.4. "Covered Software" +means Source Code Form to which the initial Contributor has attached the notice in Exhibit A, the Executable Form of such Source Code Form, and Modifications of such Source Code Form, in each case including portions thereof. + + + 1.5. "Incompatible With Secondary Licenses" +means +that the initial Contributor has attached the notice described in Exhibit B to the Covered Software; or that the Covered Software was made available under the terms of version 1.1 or earlier of the License, +but not also under the terms of a Secondary License. + + + 1.6. "Executable Form" +means any form of the work other than Source Code Form. + + + 1.7. "Larger Work" +means a work that combines Covered Software with other material, in a separate file or files, that is not +Covered Software. + + + 1.8. "License" +means this document. + + + 1.9. "Licensable" +means having the right to grant, to the maximum extent possible, whether at the time of the initial grant or subsequently, any and all of the rights conveyed by this License. + + + 1.10. "Modifications" +means any of the following: + + any file in Source Code Form that results from an addition to, deletion from, or modification of the +contents of Covered Software; or + + + any new file in Source Code Form that contains any Covered Software. + + + 1.11. "Patent Claims" of a Contributor +means any patent claim(s), including without limitation, method, process, and apparatus claims, in any patent Licensable by such Contributor that would be infringed, but for the grant of the License, by the making, using, selling, offering for sale, having made, import, or transfer of either its Contributions or its Contributor Version. + + + 1.12. "Secondary License" +means either the GNU General Public License, Version 2.0, the GNU Lesser General Public License, Version 2.1, the GNU Affero General Public License, Version 3.0, or any later versions of those licenses. + + + 1.13. "Source Code Form" +means the form of the work preferred for making modifications. + + + 1.14. "You" (or "Your") +means an individual or a legal entity exercising rights under this License. For legal entities, "You" includes any entity that controls, is controlled by, or is under common control with You. For purposes of this definition, "control" means (a) the power, direct or indirect, to cause the direction or management of such entity, whether by contract or otherwise, or (b) ownership of more than fifty percent (50%) of the outstanding shares or beneficial ownership of such entity. + + +2. License Grants and Conditions + + 2.1. Grants + + Each Contributor hereby grants You a world-wide, royalty-free, non-exclusive license: + under intellectual property rights (other than patent or trademark) Licensable by such Contributor to use, reproduce, make available, modify, display, perform, distribute, and otherwise exploit its Contributions, either on an unmodified basis, with Modifications, or as part of a Larger Work; and under Patent Claims of such Contributor to make, use, sell, offer for sale, have made, import, and otherwise transfer either its Contributions or its Contributor Version. + + + 2.2. Effective Date + + The licenses granted in Section 2.1 with respect to any Contribution become effective for each +Contribution on the date the Contributor first distributes such Contribution. + + + 2.3. Limitations on Grant Scope + + The licenses granted in this Section 2 are the only rights granted under this License. No additional rights or licenses will be implied from the distribution or licensing of Covered Software under this License. Notwithstanding Section 2.1(b) above, no patent license is granted by a Contributor: +for any code that a Contributor has removed from Covered Software; or for infringements caused by: (i) Your and any other third party's modifications of Covered Software, or (ii) the combination of its Contributions with other software (except as part of its Contributor Version); or +under Patent Claims infringed by Covered Software in the absence of its Contributions. +T. his License does not grant any rights in the trademarks, service marks, or logos of any Contributor +(except as may be necessary to comply with the notice requirements in Section 3.4). + + + 2.4. Subsequent Licenses + + No Contributor makes additional grants as a result of Your choice to distribute the Covered Software under a subsequent version of this License (see Section 10.2) or under the terms of a Secondary License (if permitted under the terms of Section 3.3). + + + 2.5. Representation + + Each Contributor represents that the Contributor believes its Contributions are its original creation(s) or it has sufficient rights to grant the rights to its Contributions conveyed by this License. + + + 2.6. Fair Use + + This License is not intended to limit any rights You have under applicable copyright doctrines of fair use, fair dealing, or other equivalents. + + + 2.7. Conditions + + Sections 3.1, 3.2, 3.3, and 3.4 are conditions of the licenses granted in Section 2.1. + + +3. Responsibilities + + + 3.1. Distribution of Source Form + + All distribution of Covered Software in Source Code Form, including any Modifications that You create or to which You contribute, must be under the terms of this License. You must inform recipients that the Source Code Form of the Covered Software is governed by the terms of this License, and how they can obtain a copy of this License. You may not attempt to alter or restrict the recipients' rights in the Source Code Form. + + 3.2. Distribution of Executable Form + + If You distribute Covered Software in Executable Form then: + such Covered Software must also be made available in Source Code Form, as described in Section 3.1, and You must inform recipients of the Executable Form how they can obtain a copy of such Source Code Form by reasonable means in a timely manner, at a charge no more than the cost of distribution to the recipient; and +You may distribute such Executable Form under the terms of this License, or sublicense it under different terms, provided that the license for the Executable Form does not attempt to limit or alter the recipients' rights in the Source Code Form under this License. + + 3.3. Distribution of a Larger Work + + You may create and distribute a Larger Work under terms of Your choice, provided that You also comply with the requirements of this License for the Covered Software. If the Larger Work is a combination of Covered Software with a work governed by one or more Secondary Licenses, and the Covered Software is not Incompatible With Secondary Licenses, this License permits You to additionally distribute such Covered Software under the terms of such Secondary License(s), so that the recipient of the Larger Work may, at their option, further distribute the Covered Software under the terms of either this License or such Secondary License(s). + + + 3.4. Notices + + You may not remove or alter the substance of any license notices (including copyright notices, patent notices, disclaimers of warranty, or limitations of liability) contained within the Source Code Form of the Covered Software, except that You may alter any license notices to the extent required to remedy known factual inaccuracies. + + + 3.5. Application of Additional Terms + + You may choose to offer, and to charge a fee for, warranty, support, indemnity or liability obligations +to one or more recipients of Covered Software. However, You may do so only on Your own behalf, and not on behalf of any Contributor. You must make it absolutely clear that any such warranty, support, indemnity, or liability obligation is offered by You alone, and You hereby agree to indemnify every Contributor for any liability incurred by such Contributor as a result of warranty, support, indemnity or liability terms You offer. You may include additional disclaimers of warranty and limitations of +liability specific to any jurisdiction. + + +4. Inability to Comply Due to Statute or Regulation + + + If it is impossible for You to comply with any of the terms of this License with respect to some or all of the Covered Software due to statute, judicial order, or regulation then You must: (a) comply with the terms of this License to the maximum extent possible; and (b) describe the limitations and the code they affect. Such description must be placed in a text file included with all distributions of the Covered Software under this License. Except to the extent prohibited by statute or regulation, such description must be sufficiently detailed for a recipient of ordinary skill to be able to understand it. + + +5. Termination + + + 5.1. The rights granted under this License will terminate automatically if You fail to comply with any of its terms. However, if You become compliant, then the rights granted under this License from a particular Contributor are reinstated (a) provisionally, unless and until such Contributor explicitly and finally terminates Your grants, and (b) on an ongoing basis, if such Contributor fails to notify You of the non-compliance by some reasonable means prior to 60 days after You have come back into compliance. Moreover, Your grants from a particular Contributor are reinstated on an ongoing basis if such Contributor notifies You of the non-compliance by some reasonable means, this is the first time +You have received notice of non-compliance with this License from such Contributor, and You become compliant prior to 30 days after Your receipt of the notice. + + + 5.2. If You initiate litigation against any entity by asserting a patent infringement claim (excluding declaratory judgment actions, counter-claims, and cross-claims) alleging that a Contributor Version directly or indirectly infringes any patent, then the rights granted to You by any and all Contributors for the Covered Software under Section 2.1 of this License shall terminate. + + + 5.3. In the event of termination under Sections 5.1 or 5.2 above, all end user license agreements (excluding distributors and resellers) which have been validly granted by You or Your distributors under this License prior to termination shall survive termination. + + +6. Disclaimer of Warranty + + Covered Software is provided under this License on an "as is" basis, without warranty of any kind, either expressed, implied, or statutory, including, without limitation, warranties that the Covered Software is free of defects, merchantable, fit for a particular purpose or non-infringing. The entire risk as to the quality and performance of the Covered Software is with You. Should any Covered Software prove defective in any respect, You (not any Contributor) assume the cost of any necessary servicing, repair, or correction. This disclaimer of warranty constitutes an essential part of this License. No use of any Covered Software is authorized under this License except under this disclaimer. + + +7. Limitation of Liability + + Under no circumstances and under no legal theory, whether tort (including negligence), contract, or otherwise, shall any Contributor, or anyone who distributes Covered Software as permitted above, be liable to You for any direct, indirect, special, incidental, or consequential damages of any character including, without limitation, damages for lost profits, loss of goodwill, work stoppage, computer failure or malfunction, or any and all other commercial damages or losses, even if such party shall have been informed of the possibility of such damages. This limitation of liability shall not apply to liability +for death or personal injury resulting from such party's negligence to the extent applicable law prohibits such limitation. Some jurisdictions do not allow the exclusion or limitation of incidental or consequential damages, so this exclusion and limitation may not apply to You. + + +8. Litigation + + Any litigation relating to this License may be brought only in the courts of a jurisdiction where the defendant maintains its principal place of business and such litigation shall be governed by laws of that jurisdiction, without reference to its conflict-of-law provisions. Nothing in this Section shall prevent a party's ability to bring cross-claims or counter-claims. + + +9. Miscellaneous + + This License represents the complete agreement concerning the subject matter hereof. If any provision of this License is held to be unenforceable, such provision shall be reformed only to the extent necessary to make it enforceable. Any law or regulation which provides that the language of a contract shall be construed against the drafter shall not be used to construe this License against a Contributor. + +10. Versions of the License + + + 10.1. New Versions + + Mozilla Foundation is the license steward. Except as provided in Section 10.3, no one other than the license steward has the right to modify or publish new versions of this License. Each version will be given a distinguishing version number. + + + 10.2. Effect of New Versions + + You may distribute the Covered Software under the terms of the version of the License under which You originally received the Covered Software, or under the terms of any subsequent version published by the license steward. + + + 10.3. Modified Versions + + If you create software not governed by this License, and you want to create a new license for such software, you may create and use a modified version of this License if you rename the license and remove any references to the name of the license steward (except to note that such modified license differs from this License). + + + 10.4. Distributing Source Code Form that is Incompatible With Secondary Licenses + + If You choose to distribute Source Code Form that is Incompatible With Secondary Licenses under the terms of this version of the License, the notice described in Exhibit B of this License must be attached. + + + Exhibit A - Source Code Form License Notice + + This Source Code Form is subject to the terms of the Mozilla Public License, v. 2.0. If a copy of the +MPL was not distributed with this file, You can obtain one at https://mozilla.org/MPL/2.0/. + + + If it is not possible or desirable to put the notice in a particular file, then You may include the notice in +a location (such as a LICENSE file in a relevant directory) where a recipient would be likely to look for such a notice. +You may add additional accurate notices of copyright ownership. Exhibit B - "Incompatible With Secondary Licenses" Notice +This Source Code Form is "Incompatible With Secondary Licenses", as defined by the Mozilla Public +License, v. 2.0. + + + + +## Private PTC CUSTOMER AGREEMENT Axeda Agent Embedded +======================================================================= + +PTC CUSTOMER AGREEMENT + +THIS PTC CUSTOMER AGREEMENT ("AGREEMENT") IS A LEGAL AGREEMENT BETWEEN THE INDIVIDUAL, OR +THE COMPANY OR OTHER ORGANIZATION ON WHOSE BEHALF SUCH INDIVIDUAL ACCEPTS THIS AGREEMENT, +THAT EITHER (A) CLICKS THE "I ACCEPT" BUTTON BELOW OR (B) INSTALLS, ACCESSES, +OR USES ANY +SOFTWARE OR DOCUMENTATION FROM PTC ("CUSTOMER"), AND PTC INC. OR, IF THE PURCHASE WAS MADE IN +A COUNTRY SPECIFIED ON SCHEDULE A TO THIS AGREEMENT, THE PTC AFFILIATE SPECIFIED ON SCHEDULE A +(AS APPLICABLE, "PTC"). +PLEASE READ THE TERMS AND CONDITIONS OF THIS AGREEMENT CAREFULLY BEFORE ACCEPTING THIS +AGREEMENT. BY CLICKING ON THE "I ACCEPT" BUTTON BELOW OR BY INSTALLING, ACCESSING, OR USING +ANY SOFTWARE OR DOCUMENTATION FROM PTC, CUSTOMER HEREBY AGREES TO BE BOUND BY THIS +AGREEMENT AND REPRESENTS THAT IT IS AUTHORIZED TO DO SO. +IF YOU DO NOT AGREE TO ALL OF THE TERMS OF THIS AGREEMENT OR IF YOU DO NOT HAVE AUTHORITY TO +BIND THE COMPANY OR OTHER ORGANIZATION ON WHOSE BEHALF YOU ARE ACCEPTING THIS AGREEMENT, +CLICK THE "I DECLINE" BUTTON AND RETURN TO PTC THE SOFTWARE AND DOCUMENTATION PRODUCTS +PROVIDED TOGETHER WITH THIS AGREEMENT IN ACCORDANCE WITH THE INSTRUCTIONS PROVIDED WHEN +YOU CLICK THE "I DECLINE" BUTTON. NOTE THAT FAILURE TO COMPLY WITH SUCH INSTRUCTIONS WITHIN +THE TIME PERIOD SPECIFIED WILL VOID ANY RIGHT YOU WOULD OTHERWISE HAVE HAD FOR A REFUND OF +ANY FEES PAID. EACH ORDER FOR LICENSED PRODUCTS MAY NOT BE CANCELLED ONCE THIS AGREEMENT +HAS BEEN ACCEPTED. +IF CUSTOMER DID NOT OBTAIN THE LICENSED PRODUCT FROM PTC DIRECTLY, FROM AN AUTHORIZED PTC +DISTRIBUTOR OR RESELLER OR FROM THE PTC ONLINE STORE (AT WWW.PTC.COM), CUSTOMER IS USING AN +ILLEGALLY OBTAINED UNLICENSED VERSION OF THE APPLICABLE LICENSED PRODUCT. PTC REGARDS +SOFTWARE PIRACY AS THE CRIME IT IS AND PURSUES (BOTH CIVILLY AND CRIMINALLY) THOSE WHO TAKE +PART IN THESE ACTIVITIES. AS PART OF THESE EFFORTS, PTC UTILIZES DATA MONITORING AND SCOURING +TECHNOLOGIES TO OBTAIN AND TRANSMIT TO PTC DATA ON USERS OF ILLEGAL COPIES OF LICENSED +PRODUCTS. IF CUSTOMER IS USING AN ILLEGAL COPY OF SOFTWARE, CEASE USING THE ILLEGAL VERSION +AND CONTACT PTC TO OBTAIN A LEGALLY LICENSED COPY. BY USING THIS SOFTWARE, YOU CONSENT TO THE +COLLECTION, USE, AND TRANSFER OF PERSONAL DATA (INCLUDING TO THE UNITED STATES) FOR THE +PURPOSES OF IDENTIFYING USERS OF ILLEGAL COPIES OF OUR SOFTWARE. SUCH CONSENT SHALL BE BINDING +ON ANY USERS OF THIS SOFTWARE, INCLUDING USERS OTHER THAN YOU. +IN ORDER TO UNDERSTAND THE PREFERENCES OF OUR SOFTWARE USERS, PTC USES DATA MONITORING +TECHNOLOGIES TO OBTAIN AND TRANSMIT DATA ON SYSTEM USE AND PERFORMANCE AND FOR GATHERING +USER DATA AND USE METRICS ON USERS OF OUR SOFTWARE. WE WILL SHARE THIS DATA WITHIN PTC, ITS +AFFILIATED COMPANIES AND OUR BUSINESS PARTNERS, INCLUDING WITHIN THE UNITED STATES AND +ELSEWHERE FOR TECHNICAL AND MARKETING PURPOSES AND WILL ENDEAVOR TO ENSURE THAT ANY SUCH +DATA TRANSFERRED IS APPROPRIATELY PROTECTED. OUR COMMERCIAL LICENSES PERMIT USERS TO OPT OUT OF THIS DATA COLLECTION AND OUR STUDENT/EDUCATIONAL VERSIONS ONLY COLLECT DATA ON +SYSTEM USE AND PERFORMANCE. OUR FREE AND TRIAL VERSIONS OF SOFTWARE DO NOT ALLOW USERS TO +OPT-OUT OF THIS DATA COLLECTION, INCLUDING USER DATA. +IF YOU ARE USING PTC SOFTWARE, VISITING A PTC WEBSITE OR COMMUNICATING ELECTRONICALLY WITH US +FROM A COUNTRY OTHER THAN THE UNITED STATES, VARIOUS COMMUNICATIONS WILL NECESSARILY +RESULT IN A TRANSFER OF THIS INFORMATION ACROSS INTERNATIONAL BOUNDARIES. +IF YOU DO NOT CONSENT TO THE COLLECTION AND/OR TRANSMISSION (INCLUDING TO THE UNITED STATES) +OF YOUR DATA AS DESCRIBED ABOVE, DO NOT DOWNLOAD OR USE PTC SOFTWARE. BY (I) USING FREE OR +TRIAL SOFTWARE OR (II) NOT OPTING-OUT OF THE COLLECTION OF CERTAIN PERSONAL DATA AS YOU ARE +ABLE TO WITH PTC COMMERCIAL SOFTWARE, YOU CONSENT TO PTC'S COLLECTION, USE, AND TRANSFER OF +YOUR PERSONAL DATA (INCLUDING TO THE UNITED STATES). +CAPITALIZED TERMS NOT DEFINED IN THE TEXT BELOW ARE DEFINED IN SCHEDULE B AT THE END OF THIS +AGREEMENT. +SCHEDULE A TO THIS AGREEMENT CONTAINS ADDITIONAL (OR ALTERNATIVE) TERMS APPLICABLE TO +SPECIFIC GEOGRAPHIES. + + + +### PTC Clickwrap Customer Agreement - Rev. 12/14 + +1. License. + + 1.1 License Grant. Subject to the terms and conditions of this Agreement, PTC hereby grants to Customer a non-exclusive, revocable, non-transferable license, without any right to sub-license, to install and use the Licensed +Products identified in the Quote +during the applicable License Term, solely for Customer's internal business purposes and solely in accordance with the applicable +usage and license-type restrictions identified in the Quote and in the Licensing Basis Webpage +("License"). Notwithstanding the foregoing: + + (a) If the Licensed Product is being provided by PTC on an "evaluation" or "trial" basis, such License will be instead to +install and use the Licensed Product solely to evaluate such Licensed Products, and Customer agrees not to use the +Licensed Product in any commercial applications or for productive purposes. + + (b) If the Licensed Software is Educational Software, Customer must be enrolled in, or employed by, an accredited, academic +institution, and shall use the Licensed Software solely for educational purposes in a degree-granting program. If Customer +does not meet one of these qualifications, Customer has no rights under this Agreement. Without limitation, non educational research or funded educational research conducted using the facilities of an academic institution or under an +academic name does not qualify as "educational purposes" and use of Educational Software for such purposes represents a +violation of the terms of this Agreement. + + (C) If the Licensed Software is sold on a "demo and test" or "non-production" basis (or similar designation), such Licensed +Software may not be used in a production environment. + + 1.2 Designated Country/Computers/Networks. Subject to Section 1.3, Customer may only install and operate Licensed Products on +the applicable Designated Computers or Designated Networks on computer systems and networks situated in the applicable +Designated Country. Customer may, from time to time, change the Designated Computer, Designated +Network, and/or the +Designated Country in which Customer seeks to install or operate a Licensed Product, provided that in each case (i) Customer shall +give prior written notice to PTC of any such change, and (ii) upon moving the Licensed Products to a different Designated Country, +Customer shall pay all applicable Uplift Fees. Notwithstanding the foregoing, Registered Users need not be located in the +Designated Country when accessing a Registered User Product. + + 1.3 Global/Restricted Global Licenses. If a Concurrent User Licensed Product is licensed by PTC on a +"Global" or "Restricted +Global" basis, Section 1.2 shall not apply to such Licensed Products and the following provisions shall apply instead: + + (i) Global Licenses. Subject to the other requirements of this Agreement, a Global License allows the +Customer to install, +operate and use such Licensed Product at any Customer site(s) throughout the world. + + (ii) Restricted Global Licenses. Subject to the other requirements of this Agreement, a Restricted +Global License allows the +Customer to install, operate and use such Licensed Product at any Customer site(s) located in the +Designated Country +and/or in any Permitted Country. "Permitted Countries" means China, India, Russia, the Czech +Republic, Poland, +Hungary, Malaysia, South Africa, Israel, Mexico, Brazil, Argentina, and Romania. + + 1.4 Additional Restrictions on Use. Customer shall not permit any persons who are not Permitted Users to access or use the +Licensed Products. Customer shall not and shall not permit any third party(ies) to: + + (i) modify or create any derivative work of any part of the Licensed Products; + + (ii) rent, lease, or loan the Licensed Products; + + (iii) use the Licensed Products, or permit them to be used, for third-party training, to deliver software implementation or +consulting services to any third parties, or for commercial time-sharing or service bureau use; + + + (iv) disassemble, decompile or reverse engineer the Licensed Products or the file format of the Licensed +Products, or otherwise +attempt to gain access to the source code or file format of the Licensed Products, except as expressly permitted in +Schedule A, if applicable; + + + (v) sell, license, sublicense, loan, assign, or otherwise transfer (whether by sale, exchange, gift, operation of law, or +otherwise) to any third party the Licensed Products, any copy thereof, or any License or other rights thereto, in whole or in +part, without in each case obtaining PTC's prior written consent, except to the extent that any of the foregoing are +explicitly authorized in the Quote and/or the Licensing Basis Webpage; + + (vi) alter, remove, or obscure any copyright, trade secret, patent, trademark, logo, proprietary and/or other legal notices on or +in any copies of the Licensed Products; and + + (vii) copy or otherwise reproduce the Licensed Products in whole or in part, except (a) as may be required for their installation +into computer memory for the purpose of executing the Licensed Products in accordance with this +Section 1, and/or (b) to +make a reasonable number of copies solely for back-up purposes (provided that any such permitted copies shall be the +property of PTC, and Customer shall reproduce thereon all PTC copyright, trade secret, patent, trademark, logo, +proprietary and/or other legal notices contained in the original copy of the Licensed Product obtained from PTC). +If Customer uses any unlicensed or unauthorized copies of any PTC software, Customer agrees that, +without limiting PTC's right to +terminate this Agreement for breach in accordance with Section 7 and without limiting any other remedies to which PTC may be entitled, Customer will pay to PTC the PTC then-current list price for all such unlicensed software, in addition to any fines or +penalties that may be imposed by law. + + 1.5 Additional Restrictions on Use Applicable to Concurrent User Products. If the Licensed Product is a +Concurrent User Product, +the following provisions apply: + + (i) The number of Permitted Users accessing or operating a Concurrent User Product at any point in time may not exceed the +number of Licenses in effect at such time for that particular Licensed Product. + + (ii) Except with respect to Integrity and Implementer Products, only Permitted Users physically located in the Designated +Country may access, operate and/or use the Licensed Products. Permitted Users who are not employees of Customer may +use the Licensed Products while physically located at Customer's site only. + + (iii) Where a Concurrent User Product is Licensed on a "fixed," "locked" or "node-locked" basis, or the +Licensed Product is +licensed as a "Designated Computer" product, such Licensed Product is licensed to operate solely on the Designated +Computer on which it is installed. + + 1.6 Additional Restrictions on Use Applicable to Registered User Products. A License is required for each individual who accesses +a Registered User product or the data contained therein, whether directly or through a web portal or other mechanism for "batching" +or otherwise achieving indirect access to the Licensed Product or such data. Generic or shared log-ins are not permitted. Customer +may add and/or substitute from time to time new Registered Users as long as the aggregate number of +Registered Users does not +exceed at any point in time the number of Licenses in effect at such time for that particular Licensed +Product and, provided further, +that if a person who was previously a Registered User returns to Registered User status, a new License fee must be paid to PTC at +PTC's then current rates. + + 1.7 Additional Restrictions on Use Applicable to Designated Server Products. Each Designated Server product may only be used on +the computer server that is designated by the Customer in connection with the initial installation of such product and that has one +unique instance of the applicable installed product application. In the event a computer server is partitioned in any manner +(physically, logically or otherwise), the reference in the preceding sentence to "computer server" shall mean each partition of such +server, and such Designated Server product may only be used on one of such partitions. Customer may, from time to time, change +the Designated Server(s) for a Designated Server Product, and/or the location thereof, provided that in each case (a) Customer shall +give prior written notice to PTC of any such change, and (b) upon transferring the Designated Server +Products to a different +Designated Country, Customer pays all applicable Uplift Fees. + + 1.8 Third Party Components and Bundled Third Party Products. Certain of the Licensed Products may contain third party software +components for which additional terms apply ("Third Party Components"). The current additional terms are set forth on the Schedule +of Third Party Terms available in the legal policies and guidelines section of http://www.ptc.com. Separately, third party software +products that PTC resells and/or bundles for distribution with the Licensed Products are licensed to +Customer directly by the +manufacturer of such third party software products ("Bundled Third Party Products"). Such Bundled +Third Party Products are also +described on the Schedule of Third Party Terms. Customer agrees that its use of Third Party +Components and/or Bundled Third +Party Products is subject to the terms of the Schedule of Third Party Terms. New Releases containing +Third Party Components or +Bundled Third Party Products may be subject to additional or different third party terms, of which PTC +shall notify the Customer at +the time such New Releases are delivered to the Customer. + + 1.9 Upgrades: If the Licensed Software was licensed as an upgrade from a previous version, Customer must first be licensed for the +Licensed Software identified by PTC as eligible for the upgrade and Customer must be active on +Support Services for such software. +After installing the upgrade, Licensed Software licensed as an upgrade replaces and/or supplements the product that formed the basis +of Customer's eligibility for the upgrade and Customer may no longer use the original Licensed +Software that formed the basis for +Customer's upgrade eligibility. + +2. Compliance. + + 2.1 License Usage Assessments. To confirm Customer's compliance with the terms and conditions hereof, Customer agrees that +PTC may perform a usage assessment with respect to Customer's use of the Licensed Products. Customer agrees to provide PTC +access to Customer's facilities and computer systems, and cooperation from Customer's employees and consultants, as reasonably +requested by PTC in order to perform such assessment, all during normal business hours, and after reasonable prior notice from PTC. +2.2 Reports. Upon written request from PTC, Customer agrees to provide to PTC an installation and/or usage report with respect to +the Licensed Products (and in the case of Registered User Products, such report shall include a list of all users for whom Customer +has issued a password or other unique identifier to enable such individual to use the Registered User +Product). Such report shall be +certified by an authorized representative of Customer as to its accuracy within ten (10) business days after receipt of any written +request from PTC. For any period in which Customer's use of the Licensed Products exceeds the number and/or the scope of the +Licenses in effect during such period for such Licensed Products, Customer agrees to pay for any such excess usage, including +applicable license and Support Services fees, and without limiting any other rights or remedies to which it is entitled, failure to pay +shall be grounds for termination in accordance with Section 7 hereof. + + +3. Intellectual Property. PTC and its licensors are the sole owners of the Licensed Products and of any copies of the Licensed +Products, and of all copyright, trade secret, patent, trademark and other intellectual or industrial property rights in and to the Licensed +Products. All copies of the Licensed Products, in whatever form provided by PTC or made by +Customer, shall remain the property of +PTC, and such copies shall be deemed to be on loan to Customer during the License Term. Customer acknowledges that the License +granted hereunder does not provide Customer with title to or ownership of the Licensed Products or any copies thereof, but only a +right of limited use consistent with the express terms and conditions of this Agreement. Customer shall have no rights to the source +code for the Licensed Products, and Customer agrees that only PTC shall have the right to maintain, enhance, or otherwise modify +the Licensed Products. + +4. Support Services; Warranty; Disclaimer of Warranties. +See Schedule A for a modified version of this Section 4 for Licensed Products licensed and used in +Germany, Austria or Switzerland. + + 4.1 Support Services. Upon PTC's acceptance of an order for Support Services or for Licensed +Products for which Usage License +Fees apply, PTC agrees that it or its designated service provider shall provide the applicable Support +Services in accordance with +Schedule C. + + 4.2 Warranty. PTC warrants to Customer that PTC is authorized to grant the License(s) and that, subject to Section 4.3, the +Licensed Products will be free from Errors for a period of ninety (90) days following PTC's initial shipment to Customer or +Customer's designee of such Licensed Products (the "Warranty Period"). + + 4.3 Warranty Exceptions. PTC shall have no warranty obligations hereunder with respect to any (i) +evaluation, "trial" or "express" +Licenses, (ii) New Releases, (iii) computer software provided to Customer in the course of PTC's delivery of Training Services, (iv) +Errors attributable to the use of the Licensed Product in an application or environment for which it was not designed or contemplated, +(v) Errors attributable to any modifications or customizations of the Licensed Products, (vi) Licensed +Products that are provided by +PTC free of charge to Customer, and/or (vii) Sun Software, Oracle Software and/or Bundled Third +Party Products. + + 4.4 Sole Remedy. PTC's and its licensors' entire liability and Customer's exclusive remedy for any breach by PTC of the warranty +given in Section 4.2 above shall be, at PTC's sole discretion, either to (a) replace the Licensed Product +(s) or (b) use diligent efforts to +repair the Error. PTC's obligations set forth in the preceding sentence shall apply only if notice of the +Error is received by PTC +within the Warranty Period and Customer supplies such additional information regarding the Error as +PTC may reasonably request. +If PTC does not replace the applicable Licensed Product(s) and/or does not repair the Error (either by providing a bug fix, a +workaround or otherwise) within a reasonable time after notice of the Error and associated information from Customer is received by +PTC, PTC will provide a refund of the license fees paid by Customer for the applicable Licensed +Product(s) upon return of such +Licensed Product(s) and any copies thereof. + + 4.5 No Additional Warranties. No third party, including any employee, partner, distributor (including any Reseller) or agent of PTC +or any of its resellers or sales agents, is authorized to give any representations, warranties or covenants greater or different than those +contained in this Agreement with respect to any Licensed Products or Services, except as specifically set forth in a written agreement +signed on behalf of Customer by an authorized officer and on behalf of PTC by its legal counsel or +Corporate Controller. + + 4.6 Disclaimer of Warranties. EXCEPT AS EXPRESSLY STATED IN SECTION 4, PTC DISCLAIMS (AND CUSTOMER +WAIVES) ALL WARRANTIES, WHETHER EXPRESS, IMPLIED, OR STATUTORY, WRITTEN OR ORAL, INCLUDING +ANY WARRANTY OF MERCHANTABILITY, SATISFACTORY QUALITY, FITNESS FOR A PARTICULAR PURPOSE, +NON-INFRINGEMENT, AND/OR ANY WARRANTY THAT CUSTOMER WILL ACHIEVE ANY PARTICULAR RETURN +ON INVESTMENT. THE LICENSED PRODUCTS ARE INTENDED TO BE USED BY TRAINED PROFESSIONALS AND +ARE NOT A SUBSTITUTE FOR PROFESSIONAL JUDGMENT, TESTING, SAFETY AND UTILITY. CUSTOMER IS +SOLELY RESPONSIBLE FOR ANY RESULTS OBTAINED FROM USING THE LICENSED +PRODUCTS, INCLUDING +THE ADEQUACY OF INDEPENDENT TESTING OF RELIABILITY AND ACCURACY OF ANY ITEM DESIGNED USING +LICENSED PRODUCTS. PTC does not warrant that the operation or other use of the Licensed +Products will be uninterrupted or +error free or will not cause damage or disruption to Customer's data, computers or networks. + +5. Indemnification; Infringement. + + 5.1 PTC's Obligation to Indemnify Customer. PTC, at its own expense, will defend any action brought against Customer based on a +claim that any Licensed Product infringes a United States, European Union or Japanese patent, copyright or trademark and, at its +option, will settle any such action or will pay any final judgment awarded against Customer, provided that: (a) PTC shall be notified +promptly in writing by Customer of any notice of any such claim; (b) PTC shall have the sole control of the defense of any action on +such claim and all negotiations for its settlement or compromise and shall bear the costs of the same +(save where one or more of the +exclusions in Section 5.3 applies); and (C) Customer shall cooperate fully at PTC's expense with PTC +in the defense, settlement or +compromise of such claim. This Section 5 states PTC's sole and exclusive liability, and Customer's sole remedy, for any and all +claims relating to infringement of any intellectual property right. + + 5.2 PTC's Right to Act to Prevent a Claim. If a claim described in Section 5.1 hereof occurs or, in +PTC's opinion, may occur, +Customer shall permit PTC, at PTC's option and expense to: (a) procure for Customer the right to continue using the Licensed +Product; (b) modify the Licensed Product so that it becomes non-infringing without materially impairing its functionality; or (C) +terminate the applicable Licenses, accept return of the Licensed Products and grant Customer a credit thereon. For Licenses purchased with a perpetual License Term, such credit shall be equal to the License fees paid by +Customer for such Licensed Product +depreciated on a straight-line, five year basis. For Licenses purchased on a term license or subscription basis, such credit shall be +equal to the prepaid license or subscription fees for the remainder of the License Term. + + 5.3 Exclusions from PTC's Obligation to Indemnify Customer. PTC shall have no liability to Customer under Section 5.1 hereof or +otherwise to the extent that any infringement or claim thereof is based upon: (a) use of the Licensed +Product in combination +with equipment or software not supplied hereunder where the Licensed Product itself would not be infringing; (b) use of the Licensed +Product in an application or environment for which it was not designed or not contemplated under this +Agreement; (C) use of other +than a current release of the Licensed Product(s) provided to Customer; (d) modification of the +Licensed Product by anyone other +than PTC or its employees or agents; or (e) any claims of infringement of any patent, copyright, trade secret, trademark or other +proprietary right in which Customer has an interest. + +6. Limitation of Liability. + + See Schedule A for a modified version of this Section 6 for Licensed Products licensed and used in +Germany, Austria or Switzerland. + + + 6.1 The warranty and indemnification provisions of Sections 4 and 5 hereof state the entire liability of +PTC, its subsidiaries and +affiliates, and each of their respective directors, officers, employees or agents, with respect to the +Licensed Products and Services, +including (without limitation) any liability for breach of warranty, or for infringement or alleged infringement of patent, copyrights, +trademarks, trade secrets and other intellectual or proprietary rights by the Licensed Products, or their use. + + 6.2 EXCEPT FOR PTC'S INDEMNIFICATION OBLIGATIONS IDENTIFIED IN SECTION 5.1 +ABOVE, THE MAXIMUM +LIABILITY OF PTC AND ITS LICENSORS ARISING OUT OF, OR RELATING TO, THE CREATION, LICENSE, +FUNCTIONING, USE OR SUPPLY OF THE LICENSED PRODUCTS OR THE PROVISION OF SERVICES OR OTHERWISE +RELATING TO THIS AGREEMENT, WHETHER BASED UPON WARRANTY, CONTRACT, TORT, OR OTHERWISE, +SHALL NOT, (I) FOR LICENSES PURCHASED ON A PERPETUAL BASIS, EXCEED THE FEES PAID BY CUSTOMER FOR +THE LICENSED PRODUCTS OR SERVICES THAT GAVE RISE TO THE CLAIM AND (II) FOR LICENSES PURCHASED +ON A TERM OR SUBSCRIPTION BASIS, EXCEED THE FEES PAID BY CUSTOMER IN THE TWELVE MONTH PERIOD +IMMEDIATELY PRECEDING THE EVENT GIVING RISE TO DAMAGES FOR THE LICENSED PRODUCTS OR SERVICES +THAT GAVE RISE TO THE CLAIM. + + 6.3 IN NO EVENT SHALL PTC, ITS LICENSORS, ITS AFFILIATES (INCLUDING ITS SUBSIDIARY COMPANIES), OR +ANY OF THEIR RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES OR AGENTS BE LIABLE FOR: (A) ANY LOSS OF +PROFIT, LOSS OF USE DAMAGES, LOSS OF GOODWILL, LOSS OF BUSINESS OPPORTUNITY, LOSS OF SALES, LOSS +OF REPUTATION OR LOSS OF ANTICIPATED SAVINGS; (B) ANY LOSS OR INACCURACY OF DATA OR BUSINESS +INFORMATION OR FAILURE OR INADEQUACY OF ANY SECURITY SYSTEM OR FEATURE; AND (C) SPECIAL, +INCIDENTAL, INDIRECT, PUNITIVE OR CONSEQUENTIAL LOSS OR DAMAGE +HOWSOEVER CAUSED; IN EACH +CASE EVEN IF PTC HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. + + 6.4 Customer agrees not to bring any suit or action against PTC, and/or its subsidiaries and affiliates, and/or any of their respective +directors, officers, employees or agents for any reason whatsoever more than one year after the cause of action arises. Customer +recognizes that fees paid by Customer for the Licensed Products and Services are based in part on the disclaimer of warranty and +limitation of liability provisions set forth herein and that, in the absence of Customer's agreement to such terms, the charges for the +Licensed Products would be significantly higher. The limitations and exclusions set forth in this Section +6 shall not apply to any +claim in respect of death or personal injury. + + +7. Term and Termination. + + 7.1 Events Causing Termination. This Agreement and all Licenses will terminate: + + (a) Automatically and without notice on the following events: (I) Customer's breach of any of clauses +(i) through (vii) of +Section 1.4 or Sections 3 or 8.4 hereof; (II) a receiver, trustee, liquidator, or such similar officer is appointed for Customer +or for any of Customer's properties or assets; (III) Customer makes a general assignment for the benefit of Customer's +creditors; (IV) Customer files a petition for its reorganization, dissolution or liquidation, or such a petition is filed against +Customer and is not dismissed within sixty (60) days thereafter; or (V) Customer ceases doing business or commence +dissolution or liquidation proceedings; or + + (b) Thirty (30) days after written notice from PTC specifying a breach (other than as listed in Section + + 7.1(a) above) of this +Agreement, including failure to make any payment due to either PTC or a Reseller in connection with the Licensed +Products in a timely manner, if that breach is not, within that thirty (30) day period, remedied to PTC's reasonable +satisfaction. + + 7.2 Effects of Expiration or Termination. Upon expiration of a given License Term and/or any expiration or termination of this +Agreement, Customer shall promptly pay all sums owed by Customer, return to PTC the original copies of all Licensed Products for +which the License Term has expired or has been terminated, destroy and/or delete all copies and backup copies thereof from Customer's computer libraries, storage facilities and/or hosting facilities, and certify in writing by an officer that Customer is in +compliance with the foregoing requirements and that such Licensed Products are no longer in +Customer's possession or in use. +7.3 Survival. Sections 2, 3, 4.6, 5, 6, 7.2, 7.3 and 8 shall survive expiration or termination of this +Agreement. + +8. General. + + 8.1 Governing Law and Jurisdiction. Unless otherwise stated in Schedule A, all disputes arising under, out of, or in any way +connected with this Agreement shall be governed by and construed in accordance with the laws of the +Commonwealth of +Massachusetts without reference to conflict of laws principles (and specifically excluding the Uniform +Computer Information +Transactions Act). The parties hereby expressly disclaim the application of the U.N. Convention for the +International Sale of Goods. +All disputes arising under, out of, or in any way connected with this Agreement shall be litigated exclusively in the state or federal +courts situated in the Commonwealth of Massachusetts, and in no other court or jurisdiction. Notwithstanding the foregoing or +anything to the contrary, PTC shall have the right to bring a claim in any court of competent jurisdiction to enforce any intellectual +property rights and/or protect any confidential information. Customer agrees that the state and federal courts situated in the +Commonwealth of Massachusetts shall have personal jurisdiction over its person, and Customer hereby irrevocably (i) submits to the +personal jurisdiction of said courts and (ii) consents to the service of process, pleadings, and notices in connection with any and all +actions initiated in said courts. The parties agree that a final judgment in any such action or proceeding shall be conclusive and +binding and may be enforced in any other jurisdiction. Each party waives its right to trial by jury in connection with any dispute +arising out of this Agreement. + + 8.2 Notices. Any notice or communication required or permitted under this Agreement shall be in writing. In the case of notice to +Customer, the notice shall be directed to the address set forth on the Customer's purchase order or to such other address as may be +provided to PTC in writing. In the case of notice to PTC, such notice shall be directed to PTC, 140 +Kendrick Street, Needham, MA +02494; Attn: Corporate Controller, with a copy to General Counsel. Any notice provided under this section shall be deemed to have +been received: (a) if given by hand, immediately; (b) if given by mail, five (5) business days after posting; (C) if given by express +courier service, the second business day following dispatch in the jurisdiction of the sender; or (d) if given by fax, upon receipt +thereof by the recipient's fax machine or as stated in the sender's transmission confirmation report as produced electronically by +sender's fax machine. + + 8.3 Assignment, Waiver, Modification. Customer may not assign, transfer, delegate or sublicense any +of Customer's rights or +obligations hereunder (including without limitation by operation of law or by sale of Customer assets, whether directly or by merger, +and a change in control of Customer shall be deemed to be an "assignment" for purposes of the foregoing) without PTC's prior +written consent, and any such attempted delegation, assignment, transfer or sublicense shall be void and a breach of this Agreement. +No waiver, consent, modification, amendment or change of the terms of this Agreement shall be binding unless in writing and signed +by PTC and Customer. PTC reserves the right to charge a transfer fee for any proposed assignment, transfer or sublicense of this +Agreement. + + 8.4 Compliance with Laws. Each party shall be responsible for its own compliance with applicable laws, regulations and other legal +requirements relating to the conduct of its business and this Agreement. Further Customer represents and warrants that it will use the +Licensed Products, as well as related technology and services, in full compliance with applicable laws and regulations. Customer +acknowledges and agrees that the Licensed Products and related technical data and services are subject to the export control laws and +regulations of the United States and any country in which the Licensed Products or related technical data or services are developed, +received, downloaded, used, or performed. Further, Customer understands and acknowledges that the release of software or +technology to a non-U.S. person within the United States or elsewhere abroad is deemed to be an export to the non-U.S. person's +home country or countries, and that the transfer of the Licensed Products or related technology to +Customer's employees, affiliates, +or any third party, may require a license from the United States Government and possibly other applicable authorities. Customer shall +be solely responsible for determining whether Customer's use or transfer of the Licensed Products or related technology or services +requires an export license or approval from U.S. or other authorities, and for securing all required authorizations. Customer hereby +warrants and represents that: (x) neither Customer nor any of Customer's directors, officers or affiliates is identified on the U.S. +Commerce Department's Denied Persons List, Entity List, or Unverified List, the U.S. State +Department's Nonproliferation +Sanctions List, the U.S. Treasury Department's List of Specially Designated Nationals and Blocked +Persons or any similar Export +Controls Division-Foreign Affairs and International Trade Canada listing that designates individuals or entities to which export +restrictions apply (collectively, the "Restricted Parties Lists"), (y) except as specifically authorized or licensed by the United States +Government and other applicable authorities, Customer will not sell, offer, transfer, deliver, release, either directly or indirectly, the +Licensed Products or related technology or services to any end-user: (A) that is either located in, a national of, or acting on behalf of +a country subject to U.S. economic embargoes, or (B) that have been designated as prohibited or restricted parties by the U.S. +Government, including but not limited to persons listed on the Restricted Parties Lists, or (C) engaged in activities related to the +design, development, stockpiling, or proliferation of nuclear, chemical, or biological weapons, or missiles or missile systems, or (D) +engaged in maritime nuclear propulsion activities. Customer represents and warrants that it will ensure that any person or entity to +which Customer has granted access to the Licensed Products or related technology or services has been made aware of, and will +comply with, this provision and U.S. and other applicable export control laws and regulations. Unless prohibited by applicable law +and without waiving sovereign immunity, Customer shall indemnify and hold harmless PTC and its employees against any damage, +loss, liability or expense (including attorneys' fees) that PTC may incur as a result of Customer's failure to comply with this Section + + 8.4. Such indemnification shall survive the expiration or termination of this Agreement. + + 8.5 Severability. It is intended that this Agreement shall not violate any applicable law and the unenforceability or invalidity of any +provision (other than the provisions obligating Customer to make payments to PTC) shall not affect the force and validity of the +remaining provisions and such provisions determined to be invalid shall be deemed severed from this +Agreement and, to the extent +possible, be replaced with terms which as closely as possible approximate the interest and economic intent of such invalid provisions. + + 8.6 Entire Agreement. This Agreement is the complete and exclusive statement of the contract between +PTC and Customer +with respect to the subject matter hereof. No waiver, consent, modification, amendment or change of this Agreement shall be binding +unless in writing and signed or otherwise expressly acknowledged by PTC and Customer. + + 8.7 Third Party Beneficiaries. It is agreed by the parties to this Agreement that PTC's third party licensors are intended +beneficiaries of this Agreement and have the right to rely upon and directly enforce its terms with respect to the products of such +licensors. + + 8.8 Marketing. Customer agrees that while this Agreement is in effect, PTC shall be authorized to identify Customer as a +customer/end-user of PTC software and services (as applicable) in public relations and marketing materials. + + 8.9 Government Licensees. If Customer is a United States Governmental entity, Customer agrees that the Licensed Products +are "commercial computer software" under the applicable federal acquisition regulations and are provided with the commercial +license rights and restrictions described elsewhere herein. If Customer is acquiring the Licensed +Product(s) under a United States +government contract, Customer agrees that Customer will include all necessary and applicable restricted rights legends on the +Licensed Products to protect PTC's proprietary rights under the FAR or other similar regulations of other federal agencies. Customer +agrees to always include such legends whenever the Licensed Products are, or are deemed to be, a deliverable under a government +contract. +Schedule A - Purchases from PTC Affiliates +If the Customer has obtained a License to any Licensed Products in one of the following countries, the entity granting the +License is specified below and, notwithstanding Section 8.1 of this Agreement, the governing law and jurisdiction shall be as set +forth below. +Country PTC Affiliate Licensing Entity Governing Law/Jurisdiction for +Disputes +Belgium, Netherlands, Luxembourg +Parametric Technology Nederland B.V. Netherlands +Austria, Germany Parametric Technology GmbH German Law*, Landgericht Munchen I, Germany +France Parametric Technology S.A. France Ireland PTC Software and Services (Ireland) Limited +Republic of Ireland +Italy Parametric Technology Italia S.r.L. Italy +Spain, Portugal Parametric Technology Espana, S.A. Spain +Switzerland Parametric Technology (Schweiz) AG German Law*, Landgericht Munchen I, Germany +United Kingdom Parametric Technology (UK) Limited United Kingdom +Remaining countries of the +European Union +PTC Software and Services (Ireland) Limited +Republic of Ireland Turkey, Kosovo, Serbia, Macedonia, Montenegro, Croatia, Bosnia and Herzegovina, and Albania +PTC Software and Services (Ireland) Limited +Republic of Ireland +The Russian Federation PTC International LLC Russian Law / International +Commercial Arbitration Court at the Chamber of Commerce and Industry of the Russian Federation in Moscow Belarus, Moldova, Ukraine, +Armenia, Georgia, Azerbaijan, Kazakhstan, Kyrgyzstan, Tajikistan, Turkmenistan, and Uzbekistan +PTC Software and Services (Ireland) Limited +Republic of Ireland +Norway, Sweden, and Denmark, Finland, Iceland, and the Faeroe Islands +PTC Sweden AB Sweden +Japan PTC Japan K.K. Japan / Tokyo District Court +Country PTC Affiliate Licensing Entity Governing Law/Jurisdiction for +Disputes +China Parametric Technology (Shanghai) Software Co., Ltd. +The People's Republic of China/China International Economic and Trade Arbitration Commission in Shanghai +Taiwan Parametric Technology Taiwan Limited Taiwan / Courts of Taipei, Taiwan +India Parametric Technology (India) Private +Limited +India +Korea Parametric Technology Korea Ltd. Republic of Korea +Other Asia Pacific Countries including Australia and New Zealand, but excluding China, Japan and Taiwan) +PTC Inc. Special Administrative Region of Hong +Kong / Hong Kong International +Arbitration Centre +Canada PTC (Canada) Inc. Ontario +Any other country PTC Inc., or such other affiliate of PTC as +PTC directs at the time of the order +Commonwealth of Massachusetts, +United States + +*Specific Provisions for Austria, Germany and Switzerland: +For Licensed Products licensed and used in Austria, Germany or Switzerland, the following provisions shall apply. The following +provisions shall have no applicability to any Licensed Products or Services purchased outside of +Austria, Germany or Switzerland. + +References to sections below are references to the applicable sections in the body of the Agreement. + +Section 1.4 (iv) above shall not apply to the extent that (i) the processes Customer undertakes are required to achieve +information necessary to achieve interoperability of an independently created computer program with other software +programs, (ii) the further requirements of Section 69e of the German Copyright Act are fulfilled and +(iii) PTC, upon +Customer's written request, has not made available the information required for this within a reasonable period. + +Sections 4.2 (Warranty), 4.4 (Sole Remedy), 4.5 (No Additional Warranties) and 4.6 (Disclaimer of +Warranties) are hereby +replaced by the following provisions: + +4.2 Warranty Period, Restarts and Investigation Duty. The limitation period for warranty claims shall be twelve (12) +months from delivery. Any replacement of the Licensed Product(s) and/or repair of Errors will not restart the warranty +period. The pre-requisite for the Customer's warranty claims (Mangelanspruche) is that: (i) the +Customer inspects the +Licensed Products according to Section 377 German Commercial Code, (ii) the defect is an Error as defined in this +Agreement, (iii) the Error already existed at the time of delivery and (iv) the Customer effects a proper notification of the +Error. Customer shall provide notifications of Errors to PTC in writing and Customer shall provide specific details of the +Error as deemed reasonable under the specific circumstances. Customer shall notify PTC of obvious +Errors in writing +within one week of delivery and of latent Errors within one week of discovery of such Error. The periods specified are +preclusion periods. + +4.4 Remedies. In the event of an Error, PTC in its sole discretion may: (a) replace the Licensed Product +(s) or (b) repair +the Error, provided that notice of the Error is received by PTC within the periods set forth in Section +4.2 and Customer +provides such additional information regarding the Error as PTC may reasonably request. If the repair +(either by providing +a bug fix, a workaround or otherwise) or replacement is not successful (after at least two repair attempts for the same Error +by PTC within a reasonable period of time), Customer shall be entitled, at Customer's choice, to either: +(i) rescission of the +affected order so that PTC provides a refund of the license fees paid by Customer for the applicable +Licensed Product(s) +upon return of such Licensed Product(s) and any copies made thereof or (ii) a reasonable reduction in the purchase price. +Replacements or repairs shall be made without acknowledgement of a legal obligation and shall not suspend the limitation +period for warranty claims related to the Licensed Products. + +4.5 No Additional Warranties. No employee, partner, distributor (including any Reseller) or agent of +PTC or any of its +resellers or sales agents is authorized to give representations, warranties or covenants greater or different than those +contained in this Agreement, except as specifically set forth in a written agreement signed on behalf of +Customer by an +authorized officer and on behalf of PTC by its legal counsel or Corporate Controller. Apart from claims for damages based +on Errors that are subject to the limitation of liability as set forth in Section 6, the obligations provided for in this Section 4 +shall be PTC's exclusive liability in case of warranty claims. + +4.6 Customer Responsibility. The Licensed Products are intended to be used by trained professionals and are not a +substitute for the exercise by Customer of professional judgement, testing, safety and utility in their use. Customer is +solely responsible for any results which were obtained by using the Licensed Products, including the adequacy of +independent testing of reliability and accuracy of any item designed using Licensed Products. + +4.7 Qualities (Beschaffenheit), Guarantees. Qualities of the Licensed Products stated in publications of +PTC or its sales +representatives, in particular in advertising, in drawings, brochures or other documents, including presentations in the +Internet, or on packaging and labeling of the Licensed Products, or which fall under trade usages, shall only be deemed to +be covered by the contractual quality of the Licensed Products if such qualities are expressly contained in an offer or an +order confirmation in writing. Guarantees, in particular guarantees as to quality, shall be binding on +PTC only to the extent +to which they (i) are contained in an offer or an order confirmation in writing, (ii) are expressly designated as "guarantee" +or "guarantee as to condition" (Beschaffenheitsgarantie), and (iii) expressly stipulate the obligations for +PTC resulting from such guarantee. + +Section 6 is hereby replaced by the following provisions: +6. Limitation of Liability + + 6.1 Liability Categories. PTC shall be liable for damages, regardless of the legal grounds, only if: (i) PTC breaches a +material contractual obligation (cardinal obligation) culpably (i.e., at least negligently), or (ii) the damage has been caused +by gross negligence or wilfull intent on the part of PTC or (iii) PTC has assumed a guarantee. + + 6.2 Predictability. PTC's liability shall be limited to the typical, foreseeable damage: (i) if PTC +breaches material +contractual obligations (cardinal obligations) with slight negligence, or (ii) if employees or agents of +PTC who are not +officers or executive staff have breached other obligations by gross negligence, or (iii) if PTC has assumed a guarantee, +unless such guarantee is expressly designated as guarantee as to condition (Beschaffenheitsgarantie). + + 6.3 Maximum Amount. In the cases of Section 6.2 (i) and (ii), PTC's liability shall be limited to a maximum amount of +EURO 1,000,000 or, in case of purely financial losses, to a maximum amount of EURO 100,000. + + 6.4 Indirect Damages. In the cases of Section 6.2, PTC shall not be liable for indirect damages, consequential damages or +loss of profit. + + 6.5 Liability Period. Customer's claims for damages against PTC and/or PTC's affiliates, regardless of the legal grounds, +shall expire at the latest one year from the time the Customer gains knowledge of the damage or, irrespective of this +knowledge, at the latest two years after the damaging event. For claims based on Errors of the Licensed +Product(s), the +warranty limitation period pursuant to Section 4.2 shall apply. + + 6.6 Mandatory Liability. PTC's liability pursuant to the German Product Liability Act +(Produkthaftungsgesetz), for injury +of life, body and health, for fraudulent concealment of a defect or for the assumption of a guarantee as to condition +(Beschaffenheitsgarantie) remains unaffected. + + 6.7 Employees. Sections 6.1 to 6.6 shall also apply in the case of any claims for damages of Customer against employees +or agents of PTC and/or PTC's affiliates. + + 6.8 Contributory Negligence. In the event of a guarantee or liability claim against PTC any contributory fault of +Customer must be taken into account accordingly, particularly in the event of inadequate fault notification or +inadequate data securing. It constitutes inadequate data securing if the client, among others, does not, by way of +appropriate state of the art security measures, take precautions against external influences, e.g. computer viruses and other +phenomena which could put individual data or an entire data stock at risk. Schedule B - Definitions + +"Concurrent User Products" means the Licensed Products licensed on a concurrent user basis, as +specified either in the Quote or at the Licensing Basis Webpage. + +"Designated Computer" means the central processing unit(s) designated in writing by Customer to PTC +at the time of installation of +the Licensed Products (as may be modified in accordance with Section 1.2 of this Agreement). + +"Designated Computer Product" means the Licensed Products licensed on a "Designated Computer" basis or otherwise designated as +"fixed," "locked" or "node-locked", as specified either in the Quote or at the Licensing Basis Webpage. Designated Computer +Products may not be remotely accessed or installed in a virtual environment. + +"Designated Country" means the country of installation specified in writing by Customer to PTC at the time Customer places its +order of the Licensed Products. The Designated Country may be changed only in accordance with +Section 1.2 of this Agreement. + +"Designated Network" means the network designated in writing by Customer to PTC at the time of installation of the Licensed +Products (as may be modified in accordance with Section 1.2 of this Agreement). + +"Designated Server" means a computer server designated in writing by Customer to PTC at the time of installation of the Licensed +Products (as may be modified in accordance with Section 1.2 of this Agreement) that has one unique instance of the applicable +installed Licensed Product application. + +"Designated Server Products" means the Licensed Products licensed on a Designated Server basis, as specified either in the Quote or +at the Licensing Basis Webpage. + +"Documentation" means the applicable Licensed Software user manuals provided or made available by electronic means by PTC at +the time of shipment of the Licensed Software. + +"Educational Software" means Licensed Products identified as "Priced for Education," "Student +Edition," "Schools Edition," + +"Schools Advanced Edition," "University Edition," "Professor's Edition/Version" or "Academic +Edition/Version," or otherwise +designated as educational or academic licenses. + +"Error" means a failure of the Licensed Software to conform substantially to the applicable +Documentation, provided that Customer +informs PTC of such failure in writing and PTC is able to replicate such failure after making reasonable efforts. + +"External User" means a Registered User who is a vendor or other third party external to the Customer and its affiliates. + +"License" shall have the meaning set out in Section 1.1 of the body of the Agreement. + +"License Term" means the time period during which the License for the applicable Licensed Products shall be in effect, as specified +in the name of the Licensed Product or in the applicable Quote (subject to earlier termination pursuant +to the terms hereof) or, if no +Quote was provided to Customer, as otherwise communicated by PTC to Customer. In the absence of a stated license term, the +License Term shall be perpetual, except that the License Term for evaluation Licenses shall be no longer than thirty days from the +date of Customer's request for an evaluation license, unless otherwise specifically designated by PTC, and the evaluation License +will cease to be operational after such term expires. The License Term of a "subscription" License is as specified in the Quote and/or +the invoice, and such License includes Support Services during such License Term at no additional fee. "License Locked Product" means a Licensed Product licensed for use with another PTC product to which the License Locked +Product is an extension. The License Locked Product will assume the licensing basis of such other product.. License Locked +Products are specified either in the Quote or at the Licensing Basis Webpage. + +"Licensed Products" means collectively the Licensed Software and the Documentation. + +"Licensed Software" means, collectively, the computer software product identified in the applicable +Quote, as well as (i) any +software product that is provided to operate with such computer software product (e.g., modules, software bundled with this software +product, etc.), but excluding any software that is a consulting services deliverable, (ii) any Error corrections pursuant to Section 4.4 +hereof, (iii) any updates, Error corrections and/or New Releases provided to Customer by PTC pursuant to Support Services +purchased by Customer and (iv) any computer software provided to Customer in the course of PTC's delivery of Training Services. + +"Licensing Basis Webpage" means the "Licensing Basis" document at http://www.ptc. com/support/customer_agreements/ +index.htm, which specifies the licensing basis of PTC's different products and states certain additional product-specific terms and +conditions. + +"Support Services" means the provision of New Releases and, depending on the level of Support +Services ordered, may also include +telephone support, web-based support tools, and correction of Errors, all in accordance with Schedule C +attached to this Agreement. + +"New Release" means a modified or enhanced version of a Licensed Product that is designated by PTC +as a new release of that +product and that PTC makes generally available to its Support Services customers. + +"Permitted User" means an individual who is authorized by Customer to use the Licensed Products, such use to be solely in +accordance with the terms and conditions of the Agreement. Permitted Users are limited to Customer's employees, consultants, +subcontractors, suppliers, business partners and customers who (i) are not competitors of PTC or employed by competitors of PTC +and (ii) are directly involved in the utilization of the Licensed Products solely in support of Customer's internal business purposes. +Customer shall at all times be responsible for its Permitted Users' compliance with this Agreement. + +"Per Instance Product" means a Licensed Product for which one License is required for each instance of a system to which the +applicable Licensed Product connects. For example, if an adapter that is licensed on a Per Instance basis enables Windchill to +connect to an ERP system and a CRM system, two licenses of such adapter will be required. The +Licensed Products that are Per +Instance Products are identified either in the Quote or at the Licensing Basis Webpage. + +"Quote" means the PTC product schedule, quote or order confirmation provided to Customer in connection with the purchase of the +applicable Licensed Product or, if no such document is provided, Customer's purchase order for such +Licensed Product, if any. + +"Registered User" means a Permitted User for whom Customer has purchased a License to use a +Registered User Product and for +whom Customer has issued a password or other unique identifier to enable such individual to use the +Registered User Product. + +"Registered User Products" means the Licensed Products licensed on a Registered User basis, as specified either in the Quote or at +the Licensing Basis Webpage. + +"Reseller" means a third-party appointed and authorized by PTC to resell or distribute any Licensed +Product. . + +"Services" means collectively Support Services and Training Services. + +"Site License" means a Licensed Product for which one License is required for each Customer location, as specified either in the +Quote or at the Licensing Basis Webpage. Multiple customer facilities located in the same city or town +(based on postal address) +shall be considered one "location," whereas locations located in different cities or towns will require multiple Site Licenses. + +"Training Services" means instruction or other training provided by PTC in the use of the Licensed +Products. "Training Services" +does not include PTC's e-Learning training products (e.g., "PTCU"), which are considered Licensed +Products for purposes of this +Agreement. + +"Uplift Fee" means a fee based upon the difference between the License fee applicable to installation of the applicable Licensed +Product in the original Designated Country and the License fee applicable to the installation of such +Licensed Product in the +Designated Country to which Customer wishes to move the Licensed Product. + +"Usage License Fee" means an ongoing fee that commences upon installation of the applicable +Licensed Product and that, during the +period for which the Usage License Fee is paid, entitles Customer to (i) continued use of the Licensed +Product in accordance with the +terms of the License and (ii) telephone support, Error corrections or workarounds, and New Releases for such software. + +Schedule C - PTC Support Services Terms and Conditions +The following additional terms and conditions apply to the provision of Support Services by PTC: Support Services Plan; Levels of Support Services. Upon PTC's acceptance of Customer's order for Support Services in respect of +the Licensed Products, PTC and/or its authorized subcontractors shall provide Support Services in accordance with these terms for a +time period of twelve (12) months or for such other period specified in Customer's order accepted by +PTC (a "Support Services +Plan"). All Support Services are provided subject to Customer's payment for such services at PTC's then-current rates, provided that +for Licensed Product licensed on a subscription basis, such License includes Support Services during such License Term at no +additional fee. If Customer does not order Support Services to commence on shipment of the Licensed +Product(s), or if Customer at +any time discontinues Support Services, and in either case subsequently wishes to obtain Support +Services, Customer must pay (i) the +then current fees for Support Services and (ii) the fees for Support Services for any period for which + +Customer has not purchased +Support Services. The then current levels of Support Services offered and the corresponding services provided thereunder are +described on http://www.ptc.com at http://www.ptc.com/support/maintenance/maintenance_support_policies.htm + +A Support Services Plan may not be cancelled by Customer following PTC's acceptance of an order for such Support Services Plan. +With respect to Registered User Products, e-Learning products and Integrity Concurrent User and +Server Licensed Products, Support +Services ordered by Customer must cover all Licenses granted to Customer for such Licensed Products. PTC is obligated to provide +Support Services only during periods for which Customer has paid the applicable Support Services fees and only in accordance with +the level of Support Services Customer has purchased. The services offered under any Support Services +Plan may change from time +to time, and PTC may cease to offer Support Services Plans at any time without notice, subject only to the obligation to refund to +Customer the unused portion of any previously paid applicable Support Services fee (on a prorated basis). + +(a) Telephone Support. If Customer purchases Support Services at a level that includes telephone support, Customer may utilize +PTC's telephone support service to report problems and seek assistance in use of the Licensed Products. The hours during which +PTC will provide telephone support will vary depending upon the level of Support Services ordered by +Customer. For all levels of +Support Services that include telephone support, PTC will provide telephone support in the languages, and during normal business +hours for the countries, listed on PTC's website at the website URL listed above. For levels of Support + +Services that include +telephone support during non-business hours, PTC will provide such support in the English language only. Regardless of the total +number of the Licensed Products licensed by Customer, Customer is entitled to telephone support only in direct connection with +Licenses that are covered by a Support Services Plan at a level that includes telephone support. + +(b) Repair of Errors. If Customer's Support Services Plan includes repair or workaround of Errors, PTC +shall use diligent efforts +to repair Errors or provide workarounds as required in such Support Services Plan, provided notice of the Error is received by PTC +during the term of a Support Services Plan and Customer supplies such additional information regarding the Error as PTC may +reasonably request. + +(C) New Releases. PTC will provide Customer with one copy of each New Release for each Licensed +Product for which +Customer is entitled to Support Services at the time the applicable language version of the New Release is made generally available. +Subject to different terms for particular products set forth at http://www.ptc.com/support/maintenance/maintenance_support_policies.htm, following shipment of the New Release, the previous +release shall remain "current" for purposes of this Agreement for a period of ninety (90) days; +thereafter only such New Release will be current. + +(d) Exclusions. + +(1) PTC is not obligated to perform investigation and/or repair of Errors (i) found by PTC to be in other than a current (as +described above), unaltered release of the Licensed Products; (ii) caused by changes to the Customer's operating systems, +environment, databases or other system components which adversely affect the Licensed Products; (iii) +caused by Customer's +modification of the Licensed Product or use thereof in combination or interconnection with software not provided by PTC; (iv) use of +the Licensed Product on a computer, operating system, software or peripherals other than a computer, operating system, software or +peripherals for which such Licensed Product was designed for and licensed for use on; (v) caused by improper or unauthorized use of +the Licensed Products; (vi) due to external causes such as, but not limited to, power failures or electric power surges; or (vii) due to a +failure by the Customer to implement recommendations in respect of solutions to Errors previously +provided by PTC to Customer. + +(2) PTC shall only be responsible for responding to problems reported by one of the two (2) technical contacts for +Customer's main location (which technical contacts and main location have previously been identified in writing to PTC by +Customer), and for sending New Releases to the "Central Support Location" designated by Customer in writing. Customer is +responsible for the distribution of New Releases to any of Customer's additional locations where +Licensed Products are authorized to +be used. Customer is responsible for providing to PTC in writing the name, address, phone number, fax number, and e-mail address +for each of Customer's designated contacts and Customer's Central Support Location. + +(3) PTC is not obligated to perform any Support Services with respect to modifications or customizations of the Licensed +Products, nor with respect to any developments resulting from Customer's use, development or customization of functionality +contained within the Licensed Products, all of which are Customer's sole responsibility + + + + +## MIT JsonCpp +============================ + + +The JsonCpp library's source code, including accompanying documentation, tests and demonstration applications, are licensed under the following conditions... + + +The author (Baptiste Lepilleur) explicitly disclaims copyright in all jurisdictions which recognize such a disclaimer. In such jurisdictions, this software is released into the Public Domain. + + +In jurisdictions which do not recognize Public Domain property (e.g. Germany as of +2010), this software is Copyright (C) 2007-2010 by Baptiste Lepilleur, and is released under the terms of the MIT License (see below). + + +In jurisdictions which recognize Public Domain property, the user of this software may choose to accept it either as 1) Public Domain, 2) under the conditions of the MIT License (see below), or 3) under the terms of dual Public Domain/MIT License conditions described here, as they choose. + + +The MIT License is about as close to Public Domain as a license can get, and is described in clear, concise terms at: + + +http://en.wikipedia.org/wiki/MIT_License + + +### The full text of the MIT License follows: +Copyright (C) 2007-2010 Baptiste Lepilleur + + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, +modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + + +The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. + + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. + +(END LICENSE TEXT) + + +The MIT license is compatible with both the GPL and commercial software, affording one all of the rights of Public Domain with the minor nuisance of being required to keep the above copyright notice and license text in the source code. Note also that by accepting the Public Domain "license" you can re-license your copy using whatever license you like. + + + +## Open source HPND License + +PIL +The Python Imaging Library (PIL) is + + +Copyright (C) 1997-2011 by Secret Labs AB Copyright (C) 1995-2011 by Fredrik Lundh + + +Pillow is the friendly PIL fork. It is + + +Copyright (C) 2010-2022 by Alex Clark and contributors +Like PIL, Pillow is licensed under the open source HPND License: + + +By obtaining, using, and/or copying this software and/or its associated documentation, you agree that you have read, understood, and will comply with the following terms and conditions: + + +Permission to use, copy, modify, and distribute this software and its associated documentation for any purpose and without fee is hereby granted, provided that the above copyright notice appears in all copies, and that +both that copyright notice and this permission notice appear in supporting documentation, and that the name of Secret Labs AB or the author not be used in advertising or publicity pertaining to distribution of the software without specific, written prior permission. + + +SECRET LABS AB AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS +SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. +IN NO EVENT SHALL SECRET LABS AB OR THE AUTHOR BE LIABLE FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM +LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE +OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. + + + + +END OF (3) ) Ion Chef(TM) Instrument Software Version 5.18 END USER LICENSE AGREEMENT +**************************************************** +**************************************************** +**************************************************** +**************************************************** +**************************************************** +(4) BEGINS: + +LIFE TECHNOLOGIES CORPORATION +END USER LICENSE AGREEMENT and LIMITED PRODUCT WARRANTY +FOR ION GENESTUDIOTM S5 INSTRUMENT SOFTWAREVERSION 5.18 INSTRUMENT OPERATING SOFTWARE +NOTICE TO USER: PLEASE READ THIS DOCUMENT CAREFULLY. THIS IS THE CONTRACT BETWEEN YOU AND LIFE TECHNOLOGIES CORPORATION ("LIFE TECHNOLOGIES") REGARDING THE OPERATING SOFTWARE FOR YOUR LIFE TECHNOLOGIES WORKSTATION OR OTHER INSTRUMENT AND BUNDLED SOFTWARE INSTALLED WITH YOUR OPERATING SOFTWARE. THIS AGREEMENT CONTAINS WARRANTY AND LIABILITY DISCLAIMERS AND LIMITATIONS. YOUR INSTALLATION AND USE OF THIS LIFE TECHNOLOGIES SOFTWARE IS SUBJECT TO THE TERMS AND CONDITIONS CONTAINED IN THIS END USER SOFTWARE LICENSE AGREEMENT, AND YOU WILL BE BOUND BY THESE TERMS AND CONDITIONS IF YOU INSTALL AND USE THE SOFTWARE. + +IF YOU DO NOT AGREE TO THESE TERMS AND CONDITIONS, YOU SHOULD PROMPTLY RETURN THIS SOFTWARE, TOGETHER WITH ALL PACKAGING, TO LIFE TECHNOLOGIES AND YOUR PURCHASE PRICE WILL BE REFUNDED. +This Life Technologies End User License Agreement accompanies a Life Technologies software product ("Software") and related explanatory materials ("Documentation"). The term "Software" also includes any upgrades, modified versions, updates, additions and copies of the Software licensed to you by Life Technologies. The term "License" or "Agreement" means this End User Software License Agreement. The term "you" or "Licensee" means the purchaser or user of this license to the Software. This Agreement includes herein by reference any additional use restrictions or Limited Use Label Licenses listed in or on user manuals, labeling, product inserts, technical notes, literature (including but not limited to Documentation) and/or splash screens related to this Software ("Supplemental Terms"). To the extent such Supplemental Terms are more restrictive than those contained herein, the more restrictive usage terms shall control. +This Software may use third-party software components from several sources. Portions of these software components are copyrighted and licensed by their respective owners. Various components require distribution of source code or if a URL is used to point the end-user to a source-code repository, and the source code is not available at such site, the distributor must, for a time determined by the license, offer to provide the source code. In such cases, please contact your Life Technologies representative. As well, various licenses require that the end-user receive a copy of the license. Such licenses, if any, may be found in Appendix 1 below. In order to use this Software, the end-user must abide by the terms and conditions of these third-party licenses. + +TITLE + +Title, ownership rights and intellectual property rights in and to the Software and Documentation shall at all times remain with Life Technologies and its subsidiaries, and their suppliers. All rights not specifically granted by this License, including Federal and international copyrights, are reserved by Life Technologies or their respective owners. + +COPYRIGHT + +The Software, including its structure, organization, code, user interface and associated Documentation, is a proprietary product of Life Technologies or its suppliers, and is protected by international laws of copyright. The law provides for civil and criminal penalties for anyone in violation of the laws of copyright. + +LICENSE + +USE OF THE SOFTWARE + +Subject to the terms and conditions of this Agreement, Life Technologies grants the purchaser of this product a non-exclusive, non-transferable (except in connection with the sale of the instrument on which it is hereby pre-installed) license, with no rights to sublicense, only to use the Software in object code (machine readable) format only on the single instrument on which it has been pre-installed by Life Technologies. + +RESTRICTIONS + +Unless permitted by applicable law, and in such cases only to the extent permitted by such law: + +7. You shall not copy, transfer (except temporarily in the event of a computer malfunction), rent, modify, distribute, electronically transmit, lend, lease, use, create derivative works based on the Software or merge the Software, or the associated Documentation, in whole or in part, whether alone or combined with any other products, except as expressly permitted in this Agreement. +8. You shall not reverse assemble, decompile, discover the source code or otherwise reverse engineer the Software. +9. You shall not remove any proprietary, copyright, trade secret or warning legend from the Software or any Documentation. +10. You agree to comply fully with all export laws and restrictions and regulations of the United States or applicable foreign agencies or authorities. You agree that you will not export or reexport, directly or indirectly, the Software and the Documentation into any country prohibited by the United States Export Administration Act and the regulations thereunder or other applicable United States law. +11. You may not use the Software or Documentation for the benefit of any third party by means of an outsourcing or service bureau relationship or for any similar commercial time-sharing or third-party training use. +12. You shall not sell, rent, transfer, resell for profit, or distribute this license or the Software, or any part thereof or any interest therein, unless the next user agrees to comply with the terms of this End User License Agreement. + +VERIFICATION + +At the written request of Life Technologies, not more frequently than annually, you shall furnish Life Technologies with a signed certification verifying that the Software is being used pursuant to the provisions of this License. + +TRIAL + +If this license is granted on a trial basis, you are hereby notified that license management software may be included to automatically cause the Software to cease functioning at the end of the trial period (and in any case you agree to discontinue usage at the end of the trial period or at the express written request of Life Technologies). + +TERMINATION + +You may terminate this Agreement by discontinuing use of the Software, removing all copies from your computers and storage media, and returning the Software and Documentation, and all copies thereof, to Life Technologies. Life Technologies may terminate this Agreement if you fail to comply with all of its terms, in which case you agree to discontinue using the Software, remove all copies from your computers and storage media, and return the Software and Documentation, and all copies thereof, to Life Technologies. + +U.S. GOVERNMENT END USERS + +The Software is a "commercial item," as that term is defined in 48 C.F.R. 2.101 (Oct. 1995), consisting of "commercial computer software" and "commercial computer software documentation," as such terms are used in 48 C.F.R. 12.212 (Sept. 1995). Consistent with 48 C.F.R. 12.212 and 48 C.F.R. 227.7202-1 through 227.7202-4 (June 1995), all U.S. Government End Users acquire the Software with only those rights set forth herein. + +EUROPEAN UNION END USERS + +If this Software is used within a country of the European Union, nothing in this Agreement shall be construed as restricting any rights available under Directive 2009/24/EC of the European Parliament and of the Council of 23 April 2009 on the legal protection of computer programs. + +LIMITED WARRANTY AND LIMITATION OF REMEDIES + +Limited Warranty. Life Technologies warrants that, except for Software provided on a trial basis, for a period of ninety days from the beginning of the applicable warranty period (as described below) the Software will, under normal use and as unmodified, function substantially in accordance with the functions and features described in the Documentation delivered with the Software when properly installed, and that for a period of ninety days from the beginning of the applicable warranty period (as described below) the tapes, CDs, diskettes or other media bearing the Software will be free of defects in materials and workmanship under normal use. +The above warranties do not apply to defects resulting from misuse, neglect, or accident, including without limitation: operation outside of the environmental or use specifications, or not in conformance with the instructions for any instrument system, software, or accessories; improper or inadequate maintenance by the user; installation of software or interfacing, or use in combination with software or products not supplied or authorized by Life Technologies; and modification or repair of the products not authorized by Life Technologies. +Warranty Period Commencement Date. The applicable warranty period for software begins on the earlier of the date of installation or three (3) months from the date of shipment for software installed by Life Technologies personnel. For software installed by the purchaser or anyone other than Life Technologies, the warranty period begins on the date the software is delivered to you. The applicable warranty period for media begins on the date the media is delivered to the purchaser. + +LIFE TECHNOLOGIES MAKES NO OTHER WARRANTIES OF ANY KIND WHATSOEVER, EXPRESS OR IMPLIED, WITH RESPECT TO THE SOFTWARE, DATA GENERATED FROM THE USE OF THE SOFTWARE ("GENERATED DATA") OR DOCUMENTATION, INCLUDING BUT NOT LIMITED TO WARRANTIES OF FITNESS FOR A PARTICULAR PURPOSE OR MERCHANTABILITY, NON-INFRINGEMENT OR NON-MISSAPROPRIATION OF INTELLECTUAL PROPERTY RIGHTS OF A THIRD PARTY, CUSTOM, TRADE, QUIET ENJOYMENT, ACCURACY OF INFORMATIONAL CONTENT, OR SYSTEM INTEGRATION. ALL OTHER WARRANTIES ARE EXPRESSLY DISCLAIMED. WITHOUT LIMITING THE GENERALITY OF THE FOREGOING, LIFE TECHNOLOGIES MAKES NO WARRANTIES THAT THE SOFTWARE WILL MEET YOUR REQUIREMENTS, THAT OPERATION OF THE SOFTWARE WILL BE UNINTERRUPTED OR ERROR FREE OR COMPLETELY SECURE, WILL OPERATE IN COMBINATION WITH THIRD PARTY HARDWARE OR SOFTWARE PRODUCTS, OR WILL CONFORM EXACTLY TO THE DOCUMENTATION, OR THAT LIFE TECHNOLOGIES WILL CORRECT ALL PROGRAM ERRORS. LIFE TECHNOLOGIES SOLE LIABILITY AND RESPONSIBILITY FOR BREACH OF WARRANTY RELATING TO THE SOFTWARE OR DOCUMENTATION SHALL BE LIMITED, AT LIFE TECHNOLOGIES SOLE OPTION, TO (1) CORRECTION OF ANY ERROR IDENTIFIED TO LIFE TECHNOLOGIES IN A WRITING FROM YOU IN A SUBSEQUENT RELEASE OF THE SOFTWARE, WHICH SHALL BE SUPPLIED TO YOU FREE OF CHARGE, (2) ACCEPTING A RETURN OF THE PRODUCT, AND REFUNDING THE PURCHASE PRICE UPON RETURN OF THE PRODUCT AND REMOVAL OF ALL COPIES OF THE SOFTWARE FROM YOUR COMPUTERS AND STORAGE DEVICES, (3) REPLACEMENT OF THE DEFECTIVE SOFTWARE WITH A FUNCTIONALLY EQUIVALENT PROGRAM AT NO CHARGE TO YOU, OR (4) PROVIDING A REASONABLE WORK AROUND WITHIN A REASONABLE TIME. LIFE TECHNOLOGIES SOLE LIABILITY AND RESPONSIBILITY UNDER THIS AGREEMENT FOR BREACH OF WARRANTY RELATING TO MEDIA IS THE REPLACEMENT OF DEFECTIVE MEDIA RETURNED WITHIN 90 DAYS OF THE DELIVERY DATE. THESE ARE YOUR SOLE AND EXCLUSIVE REMEDIES FOR ANY BREACH OF WARRANTY. WARRANTY CLAIMS MUST BE MADE WITHIN THE APPLICABLE WARRANTY PERIOD. +YOU ACKNOWLEDGE THAT LIFE TECHNOLOGIES HAS NO CONTROL OVER THE SPECIFIC CONDITIONS UNDER WHICH YOU USE THE SOFTWARE. ACCORDINGLY, EXCEPT FOR THE FOREGOING EXPRESS WARRANTY, LICENSOR CANNOT AND DOES NOT WARRANT THE PERFORMANCE OF THE SOFTWARE OR ANY PARTICULAR RESULTS THAT MAY BE OBTAINED BY THE USE OF THE SOFTWARE. THE SOFTWARE DOES NOT REPLACE YOUR OBLIGATION TO EXERCISE YOUR INDEPENDENT JUDGMENT IN USING THE SOFTWARE. The warranties made by Life Technologies may be voided by abuse or misuse of the Software. + +LIMITATION OF LIABILITY + +IN NO EVENT SHALL LIFE TECHNOLOGIES OR ITS SUPPLIERS BE RESPONSIBLE OR LIABLE, WHETHER IN CONTRACT, TORT, WARRANTY OR UNDER ANY STATUTE (INCLUDING WITHOUT LIMITATION ANY TRADE PRACTICE, UNFAIR COMPETITION OR OTHER STATUTE OF SIMILAR IMPORT) OR ON ANY OTHER BASIS FOR DAMAGES ARISING FROM PERSONAL INJURY OR DEATH OR SPECIAL, INDIRECT, INCIDENTAL, MULTIPLE, PUNITIVE, OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE POSSESSION OR USE OF, OR THE INABILITY TO USE, THE SOFTWARE, THE GENERATED DATA OR DOCUMENTATION, EVEN IF LIFE TECHNOLOGIES IS ADVISED IN ADVANCE OF THE POSSIBILITY OF SUCH DAMAGES, INCLUDING WITHOUT LIMITATION DAMAGES OR EXPENSES ARISING FROM OR RELATED TO, OR ALLEGED TO HAVE ARISEN FROM OR BE RELATED TO, LOSS OF USE, LOSS OF DATA, DOWNTIME, OR FOR LOSS OF REVENUE, PROFITS, GOODWILL OR BUSINESS OR OTHER FINANCIAL LOSS. IN ANY CASE, THE ENTIRE LIABILITY OF LIFE TECHNOLOGIES AND ITS SUPPLIERS UNDER THIS LICENSE, OR ARISING OUT OF THE USE OF THE SOFTWARE OR DOCUMENTATION OR GENERATED DATA, SHALL NOT EXCEED, IN THE AGGREGATE, THE PURCHASE PRICE OF THE PRODUCT. +SOME STATES, COUNTRIES OR JURISDICTIONS LIMIT THE SCOPE OF OR PRECLUDE LIMITATIONS OR EXCLUSION OF REMEDIES OR DAMAGES, OR OF LIABILITY, SUCH AS LIABILITY FOR GROSS NEGLIGENCE OR WILLFUL MISCONDUCT, AS OR TO THE EXTENT SET FORTH ABOVE, OR DO NOT ALLOW IMPLIED WARRANTIES TO BE EXCLUDED. IN SUCH STATES, COUNTRIES OR JURISDICTIONS, THE LIMITATION OR EXCLUSION OF WARRANTIES, REMEDIES, DAMAGES OR LIABILITY SET FORTH ABOVE MAY NOT APPLY TO YOU. HOWEVER, ALTHOUGH THEY SHALL NOT APPLY TO THE EXTENT PROHIBITED BY LAW, THEY SHALL APPLY TO THE FULLEST EXTENT PERMITTED BY LAW. YOU MAY ALSO HAVE OTHER RIGHTS THAT VARY BY STATE, COUNTRY OR OTHER JURISDICTION. +CONFIDENTIALITY + +You agree to protect Life Technologies Confidential Information with the same degree of care used to protect your own confidential information (but in no event less than a reasonable standard of care), and not to use or disclose any portion of such Confidential Information to third parties, except as expressly authorized in this Agreement. You acknowledge that the Software, including its content, structure, organization and design constitute proprietary and valuable trade secrets (and other intellectual property rights) of Life Technology and/or its licensors. The term "Confidential Information" means, collectively, non-public information that Life Technologies (and its licensors) provide and reasonably consider to be of a confidential, proprietary or trade secret nature, including but not limited to (i) the Software, and (ii) confidential elements of the Software and Life Technologies (and its licensors') technology and know-how, whether in tangible or intangible form, whether designated as confidential or not, and whether or not stored, compiled or memorialized physically, electronically, graphically, photographically, or in writing. Confidential Information does not include any information which you can demonstrate by credible evidence: (a) is, as of the time of its disclosure, or thereafter becomes part of the public domain through no fault of yours; (b) was rightfully known to you prior to the time of its disclosure, or to have been independently developed by you without use of Confidential Information; and/or (C) is subsequently learned from a third party not under a confidentiality obligation with respect to such Confidential Information. Confidential Information that is required to be disclosed by you pursuant to a duly authorized subpoena, court order, or government authority shall continue to be Confidential Information for all other purposes and you agree, prior to disclosing pursuant to a subpoena, court order, or government authority, to provide prompt written notice and assistance to Life Technologies prior to such disclosure, so that Life Technologies may seek a protective order or other appropriate remedy to protect against disclosure. + +SOFTWARE IMPROVEMENTS + +You acknowledge and agree that any ideas, enhancements, modifications, and the like disclosed by you to Life Technologies with respect to the Software ("Software Improvements and Feedback") will be the property of Life Technologies. You agree to assign, and hereby assign, all right, title, and interest worldwide in the Software Improvements and Feedback to Life Technologies and agree to assist Life Technologies, at Life Technologies' expense, in perfecting and enforcing Life Technologies rights thereto and ownership thereof. You acknowledge and agree that Life Technologies may use such Software Improvements and Feedback for its business purposes without restriction. + +GENERAL + +This Agreement shall be governed by laws of the State of California, exclusive of its conflict of laws provisions. This Agreement shall not be governed by the United Nations Convention on Contracts for the International Sale of Goods. This Agreement contains the complete agreement between the parties with respect to the subject matter hereof, and supersedes all prior or contemporaneous agreements or understandings, whether oral or written. If any provision of this Agreement is held by a court of competent jurisdiction to be contrary to law, that provision will be enforced to the maximum extent permissible and the remaining provisions of this Agreement will remain in full force and effect. The controlling language of this Agreement, and any proceedings relating to this Agreement, shall be English. You agree to bear any and all costs of translation, if necessary. The headings to the sections of this Agreement are used for convenience only and shall have no substantive meaning. All questions concerning this Agreement shall be directed to: Life Technologies Corporation, 5781 Van Allen Way, Carlsbad, CA 92008, Attention: Legal Department. +Unpublished rights reserved under the copyright laws of the United States. Life Technologies Corporation, 5781 Van Allen Way, Carlsbad, CA 92008. +Life Technologies is a trademark of Life Technologies Corporation or its subsidiaries in the U.S. and certain other countries. +All other trademarks are the sole property of their respective owners. + +May 26, 2022 + +Appendix 1 + +Life Technologies Corporation +Third Party Copyright Notices and Licenses + +Ion GeneStudioTM S5 Instrument Software VERSION 5.18 INSTRUMENT OPERATING SOFTWARE +This software uses third party software components from several sources. Portions of these software components are copyrighted and licensed by their respective owners as indicated below. Various licenses require distribution of source code or if a link is used to point the end-user to a source-code repository, and the source code is not available at such site, the distributor must, for a time determined by license, offer to provide source code. In such cases, please contact your Life Technologies representative. As well, various licenses require that the end-user receive a copy of the license or certain notices. Such licenses and notices may be found in this appendix. + +MIT/X derivate license libcurl +The curl license +COPYRIGHT AND PERMISSION NOTICE + + +Copyright (C) 1996 - 2022, Daniel Stenberg, daniel@haxx.se, and many contributors, see the THANKS +file. + + +All rights reserved. + + +Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. + + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT OF THIRD PARTY RIGHTS. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. + + +Except as contained in this notice, the name of a copyright holder shall not be used in advertising or otherwise to promote the sale, use or other dealings in this Software without prior written authorization of the copyright holder. + + + +## MIT +json library + +Copyright (C) 2007-2010 Baptiste Lepilleur and The JsonCpp Authors + + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, +modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + + +The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. + + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. + +======================================================================== +(END LICENSE TEXT) + + +The MIT license is compatible with both the GPL and commercial software, affording one all of the rights of Public Domain with the minor nuisance of being required to keep the above copyright notice and license text in the source code. Note also that by accepting the Public Domain "license" you can re-license your copy using whatever license you like. + + + +## LGPL-2.1 + +libjpeg + +Format-Specification: http://svn.debian.org/wsvn/dep/web/deps/dep5.mdwn?op=file&rev=135 + +Name: libjpeg8-empty + + +Files: * + +Copyright: 2011 Linaro Limited + +License: LGPL-2.1 + +This library is free software; you can redistribute it and/or modify it under the terms of the GNU Library General Public License (LGPL) as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. + +* This library is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Library General Public License for more details. +* You should have received a copy of the GNU Library General Public License along with this library; see the file COPYING.LIB. If not, write to +the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. +* On Debian systems, the complete text of the GNU Library General Public +License, version 2, can be found in /usr/share/common-licenses/LGPL-2.1. + + + +## LGPL-2.1 libpthread +This is the Debian prepackaged version of the Embedded GNU C Library version 2.19. + + +It was put together by the GNU Libc Maintainers +from + + +* Most of the GNU C library is under the following copyright: + + +Copyright (C) 1991,92,93,94,95,96,97,98,99,2000,2001,2002,2003,2004,2005, +2006,2007,2008,2009,2010,2011 Free Software Foundation, Inc. + + +The GNU C Library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. + + +The GNU C Library is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. + + +You should have received a copy of the GNU Lesser General Public License along with the GNU C Library; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA +02110-1301 USA + +On Debian systems, the complete text of the GNU Library +General Public License can be found in `/usr/share/common-licenses/LGPL-2.1'. + + +* The utilities associated with GNU C library is under the following copyright: + + +Copyright (C) 1991,92,93,94,95,96,97,98,99,2000,2001,2002,2003,2004,2005, +2006,2007,2008,2009,2010,2011 Free Software Foundation, Inc. + + +This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; version 2 of the License, or +(at your option) any later version. + + +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. + + +You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + + +On Debian systems, the complete text of the GNU Library +General Public License can be found in `/usr/share/common-licenses/GPL-2'. + + +* All code incorporated from 4.4 BSD is distributed under the following license: + + +Copyright (C) 1991 Regents of the University of California. All rights reserved. + + +Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: + + +1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. +2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. +3. [This condition was removed.] +4. Neither the name of the University nor the names of its contributors may be used to endorse or promote products derived from this software +without specific prior written permission. + + +THIS SOFTWARE IS PROVIDED BY THE REGENTS AND CONTRIBUTORS ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +PURPOSE +ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR +CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS +OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, +STRICT +LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +* The DNS resolver code, taken from BIND 4.9.5, is copyrighted both by UC Berkeley and by Digital Equipment Corporation. The DEC portions are under the following license: +Portions Copyright (C) 1993 by Digital Equipment Corporation. Permission to use, copy, modify, and distribute this software for any +purpose with or without fee is hereby granted, provided that the above +copyright notice and this permission notice appear in all copies, and that the name of Digital Equipment Corporation not be used in advertising or publicity pertaining to distribution of the document or software without specific, written prior permission. + + +THE SOFTWARE IS PROVIDED ``AS IS'' AND DIGITAL EQUIPMENT CORP. +DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL DIGITAL EQUIPMENT CORPORATION BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER +RESULTING +FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. + + +* The Sun RPC support (from rpcsrc-4.0) is covered by the following license: +Copyright (C) 2010, Oracle America, Inc. + + +Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: + + +* Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. +* Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. +* Neither the name of the "Oracle America, Inc." nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. + + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS +FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +* The following CMU license covers some of the support code for Mach, derived from Mach 3.0: + + +Mach Operating System +Copyright (C) 1991,1990,1989 Carnegie Mellon University +All Rights Reserved. + + +Permission to use, copy, modify and distribute this software and its documentation is hereby granted, provided that both the copyright notice and this permission notice appear in all copies of the software, derivative works or modified versions, and any portions thereof, and that both notices appear in supporting documentation. + + +CARNEGIE MELLON ALLOWS FREE USE OF THIS SOFTWARE IN ITS ``AS IS'' CONDITION. CARNEGIE MELLON DISCLAIMS ANY LIABILITY OF ANY KIND FOR ANY DAMAGES WHATSOEVER RESULTING FROM THE USE OF THIS SOFTWARE. + + +Carnegie Mellon requests users of this software to return to + + +Software Distribution Coordinator School of Computer Science Carnegie Mellon University Pittsburgh PA 15213-3890 + + +or Software.Distribution@CS.CMU.EDU any improvements or extensions that they make and grant Carnegie Mellon the rights to redistribute these changes. +* The file if_ppp.h is under the following CMU license: Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions +are met: +1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. +2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. +3. Neither the name of the University nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. + + +THIS SOFTWARE IS PROVIDED BY CARNEGIE MELLON UNIVERSITY AND CONTRIBUTORS ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE UNIVERSITY OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN +IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +* The following license covers the files from Intel's "Highly Optimized +Mathematical Functions for Itanium" collection: + +Intel License Agreement + + +Copyright (C) 2000, Intel Corporation + + +All rights reserved. + + +Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: + + +* Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. + + +* Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. + + +* The name of Intel Corporation may not be used to endorse or promote products derived from this software without specific prior written permission. + + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL INTEL OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +* The files inet/getnameinfo.c and sysdeps/posix/getaddrinfo.c are copyright +(C) by Craig Metz and are distributed under the following license: + + +* The Inner Net License, Version 2.00 + + +The author(s) grant permission for redistribution and use in source and +binary forms, with or without modification, of the software and documentation provided that the following conditions are met: + + +0. If you receive a version of the software that is specifically labelled +as not being for redistribution (check the version message and/or README), +you are not permitted to redistribute that version of the software in any way or form. +1. All terms of the all other applicable copyrights and licenses must be followed. +2. Redistributions of source code must retain the authors' copyright notice(s), this list of conditions, and the following disclaimer. +3. Redistributions in binary form must reproduce the authors' copyright notice(s), this list of conditions, and the following disclaimer in the documentation and/or other materials provided with the distribution. +4. [The copyright holder has authorized the removal of this clause.] +5. Neither the name(s) of the author(s) nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. + + +THIS SOFTWARE IS PROVIDED BY ITS AUTHORS AND CONTRIBUTORS ``AS IS'' AND ANY +EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +ARE +DISCLAIMED. IN NO EVENT SHALL THE AUTHORS OR CONTRIBUTORS BE LIABLE FOR ANY +DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES +(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; +LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON +ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS +SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. If these license terms cause you a real problem, contact the author. */ + +## MIT +libxml + +https://gitlab.gnome.org/GNOME/libxml2/-/wikis/home + + +The MIT License +OSI Approved License LogoLicense Copyright: Unknown. License License: Unknown. +License Contact: Unknown. + +SPDX short identifier: MIT Further resources... + +Begin license text. +Copyright + + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + + +The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. + + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. + + +End license text. + + + + +## LGPL-2.1+ +libudev + +Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: systemd +Upstream-Contact: systemd-devel@lists.freedesktop.org +Source: https://www.freedesktop.org/wiki/Software/systemd/ + + +Files: debian/* +Copyright: 2010-2013 Tollef Fog Heen +2013-2015 Michael Biebl +2013 Michael Stapelberg License: LGPL-2.1+ + + +Files: * + +Copyright: 2008-2015 Kay Sievers + +2010-2015 Lennart Poettering +2012-2015 Zbigniew Ja (TM) drzejewski-Szmek +2013-2015 Tom Gundersen +2013-2015 Daniel Mack +2010-2015 Harald Hoyer +2013-2015 David Herrmann +2013, 2014 Thomas H.P. Andersen +2013, 2014 Daniel Buch +2014 Susant Sahani +2009-2015 Intel Corporation +2000, 2005 Red Hat, Inc. +2009 Alan Jenkins +2010 ProFUSION embedded systems +2010 Maarten Lankhorst +1995-2004 Miquel van Smoorenburg +1999 Tom Tromey +2011 Michal Schmidt +2012 B. Poettering +2012 Holger Hans Peter Freyther +2012 Dan Walsh +2012 Roberto Sassu +2013 David Strauss +2013 Marius Vollmer +2013 Jan Janssen +2013 Simon Peeters +License: LGPL-2.1+ + + +Files: src/basic/siphash24.h src/basic/siphash24.c +Copyright: 2012 Jean-Philippe Aumasson +2012 Daniel J. Bernstein License: CC0-1.0 + + +Files: src/basic/securebits.h +Copyright: Linus Torvalds License: GPL-2 + + +Files: src/basic/ioprio.h +Copyright: Jens Axboe License: GPL-2 + + +Files: src/shared/linux/auto_dev-ioctl.h +Copyright: 2008 Red Hat, Inc. +2008 Ian Kent License: GPL-2+ + + +Files: src/basic/sparse-endian.h +Copyright: 2012 Josh Triplett License: Expat + + +Files: src/journal/lookup3.c src/journal/lookup3.h +Copyright: none +License: public-domain +You can use this free for any purpose. It's in the public domain. It has no warranty. + + +Files: src/udev/* +Copyright: 2003-2012 Kay Sievers +2003-2004 Greg Kroah-Hartman +2004 Chris Friesen +2004, 2009, 2010 David Zeuthen +2005, 2006 SUSE Linux Products GmbH +2003 IBM Corp. +2007 Hannes Reinecke +2009 Canonical Ltd. +2009 Scott James Remnant +2009 Martin Pitt +2009 Piter Punk +2009, 2010 Lennart Poettering +2009 Filippo Argiolas +2010 Maxim Levitsky +2011 ProFUSION embedded systems +2011 Karel Zak +2014 Zbigniew Ja (TM) drzejewski-Szmek +2014 David Herrmann +2014 Carlos Garnacho License: GPL-2+ + + +Files: src/udev/udev-ctrl.c src/udev/udevadm-hwdb.c src/udev/udev-builtin.c src/udev/udev-builtin-net_id.c +src/udev/udev-builtin-net_setup_link.c src/udev/udev-builtin-hwdb.c src/udev/udev-builtin-btrfs.c src/udev/udev-builtin-keyboard.c +src/udev/net/link-config.h src/udev/net/link-config.c src/udev/net/ethtool-util.c src/udev/net/ethtool-util.h +Copyright: 2007-2013 Kay Sievers +2013 Tom Gundersen License: LGPL-2.1+ + + +Files: src/udev/scsi_id/scsi.h Copyright: 2003 IBM Corp. License: GPL-2 + + +License: Expat + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to +deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + +* The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. +* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS +IN THE SOFTWARE. + + +## License: GPL-2 +This program is free software; you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by the Free Software Foundation; version 2 of the License. +* This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. +You should have received a copy of the GNU General Public License +along with this program; if not, write to the Free Software Foundation, Inc., +51 Franklin St, Fifth Floor, Boston, MA 02110-1301, USA. +*On Debian and systems the full text of the GNU General Public +License version 2 can be found in the file +`/usr/share/common-licenses/GPL-2` + + +## License: GPL-2+ +This program is free software; you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2, or (at your option) +any later version. + +* This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. +* You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, +Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. +* On Debian systems, the complete text of the GNU General Public License version 2 can be found in `/usr/share/common-licenses/GPL-2` (TM) . + + +## License: LGPL-2.1+ +This program is free software; you can redistribute it and/or modify +it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1, or (at your option) +any later version. + +* This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. +* You should have received a copy of the GNU Lesser General Public License along with this program; if not, write to the Free Software Foundation, +Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. +* On Debian systems, the complete text of the GNU Lesser General Public +License version 2.1 can be found in `/usr/share/common-licenses/LGPL-2.1`(TM) . + +## License: CC0-1.0 +To the extent possible under law, the author(s) have dedicated all copyright and related and neighboring rights to this software to the public domain worldwide. This software is distributed without any warranty. + +* You should have received a copy of the CC0 Public Domain Dedication along with this software. If not, see . +* On Debian systems, the complete text of the CC0 1.0 Universal license can be found in `/usr/share/common-licenses/CC0-1.0` (TM) . + + +## Libpng license libpng12 + +COPYRIGHT NOTICE, DISCLAIMER, and LICENSE + + +### PNG Reference Library License version 2 + + +* Copyright (C) 1995-2019 The PNG Reference Library Authors. +* Copyright (C) 2018-2019 Cosmin Truta. +* Copyright (C) 2000-2002, 2004, 2006-2018 Glenn Randers-Pehrson. +* Copyright (C) 1996-1997 Andreas Dilger. +* Copyright (C) 1995-1996 Guy Eric Schalnat, Group 42, Inc. + + +The software is supplied "as is", without warranty of any kind, express or implied, including, without limitation, the warranties of merchantability, fitness for a particular purpose, title, and +non-infringement. In no event shall the Copyright owners, or anyone distributing the software, be liable for any damages or other liability, whether in contract, tort or otherwise, arising from, out of, or in connection with the software, or the use or other dealings in the software, even if advised of the possibility of such damage. + + +Permission is hereby granted to use, copy, modify, and distribute this software, or portions hereof, for any purpose, without fee, subject to the following restrictions: + + +1. The origin of this software must not be misrepresented; you must not claim that you wrote the original software. If you +use this software in a product, an acknowledgment in the product documentation would be appreciated, but is not required. +2. Altered source versions must be plainly marked as such, and must not be misrepresented as being the original software. + + +3. This Copyright notice may not be removed or altered from any source or altered source distribution. + + + +## PNG Reference Library License version 1 (for libpng 0.5 through 1.6.35) + + +libpng versions 1.0.7, July 1, 2000, through 1.6.35, July 15, 2018 are Copyright (C) 2000-2002, 2004, 2006-2018 Glenn Randers-Pehrson, are derived from libpng-1.0.6, and are distributed according to the same disclaimer and license as libpng-1.0.6 with the following individuals added to the list of Contributing Authors: + + +Simon-Pierre Cadieux +Eric S. Raymond Mans Rullgard Cosmin Truta Gilles Vollant James Yu +Mandar Sahastrabuddhe +Google Inc. Vadim Barkov + + +and with the following additions to the disclaimer: + + +There is no warranty against interference with your enjoyment of the library or against infringement. There is no warranty that our efforts or the library will fulfill any of your particular purposes +or needs. This library is provided with all faults, and the entire risk of satisfactory quality, performance, accuracy, and effort is with the user. + + +Some files in the "contrib" directory and some configure-generated files that are distributed with libpng have other copyright owners, and are released under other open source licenses. + + +libpng versions 0.97, January 1998, through 1.0.6, March 20, 2000, are Copyright (C) 1998-2000 Glenn Randers-Pehrson, are derived from libpng-0.96, and are distributed according to the same disclaimer and license as libpng-0.96, with the following individuals added to the list of Contributing Authors: + +Tom Lane +Glenn Randers-Pehrson +Willem van Schaik + + +libpng versions 0.89, June 1996, through 0.96, May 1997, are +Copyright (C) 1996-1997 Andreas Dilger, are derived from libpng-0.88, and are distributed according to the same disclaimer and license as libpng-0.88, with the following individuals added to the list of Contributing Authors: + + +John Bowler Kevin Bracey Sam Bushell +Magnus Holmgren +Greg Roelofs +Tom Tanner + + +Some files in the "scripts" directory have other copyright owners, but are released under this license. + + +libpng versions 0.5, May 1995, through 0.88, January 1996, are +Copyright (C) 1995-1996 Guy Eric Schalnat, Group 42, Inc. + + +For the purposes of this copyright and license, "Contributing Authors" is defined as the following set of individuals: + + +Andreas Dilger Dave Martindale Guy Eric Schalnat Paul Schmidt +Tim Wegner + +The PNG Reference Library is supplied "AS IS". The Contributing Authors and Group 42, Inc. disclaim all warranties, expressed or implied, including, without limitation, the warranties of merchantability and of fitness for any purpose. The Contributing Authors and Group 42, Inc. assume no liability for direct, indirect, incidental, special, exemplary, or consequential damages, which may result from the use of the PNG Reference Library, even if advised of the possibility of such damage. + + +Permission is hereby granted to use, copy, modify, and distribute this source code, or portions hereof, for any purpose, without fee, subject to the following restrictions: + + +1. The origin of this source code must not be misrepresented. + + +2. Altered versions must be plainly marked as such and must not be misrepresented as being the original source. + + +3. This Copyright notice may not be removed or altered from any source or altered source distribution. + + +The Contributing Authors and Group 42, Inc. specifically permit, without fee, and encourage the use of this source code as a component to supporting the PNG file format in commercial products. If you use +this source code in a product, acknowledgment is not required but would be appreciated. + + +LGPL-2.1 libnuma +This package was debianized by Ian Wienand +on Wed, 15 Dec 2004. + + +libnuma sources are available from https://github.com/numactl/numactl + + +Upstream Authors: +Andi Kleen Copyright (C) 2004 Andi Kleen +numactl and the demo programs are under the GNU General Public License, v.2 libnuma is under the GNU Lesser General Public License, v2.1. +The manpages are under the same license as the Linux manpages (see the files) + + +This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, +or (at your option) any later version. The full text of the License may be found in /usr/share/common-licenses/GPL. + + +The redistribution of portions of this program are controlled by the GNU Lesser General Public License as published by the Free Software Foundation. The full text of the License may be found in + + +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. + + +Parts of the numademo program are derived from the STREAM benchmark, available from + +http://www.cs.virginia.edu/stream/ + + +Proprietary license from PTC Axeda Agent Embedded +PTC CUSTOMER AGREEMENT + +THIS PTC CUSTOMER AGREEMENT ("AGREEMENT") IS A LEGAL AGREEMENT BETWEEN THE INDIVIDUAL, OR THE COMPANY OR OTHER ORGANIZATION ON WHOSE BEHALF SUCH INDIVIDUAL ACCEPTS THIS AGREEMENT, THAT EITHER (A) CLICKS THE "I ACCEPT" BUTTON BELOW OR (B) INSTALLS, ACCESSES, OR USES ANY SOFTWARE OR DOCUMENTATION FROM PTC ("CUSTOMER"), AND PTC INC. OR, IF THE PURCHASE WAS MADE IN A COUNTRY SPECIFIED ON SCHEDULE A TO THIS AGREEMENT, THE PTC AFFILIATE SPECIFIED ON SCHEDULE A (AS APPLICABLE, "PTC"). + +PLEASE READ THE TERMS AND CONDITIONS OF THIS AGREEMENT CAREFULLY BEFORE ACCEPTING THIS AGREEMENT. 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BY (I) USING FREE OR TRIAL SOFTWARE OR (II) NOT OPTING-OUT OF THE COLLECTION OF CERTAIN PERSONAL DATA AS YOU ARE ABLE TO WITH PTC COMMERCIAL SOFTWARE, YOU CONSENT TO PTC'S COLLECTION, USE, AND TRANSFER OF YOUR PERSONAL DATA (INCLUDING TO THE UNITED STATES). + +CAPITALIZED TERMS NOT DEFINED IN THE TEXT BELOW ARE DEFINED IN SCHEDULE B AT THE END OF THIS AGREEMENT. + +SCHEDULE A TO THIS AGREEMENT CONTAINS ADDITIONAL (OR ALTERNATIVE) TERMS APPLICABLE TO SPECIFIC GEOGRAPHIES. + + +1. License. + + 1.1 License Grant. Subject to the terms and conditions of this Agreement, PTC hereby grants to Customer a non-exclusive, revocable, non-transferable license, without any right to sub-license, to install and use the Licensed Products identified in the Quote during the applicable License Term, solely for Customer's internal business purposes and solely in accordance with the applicable usage and license-type restrictions identified in the Quote and in the Licensing Basis Webpage ("License"). Notwithstanding the foregoing: + + (a) If the Licensed Product is being provided by PTC on an "evaluation" or "trial" basis, such License will be instead to install and use the Licensed Product solely to evaluate such Licensed Products, and Customer agrees not to use the Licensed Product in any commercial applications or for productive purposes. + + (b) If the Licensed Software is Educational Software, Customer must be enrolled in, or employed by, an accredited, academic institution, and shall use the Licensed Software solely for educational purposes in a degree-granting program. If Customer does not meet one of these qualifications, Customer has no rights under this Agreement. Without limitation, non- educational research or funded educational research conducted using the facilities of an academic institution or under an academic name does not qualify as "educational purposes" and use of Educational Software for such purposes represents a violation of the terms of this Agreement. + + (C) If the Licensed Software is sold on a "demo and test" or "non-production" basis (or similar designation), such Licensed +Software may not be used in a production environment. + + 1.2 Designated Country/Computers/Networks. Subject to Section 1.3, Customer may only install and operate Licensed Products on the applicable Designated Computers or Designated Networks on computer systems and networks situated in the applicable Designated Country. Customer may, from time to time, change the Designated Computer, Designated Network, and/or the Designated Country in which Customer seeks to install or operate a Licensed Product, provided that in each case (i) Customer shall give prior written notice to PTC of any such change, and (ii) upon moving the Licensed Products to a different Designated Country, Customer shall pay all applicable Uplift Fees. Notwithstanding the foregoing, Registered Users need not be located in the Designated Country when accessing a Registered User Product. + + 1.3 Global/Restricted Global Licenses. If a Concurrent User Licensed Product is licensed by PTC on a "Global" or "Restricted +Global" basis, Section 1.2 shall not apply to such Licensed Products and the following provisions shall apply instead: + + (i) Global Licenses. Subject to the other requirements of this Agreement, a Global License allows the Customer to install, operate and use such Licensed Product at any Customer site(s) throughout the world. + + (ii) Restricted Global Licenses. Subject to the other requirements of this Agreement, a Restricted Global License allows the Customer to install, operate and use such Licensed Product at any Customer site(s) located in the Designated Country and/or in any Permitted Country. "Permitted Countries" means China, India, Russia, the Czech Republic, Poland, Hungary, Malaysia, South Africa, Israel, Mexico, Brazil, Argentina, and Romania. + + 1.4 Additional Restrictions on Use. Customer shall not permit any persons who are not Permitted Users to access or use the +Licensed Products. Customer shall not and shall not permit any third party(ies) to: + + (i) modify or create any derivative work of any part of the Licensed Products; (ii) rent, lease, or loan the Licensed Products; + + (iii) use the Licensed Products, or permit them to be used, for third-party training, to deliver software implementation or consulting services to any third parties, or for commercial time-sharing or service bureau use; + + (iv) disassemble, decompile or reverse engineer the Licensed Products or the file format of the Licensed Products, or otherwise attempt to gain access to the source code or file format of the Licensed Products, except as expressly permitted in Schedule A, if applicable; + + (v) sell, license, sublicense, loan, assign, or otherwise transfer (whether by sale, exchange, gift, operation of law, or otherwise) to any third party the Licensed Products, any copy thereof, or any License or other rights thereto, in whole or in part, without in each case obtaining PTC's prior written consent, except to the extent that any of the foregoing are explicitly authorized in the Quote and/or the Licensing Basis Webpage; + + (vi) alter, remove, or obscure any copyright, trade secret, patent, trademark, logo, proprietary and/or other legal notices on or in any copies of the Licensed Products; and + + (vii) copy or otherwise reproduce the Licensed Products in whole or in part, except (a) as may be required for their installation into computer memory for the purpose of executing the Licensed Products in accordance with this Section 1, and/or (b) to make a reasonable number of copies solely for back-up purposes (provided that any such permitted copies shall be the property of PTC, and Customer shall reproduce thereon all PTC copyright, trade secret, patent, trademark, logo, proprietary and/or other legal notices contained in the original copy of the Licensed Product obtained from PTC). + + If Customer uses any unlicensed or unauthorized copies of any PTC software, Customer agrees that, without limiting PTC's right to terminate this Agreement for breach in accordance with Section 7 and without limiting any other remedies to which PTC may be +entitled, Customer will pay to PTC the PTC then-current list price for all such unlicensed software, in addition to any fines or penalties that may be imposed by law. + + 1.5 Additional Restrictions on Use Applicable to Concurrent User Products. If the Licensed Product is a Concurrent User Product, the following provisions apply: + + (i) The number of Permitted Users accessing or operating a Concurrent User Product at any point in time may not exceed the number of Licenses in effect at such time for that particular Licensed Product. + + (ii) Except with respect to Integrity and Implementer Products, only Permitted Users physically located in the Designated Country may access, operate and/or use the Licensed Products. Permitted Users who are not employees of Customer may use the Licensed Products while physically located at Customer's site only. + + (iii) Where a Concurrent User Product is Licensed on a "fixed," "locked" or "node-locked" basis, or the Licensed Product is licensed as a "Designated Computer" product, such Licensed Product is licensed to operate solely on the Designated Computer on which it is installed. + + 1.6 Additional Restrictions on Use Applicable to Registered User Products. A License is required for each individual who accesses a Registered User product or the data contained therein, whether directly or through a web portal or other mechanism for "batching" or otherwise achieving indirect access to the Licensed Product or such data. Generic or shared log-ins are not permitted. Customer may add and/or substitute from time to time new Registered Users as long as the aggregate number of Registered Users does not exceed at any point in time the number of Licenses in effect at such time for that particular Licensed Product and, provided further, that if a person who was previously a Registered User returns to Registered User status, a new License fee must be paid to PTC at PTC's then current rates. + + 1.7 Additional Restrictions on Use Applicable to Designated Server Products. Each Designated Server product may only be used on the computer server that is designated by the Customer in connection with the initial installation of such product and that has one unique instance of the applicable installed product application. In the event a computer server is partitioned in any manner (physically, logically or otherwise), the reference in the preceding sentence to "computer server" shall mean each partition of such server, and such Designated Server product may only be used on one of such partitions. Customer may, from time to time, change the Designated Server(s) for a Designated Server Product, and/or the location thereof, provided that in each case +(a) Customer shall give prior written notice to PTC of any such change, and (b) upon transferring the Designated Server Products to a different Designated Country, Customer pays all applicable Uplift Fees. + + 1.8 Third Party Components and Bundled Third Party Products. Certain of the Licensed Products may contain third party software components for which additional terms apply ("Third Party Components"). The current additional terms are set forth on the Schedule of Third Party Terms available in the legal policies and guidelines section of http://www.ptc.com. Separately, third party software products that PTC resells and/or bundles for distribution with the Licensed Products are licensed to Customer directly by the manufacturer of such third party software products ("Bundled Third Party Products"). Such Bundled Third Party Products are also described on the Schedule of Third Party Terms. Customer agrees that its use of Third Party Components and/or Bundled Third Party Products is subject to the terms of the Schedule of Third Party Terms. New Releases containing Third Party Components or Bundled Third Party Products may be subject to additional or different third party terms, of which PTC shall notify the Customer at the time such New Releases are delivered to the Customer. + + 1.9 Upgrades: If the Licensed Software was licensed as an upgrade from a previous version, Customer must first be licensed for the Licensed Software identified by PTC as eligible for the upgrade and Customer must be active on Support Services for such software. After installing the upgrade, Licensed Software licensed as an upgrade replaces and/or supplements the product that formed the basis of Customer's eligibility for the upgrade and Customer may no longer use the original Licensed Software that formed the basis for Customer's upgrade eligibility. + +2. Compliance. + + 2.1 License Usage Assessments. To confirm Customer's compliance with the terms and conditions hereof, Customer agrees that PTC may perform a usage assessment with respect to Customer's use of the Licensed Products. Customer agrees to provide PTC access to Customer's facilities and computer systems, and cooperation from Customer's employees and consultants, as reasonably requested by PTC in order to perform such assessment, all during normal business hours, and after reasonable prior notice from PTC. + + 2.2 Reports. Upon written request from PTC, Customer agrees to provide to PTC an installation and/or usage report with respect to the Licensed Products (and in the case of Registered User Products, such report shall include a list of all users for whom Customer has issued a password or other unique identifier to enable such individual to use the Registered User Product). Such report shall be certified by an authorized representative of Customer as to its accuracy within ten (10) business days after receipt of any written request from PTC. For any period in which Customer's use of the Licensed Products exceeds the number and/or the scope of the Licenses in effect during such period for such Licensed Products, Customer agrees to pay for any such excess usage, including applicable license and Support Services fees, and without limiting any other rights or remedies to which it is entitled, failure to pay shall be grounds for termination in accordance with Section 7 hereof. + +3. Intellectual Property. PTC and its licensors are the sole owners of the Licensed Products and of any copies of the Licensed Products, and of all copyright, trade secret, patent, trademark and other intellectual or industrial property rights in and to the Licensed Products. All copies of the Licensed Products, in whatever form provided by PTC or made by Customer, shall remain the property of PTC, and such copies shall be deemed to be on loan to Customer during the License Term. Customer acknowledges that the License granted hereunder does not provide Customer with title to or ownership of the Licensed Products or any copies thereof, but only a right of limited use consistent with the express terms and conditions of this Agreement. Customer shall have no rights to the source code for the Licensed Products, and Customer agrees that only PTC shall have the right to maintain, enhance, or otherwise modify the Licensed Products. + +4. Support Services; Warranty; Disclaimer of Warranties. + + See Schedule A for a modified version of this Section 4 for Licensed Products licensed and used in Germany, Austria or Switzerland. + + 4.1 Support Services. Upon PTC's acceptance of an order for Support Services or for Licensed Products for which Usage License Fees apply, PTC agrees that it or its designated service provider shall provide the applicable Support Services in accordance with Schedule C. + + 4.2 Warranty. PTC warrants to Customer that PTC is authorized to grant the License(s) and that, subject to Section 4.3, the Licensed Products will be free from Errors for a period of ninety (90) days following PTC's initial shipment to Customer or Customer's designee of such Licensed Products (the "Warranty Period"). + + 4.3 Warranty Exceptions. PTC shall have no warranty obligations hereunder with respect to any (i) evaluation, "trial" or "express" Licenses, (ii) New Releases, (iii) computer software provided to Customer in the course of PTC's delivery of Training Services, (iv) Errors attributable to the use of the Licensed Product in an application or environment for which it was not designed or contemplated, (v) Errors attributable to any modifications or customizations of the Licensed Products, (vi) Licensed Products that are provided by PTC free of charge to Customer, and/or (vii) Sun Software, Oracle Software and/or Bundled Third Party Products. + + 4.4 Sole Remedy. PTC's and its licensors' entire liability and Customer's exclusive remedy for any breach by PTC of the warranty given in Section 4.2 above shall be, at PTC's sole discretion, either to (a) replace the Licensed Product(s) or (b) use diligent efforts to repair the Error. PTC's obligations set forth in the preceding sentence shall apply only if notice of the Error is received by PTC within the Warranty Period and Customer supplies such additional information regarding the Error as PTC may reasonably request. If PTC does not replace the applicable Licensed Product(s) and/or does not repair the Error (either by providing a bug fix, a workaround or otherwise) within a reasonable time after notice of the Error and associated information from Customer is received by PTC, PTC will provide a refund of the license fees paid by Customer for the applicable Licensed Product(s) upon return of such Licensed Product(s) and any copies thereof. + + 4.5 No Additional Warranties. No third party, including any employee, partner, distributor (including any Reseller) or agent of PTC or any of its resellers or sales agents, is authorized to give any representations, warranties or covenants greater or different than those contained in this Agreement with respect to any Licensed Products or Services, except as specifically set forth in a written agreement signed on behalf of Customer by an authorized officer and on behalf of PTC by its legal counsel or Corporate Controller. + + 4.6 Disclaimer of Warranties. EXCEPT AS EXPRESSLY STATED IN SECTION 4, PTC DISCLAIMS (AND CUSTOMER WAIVES) ALL WARRANTIES, WHETHER EXPRESS, IMPLIED, OR STATUTORY, WRITTEN OR ORAL, INCLUDING ANY WARRANTY OF MERCHANTABILITY, SATISFACTORY QUALITY, FITNESS FOR A PARTICULAR PURPOSE, NON-INFRINGEMENT, AND/OR ANY WARRANTY THAT CUSTOMER WILL ACHIEVE ANY PARTICULAR RETURN ON INVESTMENT. THE LICENSED PRODUCTS ARE INTENDED TO BE USED BY TRAINED PROFESSIONALS AND ARE NOT A SUBSTITUTE FOR PROFESSIONAL JUDGMENT, TESTING, SAFETY AND UTILITY. CUSTOMER IS SOLELY RESPONSIBLE FOR ANY RESULTS OBTAINED FROM USING THE LICENSED PRODUCTS, INCLUDING THE ADEQUACY OF INDEPENDENT TESTING OF RELIABILITY AND ACCURACY OF ANY ITEM DESIGNED USING LICENSED PRODUCTS. PTC does not warrant that the operation or other use of the Licensed Products will be uninterrupted or error free or will not cause damage or disruption to Customer's data, computers or networks. + +5. Indemnification; Infringement. + + 5.1 P TC's Ob li gati on to Ind emn ify C u sto mer . PTC, at its own expense, will defend any action brought against Customer based on a claim that any Licensed Product infringes a United States, European Union or Japanese patent, copyright or trademark and, at its option, will settle any such action or will pay any final judgment awarded against Customer, provided that: (a) PTC shall be notified promptly in writing by Customer of any notice of any such claim; (b) PTC shall have the sole control of the defense of any action on such claim and all negotiations for its settlement or compromise and shall bear the costs of the same (save where one or more of the exclusions in Section 5.3 applies); and (C) Customer shall cooperate fully at PTC's expense with PTC in the defense, settlement or compromise of such claim. This Section 5 states PTC's sole and exclusive liability, and Customer's sole remedy, for any and all claims relating to infringement of any intellectual property right. + + 5.2 P TC's Righ t to Act to P reven t a Clai m + + + If a claim described in Section 5.1 hereof occurs or, in PTC's opinion, may occur, +Customer shall permit PTC, at PTC's option and expense to: (a) procure for Customer the right to continue using the Licensed Product; (b) modify the Licensed Product so that it becomes non-infringing without materially impairing its functionality; or (C) terminate the applicable Licenses, accept return of the Licensed Products and grant Customer a credit thereon. For Licenses purchased with a perpetual License Term, such credit shall be equal to the License fees paid by Customer for such Licensed Product depreciated on a straight-line, five year basis. For Licenses purchased on a term license or subscription basis, such credit shall be equal to the prepaid license or subscription fees for the remainder of the License Term. + + 5.3 Exclu sio n s fro m P TC's Ob li gati o n to In d emn ify Cu sto mer . PTC shall have no liability to Customer under Section 5.1 hereof or otherwise to the extent that any infringement or claim thereof is based upon: (a) use of the Licensed Product in combination with equipment or software not supplied hereunder where the Licensed Product itself would not be infringing; (b) use of the Licensed Product in an application or environment for which it was not designed or not contemplated under this Agreement; (C) use of other than a current release of the Licensed Product(s) provided to Customer; (d) modification of the Licensed Product by anyone other than PTC or its employees or agents; or (e) any claims of infringement of any patent, copyright, trade secret, trademark or other proprietary right in which Customer has an interest. + + +6. Limitation of Liability. + + See Schedule A for a modified version of this Section 6 for Licensed Products licensed and used in Germany, Austria or Switzerland. + + 6.1 The warranty and indemnification provisions of Sections 4 and 5 hereof state the entire liability of PTC, its subsidiaries and affiliates, and each of their respective directors, officers, employees or agents, with respect to the Licensed Products and Services, including (without limitation) any liability for breach of warranty, or for infringement or alleged infringement of patent, copyrights, trademarks, trade secrets and other intellectual or proprietary rights by the Licensed Products, or their use. + + 6.2 EXCEPT FOR PTC'S INDEMNIFICATION OBLIGATIONS IDENTIFIED IN SECTION 5.1 ABOVE, THE MAXIMUM LIABILITY OF PTC AND ITS LICENSORS ARISING OUT OF, OR RELATING TO, THE CREATION, LICENSE, FUNCTIONING, USE OR SUPPLY OF THE LICENSED PRODUCTS OR THE PROVISION OF SERVICES OR OTHERWISE RELATING TO THIS AGREEMENT, WHETHER BASED UPON WARRANTY, CONTRACT, TORT, OR OTHERWISE, SHALL NOT, (I) FOR LICENSES PURCHASED ON A PERPETUAL BASIS, EXCEED THE FEES PAID BY CUSTOMER FOR THE LICENSED PRODUCTS OR SERVICES THAT GAVE RISE TO THE CLAIM AND (II) FOR LICENSES PURCHASED ON A TERM OR SUBSCRIPTION BASIS, EXCEED THE FEES PAID BY CUSTOMER IN THE TWELVE MONTH PERIOD IMMEDIATELY PRECEDING THE EVENT GIVING RISE TO DAMAGES FOR THE LICENSED PRODUCTS OR SERVICES THAT GAVE RISE TO THE CLAIM. + + 6.3 IN NO EVENT SHALL PTC, ITS LICENSORS, ITS AFFILIATES (INCLUDING ITS SUBSIDIARY COMPANIES), OR ANY OF THEIR RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES OR AGENTS BE LIABLE FOR: (A) ANY LOSS OF PROFIT, LOSS OF USE DAMAGES, LOSS OF GOODWILL, LOSS OF BUSINESS OPPORTUNITY, LOSS OF SALES, LOSS OF REPUTATION OR LOSS OF ANTICIPATED SAVINGS; (B) ANY LOSS OR INACCURACY OF DATA OR BUSINESS INFORMATION OR FAILURE OR INADEQUACY OF ANY SECURITY SYSTEM OR FEATURE; AND (C) SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE OR CONSEQUENTIAL LOSS OR DAMAGE HOWSOEVER CAUSED; IN EACH CASE EVEN IF PTC HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. + + 6.4 Customer agrees not to bring any suit or action against PTC, and/or its subsidiaries and affiliates, and/or any of their respective directors, officers, employees or agents for any reason whatsoever more than one year after the cause of action arises. Customer recognizes that fees paid by Customer for the Licensed Products and Services are based in part on the disclaimer of warranty and limitation of liability provisions set forth herein and that, in the absence of Customer's agreement to such terms, the charges for the Licensed Products would be significantly higher. The limitations and exclusions set forth in this Section 6 shall not apply to any claim in respect of death or personal injury. + +7. Term and Termination. + + 7.1 Events Causing Termination. This Agreement and all Licenses will terminate: + + (a) Automatically and without notice on the following events: (I) Customer's breach of any of clauses (i) through (vii) of Section 1.4 or Sections 3 or 8.4 hereof; (II) a receiver, trustee, liquidator, or such similar officer is appointed for Customer or for any of Customer's properties or assets; (III) Customer makes a general assignment for the benefit of Customer's creditors; (IV) Customer files a petition for its reorganization, dissolution or liquidation, or such a petition is filed against Customer and is not dismissed within sixty (60) days thereafter; or (V) Customer ceases doing business or commence dissolution or liquidation proceedings; or + + (b) Thirty (30) days after written notice from PTC specifying a breach (other than as listed in Section 7.1(a) above) of this Agreement, including failure to make any payment due to either PTC or a Reseller in connection with the Licensed Products in a timely manner, if that breach is not, within that thirty (30) day period, remedied to PTC's reasonable satisfaction. + + 7.2 Effects of Expiration or Termination. Upon expiration of a given License Term and/or any expiration or termination of this Agreement, Customer shall promptly pay all sums owed by Customer, return to PTC the original copies of all Licensed Products for which the License Term has expired or has been terminated, destroy and/or delete all copies and backup copies thereof from Customer's computer libraries, storage facilities and/or hosting facilities, and certify in writing by an officer that Customer is in +compliance with the foregoing requirements and that such Licensed Products are no longer in Customer's possession or in use. + + 7.3 Survival. Sections 2, 3, 4.6, 5, 6, 7.2, 7.3 and 8 shall survive expiration or termination of this Agreement. + +8. General. + + 8.1 Governing Law and Jurisdiction. Unless otherwise stated in Schedule A, all disputes arising under, out of, or in any way connected with this Agreement shall be governed by and construed in accordance with the laws of the Commonwealth of Massachusetts without reference to conflict of laws principles (and specifically excluding the Uniform Computer Information Transactions Act). The parties hereby expressly disclaim the application of the U.N. Convention for the International Sale of Goods. All disputes arising under, out of, or in any way connected with this Agreement shall be litigated exclusively in the state or federal courts situated in the Commonwealth of Massachusetts, and in no other court or jurisdiction. Notwithstanding the foregoing or anything to the contrary, PTC shall have the right to bring a claim in any court of competent jurisdiction to enforce any intellectual property rights and/or protect any confidential information. Customer agrees that the state and federal courts situated in the Commonwealth of Massachusetts shall have personal jurisdiction over its person, and Customer hereby irrevocably (i) submits to the personal jurisdiction of said courts and (ii) consents to the service of process, pleadings, and notices in connection with any and all actions initiated in said courts. The parties agree that a final judgment in any such action or proceeding shall be conclusive and binding and may be enforced in any other jurisdiction. Each party waives its right to trial by jury in connection with any dispute arising out of this Agreement. + + 8.2 Notices. Any notice or communication required or permitted under this Agreement shall be in writing. In the case of notice to Customer, the notice shall be directed to the address set forth on the Customer's purchase order or to such other address as may be provided to PTC in writing. In the case of notice to PTC, such notice shall be directed to PTC, 140 Kendrick Street, Needham, MA +02494; Attn: Corporate Controller, with a copy to General Counsel. Any notice provided under this section shall be deemed to have been received: (a) if given by hand, immediately; (b) if given by mail, five (5) business days after posting; (C) if given by express courier service, the second business day following dispatch in the jurisdiction of the sender; or (d) if given by fax, upon receipt +thereof by the recipient's fax machine or as stated in the sender's transmission confirmation report as produced electronically by sender's fax machine. + + 8.3 Assignment, Waiver, Modification. Customer may not assign, transfer, delegate or sublicense any of Customer's rights or obligations hereunder (including without limitation by operation of law or by sale of Customer assets, whether directly or by merger, and a change in control of Customer shall be deemed to be an "assignment" for purposes of the foregoing) without PTC's prior written consent, and any such attempted delegation, assignment, transfer or sublicense shall be void and a breach of this Agreement. No waiver, consent, modification, amendment or change of the terms of this Agreement shall be binding unless in writing and signed by PTC and Customer. PTC reserves the right to charge a transfer fee for any proposed assignment, transfer or sublicense of this Agreement. + + 8.4 Compliance with Laws. Each party shall be responsible for its own compliance with applicable laws, regulations and other legal requirements relating to the conduct of its business and this Agreement. Further Customer represents and warrants that it will use the Licensed Products, as well as related technology and services, in full compliance with applicable laws and regulations. Customer acknowledges and agrees that the Licensed Products and related technical data and services are subject to the export control laws and regulations of the United States and any country in which the Licensed Products or related technical data or services are developed, received, downloaded, used, or performed. Further, Customer understands and acknowledges that the release of software or technology to a non-U.S. person within the United States or elsewhere abroad is deemed to be an export to the non-U.S. person's home country or countries, and that the transfer of the Licensed Products or related technology to Customer's employees, affiliates, or any third party, may require a license from the United States Government and possibly other applicable authorities. Customer shall be solely responsible for determining whether Customer's use or transfer of the Licensed Products or related technology or services requires an export license or approval from U.S. or other authorities, and for securing all required authorizations. Customer hereby warrants and represents that: (x) neither Customer nor any of Customer's directors, officers or affiliates is identified on the U.S. Commerce Department's Denied Persons List, Entity List, or Unverified List, the U.S. State Department's Nonproliferation Sanctions List, the U.S. Treasury Department's List of Specially Designated Nationals and Blocked Persons or any similar Export Controls Division-Foreign Affairs and International Trade Canada listing that designates individuals or entities to which export restrictions apply (collectively, the "Restricted Parties Lists"), (y) except as specifically authorized or licensed by the United States Government and other applicable authorities, Customer will not sell, offer, transfer, deliver, release, either directly or indirectly, the Licensed Products or related technology or services to any end-user: (A) that is either located in, a national of, or acting on behalf of a country subject to U.S. economic embargoes, or (B) that have been designated as prohibited or restricted parties by the U.S. Government, including but not limited to persons listed on the Restricted Parties Lists, or (C) engaged in activities related to the design, development, stockpiling, or proliferation of nuclear, chemical, or biological weapons, or missiles or missile systems, or (D) engaged in maritime nuclear propulsion activities. Customer represents and warrants that it will ensure that any person or entity to which Customer has granted access to the Licensed Products or related technology or services has been made aware of, and will comply with, this provision and U.S. and other applicable export control laws and regulations. Unless prohibited by applicable law and without waiving sovereign immunity, Customer shall indemnify and hold harmless PTC and its employees against any damage, loss, liability or expense (including attorneys' fees) that PTC may incur as a result of Customer's failure to comply with this Section + + 8.4. Such indemnification shall survive the expiration or termination of this Agreement. + + 8.5 Severability. It is intended that this Agreement shall not violate any applicable law and the unenforceability or invalidity of any provision (other than the provisions obligating Customer to make payments to PTC) shall not affect the force and validity of the remaining provisions and such provisions determined to be invalid shall be deemed severed from this Agreement and, to the extent possible, be replaced with terms which as closely as possible approximate the interest and economic intent of such invalid provisions. + + 8.6 Entire Agreement. This Agreement is the complete and exclusive statement of the contract between PTC and Customer with respect to the subject matter hereof. No waiver, consent, modification, amendment or change of this Agreement shall be binding unless in writing and signed or otherwise expressly acknowledged by PTC and Customer. + + 8.7 Third Party Beneficiaries. It is agreed by the parties to this Agreement that PTC's third party licensors are intended beneficiaries of this Agreement and have the right to rely upon and directly enforce its terms with respect to the products of such licensors. + + 8.8 Marketing. Customer agrees that while this Agreement is in effect, PTC shall be authorized to identify Customer as a customer/end-user of PTC software and services (as applicable) in public relations and marketing materials. + + 8.9 Government Licensees. If Customer is a United States Governmental entity, Customer agrees that the Licensed Products are "commercial computer software" under the applicable federal acquisition regulations and are provided with the commercial license rights and restrictions described elsewhere herein. If Customer is acquiring the Licensed Product(s) under a United States government contract, Customer agrees that Customer will include all necessary and applicable restricted rights legends on the Licensed Products to protect PTC's proprietary rights under the FAR or other similar regulations of other federal agencies. Customer agrees to always include such legends whenever the Licensed Products are, or are deemed to be, a deliverable under a government contract. + + +Schedule A - Purchases from PTC Affiliates + +If the Customer has obtained a License to any Licensed Products in one of the following countries, the entity granting the License is specified below and, notwithstanding Section 8.1 of this Agreement, the governing law and jurisdiction shall be as set forth below. + +Country PTC Affiliate Licensing Entity Governing Law/Jurisdiction for + Disputes +Belgium, Netherlands, Parametric Technology Nederland B.V. Netherlands +Luxembourg +Austria, Germany Parametric Technology GmbH German Law*, Landgericht Munchen I, +Germany +France Parametric Technology S.A. France +Ireland PTC Software and Services (Ireland) +Limited Republic of Ireland +Italy Parametric Technology Italia S.r.L. Italy +Spain, Portugal Parametric Technology Espana, S.A. Spain +Switzerland Parametric Technology (Schweiz) AG German Law*, Landgericht Munchen I, +Germany +United Kingdom Parametric Technology (UK) Limited United Kingdom +Remaining countries of the PTC Software and Services (Ireland) +Limited Republic of Ireland +European Union +Turkey, Kosovo, Serbia, PTC Software and Services (Ireland) +Limited Republic of Ireland +Macedonia, Montenegro, Croatia, Bosnia and Herzegovina, and +Albania +The Russian Federation PTC International LLC Russian Law / International +Commercial Arbitration Court at the +Chamber of Commerce and Industry of the Russian Federation in Moscow + +Belarus Moldova, Ukraine, PTC Software and Services (Ireland) +Limited Republic of Ireland +Armenia, Georgia, Azerbaijan, +Kazakhstan, Kyrgyz stan, +Tajikistan, Turkmenistan, and +Uzbekistan +Norway, Sweden, and Denmark, PTC Sweden AB Sweden +Finland, Iceland, and the Faeroe +Islands +Japan PTC Japan K.K. Japan / Tokyo District Court + + +Country PTC Affiliate Licensing Entity Governing Law/Jurisdiction for + Disputes +China Parametric Technology (Shanghai) The People's Republic of China/China +International Economic and Trade +Arbitration Commission in Shanghai + Software Co., Ltd. +Taiwan Parametric Technology Taiwan Limited Taiwan / Courts of Taipei, Taiwan +India Parametric Technology (India) Private +Limited India +Korea Parametric Technology Korea Ltd. Republic of Korea +Other Asia Pacific Countries PTC Inc. Special Administrative Region of Hong +Kong / Hong Kong International +Arbitration Centre +including Australia and New +Zealand, but excluding China, +Japan and Taiwan) +Canada PTC (Canada) Inc. Ontario +Any other country PTC Inc., or such other affiliate of PTC as +PTC directs at the time of the order Commonwealth of Massachu setts, + United States + +* Specific Provisions for Austria, Germany and Switzerland: + +For Licensed Products licensed and used in Austria, Germany or Switzerland, the following provisions shall apply. The following provisions shall have no applicability to any Licensed Products or Services purchased outside of Austria, Germany or Switzerland. References to sections below are references to the applicable sections in the body of the Agreement. + +* Section 1.4 (iv) above shall not apply to the extent that (i) the processes Customer undertakes are required to achieve information necessary to achieve interoperability of an independently created computer program with other software programs, (ii) the further requirements of Section 69e of the German Copyright Act are fulfilled and (iii) PTC, upon Customer's written request, has not made available the information required for this within a reasonable period. + +* Sections 4.2 (Warranty), 4.4 (Sole Remedy), 4.5 (No Additional Warranties) and 4.6 (Disclaimer of Warranties) are hereby replaced by the following provisions: + +4.2 Warranty Period, Restarts and Investigation Duty. The limitation period for warranty claims shall be twelve (12) months from delivery. Any replacement of the Licensed Product(s) and/or repair of Errors will not restart the warranty period. The pre-requisite for the Customer's warranty claims (Mangelanspruche) is that: (i) the Customer inspects the Licensed Products according to Section 377 German Commercial Code, (ii) the defect is an Error as defined in this Agreement, (iii) the Error already existed at the time of delivery and (iv) the Customer effects a proper notification of the Error. Customer shall provide notifications of Errors to PTC in writing and Customer shall provide specific details of the Error as deemed reasonable under the specific circumstances. Customer shall notify PTC of obvious Errors in writing within one week of delivery and of latent Errors within one week of discovery of such Error. The periods specified are preclusion periods. + +4.4 Remedies. In the event of an Error, PTC in its sole discretion may: (a) replace the Licensed Product(s) or (b) repair the Error, provided that notice of the Error is received by PTC within the periods set forth in Section 4.2 and Customer provides such additional information regarding the Error as PTC may reasonably request. If the repair (either by providing a bug fix, a workaround or otherwise) or replacement is not successful (after at least two repair attempts for the same Error by PTC within a reasonable period of time), Customer shall be entitled, at Customer's choice, to either: (i) rescission of the affected order so that PTC provides a refund of the license fees paid by Customer for the applicable Licensed Product(s) upon return of such Licensed Product(s) and any copies made thereof or (ii) a reasonable reduction in the purchase price. Replacements or repairs shall be made without acknowledgement of a legal obligation and shall not suspend the limitation period for warranty claims related to the Licensed Products. + +4.5 No Additional Warranties. No employee, partner, distributor (including any Reseller) or agent of PTC or any of its resellers or sales agents is authorized to give representations, warranties or covenants greater or different than those contained in this Agreement, except as specifically set forth in a written agreement signed on behalf of Customer by an authorized officer and on behalf of PTC by its legal counsel or Corporate Controller. Apart from claims for damages based on Errors that are subject to the limitation of liability as set forth in Section 6, the obligations provided for in this Section 4 shall be PTC's exclusive liability in case of warranty claims. + +4.6 Customer Responsibility. The Licensed Products are intended to be used by trained professionals and are not a substitute for the exercise by Customer of professional judgement, testing, safety and utility in their use. Customer is solely responsible for any results which were obtained by using the Licensed Products, including the adequacy of independent testing of reliability and accuracy of any item designed using Licensed Products. + +4.7 Qualities (Beschaffenheit), Guarantees. Qualities of the Licensed Products stated in publications of PTC or its sales representatives, in particular in advertising, in drawings, brochures or other documents, including presentations in the Internet, or on packaging and labeling of the Licensed Products, or which fall under trade usages, shall only be deemed to be covered by the contractual quality of the Licensed Products if such qualities are expressly contained in an offer or an order confirmation in writing. Guarantees, in particular guarantees as to quality, shall be binding on PTC only to the extent to which they (i) are contained in an offer or an order confirmation in writing, (ii) are expressly designated as "guarantee" or "guarantee as to condition" (Beschaffenheitsgarantie), and (iii) expressly stipulate the obligations for PTC resulting from such guarantee. + +* Section 6 is hereby replaced by the following provisions: + +6.Limitation of Liability + +6.1 Liability Categories. PTC shall be liable for damages, regardless of the legal grounds, only if: (i) PTC breaches a material contractual obligation (cardinal obligation) culpably (i.e., at least negligently), or (ii) the damage has been caused by gross negligence or wilfull intent on the part of PTC or (iii) PTC has assumed a guarantee. + +6.2 Predictability. PTC's liability shall be limited to the typical, foreseeable damage: (i) if PTC breaches material contractual obligations (cardinal obligations) with slight negligence, or (ii) if employees or agents of PTC who are not officers or executive staff have breached other obligations by gross negligence, or (iii) if PTC has assumed a guarantee, unless such guarantee is expressly designated as guarantee as to condition (Beschaffenheitsgarantie). + +6.3 Maximum Amount. In the cases of Section 6.2 (i) and (ii), PTC's liability shall be limited to a maximum amount of +EURO 1,000,000 or, in case of purely financial losses, to a maximum amount of EURO 100,000. + +6.4 Indirect Damages. In the cases of Section 6.2, PTC shall not be liable for indirect damages, consequential damages or loss of profit. + +6.5 Liability Period. Customer's claims for damages against PTC and/or PTC's affiliates, regardless of the legal grounds, shall expire at the latest one year from the time the Customer gains knowledge of the damage or, irrespective of this knowledge, at the latest two years after the damaging event. For claims based on Errors of the Licensed Product(s), the warranty limitation period pursuant to Section 4.2 shall apply. + +6.6 Mandatory Liability. PTC's liability pursuant to the German Product Liability Act (Produkthaftungsgesetz), for injury of life, body and health, for fraudulent concealment of a defect or for the assumption of a guarantee as to condition (Beschaffenheitsgarantie) remains unaffected. + +6.7 Employees. Sections 6.1 to 6.6 shall also apply in the case of any claims for damages of Customer against employees +or agents of PTC and/or PTC's affiliates. + +6.8 Contributory Negligence. In the event of a guarantee or liability claim against PTC any contributory fault of Customer must be taken into account accordingly, particularly in the event of inadequate fault notification or inadequate data securing. It constitutes inadequate data securing if the client, among others, does not, by way of appropriate state of the art security measures, take precautions against external influences, e.g. computer viruses and other phenomena which could put individual data or an entire data stock at risk. + +Schedule B - Definitions + +"Concurrent User Products" means the Licensed Products licensed on a concurrent user basis, as specified either in the Quote or at +the Licensing Basis Webpage. + +"Designated Computer" means the central processing unit(s) designated in writing by Customer to PTC at the time of installation of the Licensed Products (as may be modified in accordance with Section 1.2 of this Agreement). + +"Designated Computer Product" means the Licensed Products licensed on a "Designated Computer" basis or otherwise designated as "fixed," "locked" or "node-locked", as specified either in the Quote or at the Licensing Basis Webpage. Designated Computer Products may not be remotely accessed or installed in a virtual environment. + +"Designated Country" means the country of installation specified in writing by Customer to PTC at the time Customer places its +order of the Licensed Products. The Designated Country may be changed only in accordance with Section 1.2 of this Agreement. + +"Designated Network" means the network designated in writing by Customer to PTC at the time of installation of the Licensed +Products (as may be modified in accordance with Section 1.2 of this Agreement). + +"Designated Server" means a computer server designated in writing by Customer to PTC at the time of installation of the Licensed Products (as may be modified in accordance with Section 1.2 of this Agreement) that has one unique instance of the applicable installed Licensed Product application. + +"Designated Server Products" means the Licensed Products licensed on a Designated Server basis, as specified either in the Quote or +at the Licensing Basis Webpage. + +"Documentation" means the applicable Licensed Software user manuals provided or made available by electronic means by PTC at the time of shipment of the Licensed Software. + +"Educational Software" means Licensed Products identified as "Priced for Education," "Student Edition," "Schools Edition," "Schools Advanced Edition," "University Edition," "Professor's Edition/Version" or "Academic Edition/Version," or otherwise designated as educational or academic licenses. + +"Error" means a failure of the Licensed Software to conform substantially to the applicable Documentation, provided that Customer informs PTC of such failure in writing and PTC is able to replicate such failure after making reasonable efforts. + +"External User" means a Registered User who is a vendor or other third party external to the Customer and its affiliates. "License" shall have the meaning set out in Section 1.1 of the body of the Agreement. +"License Term" means the time period during which the License for the applicable Licensed Products shall be in effect, as specified in the name of the Licensed Product or in the applicable Quote (subject to earlier termination pursuant to the terms hereof) or, if no Quote was provided to Customer, as otherwise communicated by PTC to Customer. In the absence of a stated license term, the License Term shall be perpetual, except that the License Term for evaluation Licenses shall be no longer than thirty days from the date of Customer's request for an evaluation license, unless otherwise specifically designated by PTC, and the evaluation License will cease to be operational after such term expires. The License Term of a "subscription" License is as specified in the Quote and/or the invoice, and such License includes Support Services during such License Term at no additional fee. + +"License Locked Product" means a Licensed Product licensed for use with another PTC product to which the License Locked Product is an extension. The License Locked Product will assume the licensing basis of such other product.. License Locked Products are specified either in the Quote or at the Licensing Basis Webpage. + +"Licensed Products" means collectively the Licensed Software and the Documentation. + +"Licensed Software" means, collectively, the computer software product identified in the applicable Quote, as well as (i) any software product that is provided to operate with such computer software product (e.g., modules, software bundled with this software product, etc.), but excluding any software that is a consulting services deliverable, (ii) any Error corrections pursuant to Section 4.4 hereof, (iii) any updates, Error corrections and/or New Releases provided to Customer by PTC pursuant to Support Services purchased by Customer and (iv) any computer software provided to Customer in the course of PTC's delivery of Training Services. + +"Licensing Basis Webpage" means the "Licensing Basis" document at http://www.ptc.com/support/customer_agreements/ +index.htm, which specifies the licensing basis of PTC's different products and states certain additional product-specific terms and conditions. + +"Support Services" means the provision of New Releases and, depending on the level of Support Services ordered, may also include telephone support, web-based support tools, and correction of Errors, all in accordance with Schedule C attached to this Agreement. + +"New Release" means a modified or enhanced version of a Licensed Product that is designated by PTC as a new release of that +product and that PTC makes generally available to its Support Services customers. + +"Permitted User" means an individual who is authorized by Customer to use the Licensed Products, such use to be solely in accordance with the terms and conditions of the Agreement. Permitted Users are limited to Customer's employees, consultants, subcontractors, suppliers, business partners and customers who (i) are not competitors of PTC or employed by competitors of PTC and (ii) are directly involved in the utilization of the Licensed Products solely in support of Customer's internal business purposes. Customer shall at all times be responsible for its Permitted Users' compliance with this Agreement. + +"Per Instance Product" means a Licensed Product for which one License is required for each instance of a system to which the applicable Licensed Product connects. For example, if an adapter that is licensed on a Per Instance basis enables Windchill to connect to an ERP system and a CRM system, two licenses of such adapter will be required. The Licensed Products that are Per Instance Products are identified either in the Quote or at the Licensing Basis Webpage. + +"Quote" means the PTC product schedule, quote or order confirmation provided to Customer in connection with the purchase of the applicable Licensed Product or, if no such document is provided, Customer's purchase order for such Licensed Product, if any. + +"Registered User" means a Permitted User for whom Customer has purchased a License to use a Registered User Product and for +whom Customer has issued a password or other unique identifier to enable such individual to use the Registered User Product. + +"Registered User Products" means the Licensed Products licensed on a Registered User basis, as specified either in the Quote or at +the Licensing Basis Webpage. + +"Reseller" means a third-party appointed and authorized by PTC to resell or distribute any Licensed Product. . + +"Services" means collectively Support Services and Training Services. + +"Site License" means a Licensed Product for which one License is required for each Customer location, as specified either in the Quote or at the Licensing Basis Webpage. Multiple customer facilities located in the same city or town (based on postal address) shall be considered one "location," whereas locations located in different cities or towns will require multiple Site Licenses. + +"Training Services" means instruction or other training provided by PTC in the use of the Licensed Products. "Training Services" does not include PTC's e-Learning training products (e.g., "PTCU"), which are considered Licensed Products for purposes of this Agreement. + +"Uplift Fee" means a fee based upon the difference between the License fee applicable to installation of the applicable Licensed Product in the original Designated Country and the License fee applicable to the installation of such Licensed Product in the Designated Country to which Customer wishes to move the Licensed Product. + +"Usage License Fee" means an ongoing fee that commences upon installation of the applicable Licensed Product and that, during the period for which the Usage License Fee is paid, entitles Customer to (i) continued use of the Licensed Product in accordance with the terms of the License and (ii) telephone support, Error corrections or workarounds, and New Releases for such software. + + +Schedule C - PTC Support Services Terms and Conditions +The following additional terms and conditions apply to the provision of Support Services by PTC: + +Support Services Plan; Levels of Support Services. Upon PTC's acceptance of Customer's order for Support Services in respect of the Licensed Products, PTC and/or its authorized subcontractors shall provide Support Services in accordance with these terms for a time period of twelve (12) months or for such other period specified in Customer's order accepted by PTC (a "Support Services Plan"). All Support Services are provided subject to Customer's payment for such services at PTC's then-current rates, provided that for Licensed Product licensed on a subscription basis, such License includes Support Services during such License Term at no additional fee. If Customer does not order Support Services to commence on shipment of the Licensed Product(s), or if Customer at any time discontinues Support Services, and in either case subsequently wishes to obtain Support Services, Customer must pay (i) the then current fees for Support Services and (ii) the fees for Support Services for any period for which Customer has not purchased Support Services. The then current levels of Support Services offered and the corresponding services provided thereunder are described on http://www.ptc.com at + +http://www.ptc.com/support/maintenance/maintenance_support_policies.htm + +A Support Services Plan may not be cancelled by Customer following PTC's acceptance of an order for such Support Services Plan. With respect to Registered User Products, e-Learning products and Integrity Concurrent User and Server Licensed Products, Support Services ordered by Customer must cover all Licenses granted to Customer for such Licensed Products. PTC is obligated to provide Support Services only during periods for which Customer has paid the applicable Support Services fees and only in accordance with the level of Support Services Customer has purchased. The services offered under any Support Services Plan may change from time to time, and PTC may cease to offer Support Services Plans at any time without notice, subject only to the obligation to refund to Customer the unused portion of any previously paid applicable Support Services fee (on a prorated basis). + +(a) Telephone Support. If Customer purchases Support Services at a level that includes telephone support, Customer may utilize PTC's telephone support service to report problems and seek assistance in use of the Licensed Products. The hours during which PTC will provide telephone support will vary depending upon the level of Support Services ordered by Customer. For all levels of Support Services that include telephone support, PTC will provide telephone support in the languages, and during normal business hours for the countries, listed on PTC's website at the website URL listed above. For levels of Support Services that include telephone support during non-business hours, PTC will provide such support in the English language only. Regardless of the total number of the Licensed Products licensed by Customer, Customer is entitled to telephone support only in direct connection with Licenses that are covered by a Support Services Plan at a level that includes telephone support. + +(b) Repair of Errors. If Customer's Support Services Plan includes repair or workaround of Errors, PTC shall use diligent efforts to repair Errors or provide workarounds as required in such Support Services Plan, provided notice of the Error is received by PTC during the term of a Support Services Plan and Customer supplies such additional information regarding the Error as PTC may reasonably request. + +(C) New Releases. PTC will provide Customer with one copy of each New Release for each Licensed Product for which Customer is entitled to Support Services at the time the applicable language version of the New Release is made generally available. Subject to different terms for particular products set forth at http://www.ptc.com/support/maintenance/maintenance_support_policies.htm, following shipment of the New Release, the previous release shall remain "current" for purposes of this Agreement for a period of ninety (90) days; thereafter only such New Release will be current. + +(d) Exclusions. + +(1) PTC is not obligated to perform investigation and/or repair of Errors (i) found by PTC to be in other than a current (as described above), unaltered release of the Licensed Products; (ii) caused by changes to the Customer's operating systems, environment, databases or other system components which adversely affect the Licensed Products; (iii) caused by Customer's modification of the Licensed Product or use thereof in combination or interconnection with software not provided by PTC; (iv) use of the Licensed Product on a computer, operating system, software or peripherals other than a computer, operating system, software or peripherals for which such Licensed Product was designed for and licensed for use on; (v) caused by improper or unauthorized use of the Licensed Products; (vi) due to external causes such as, but not limited to, power failures or electric power surges; or (vii) due to a failure by the Customer to implement recommendations in respect of solutions to Errors previously provided by PTC to Customer. + +(2) PTC shall only be responsible for responding to problems reported by one of the two (2) technical contacts for Customer's main location (which technical contacts and main location have previously been identified in writing to PTC by Customer), and for sending New Releases to the "Central Support Location" designated by Customer in writing. Customer is responsible for the distribution of New Releases to any of Customer's additional locations where Licensed Products are authorized to be used. Customer is responsible for providing to PTC in writing the name, address, phone number, fax number, and e-mail address for each of Customer's designated contacts and Customer's Central Support Location. + +(3) PTC is not obligated to perform any Support Services with respect to modifications or customizations of the Licensed Products, nor with respect to any developments resulting from Customer's use, development or customization of functionality contained within the Licensed Products, all of which are Customer's sole responsibility. + + +END OF (4) Ion GeneStudio(TM) S5 V5.18 END USER LICENSE AGREEMENT +**************************************************** + diff --git a/TSVersion b/TSVersion index 0e4f8068..fd182799 100644 --- a/TSVersion +++ b/TSVersion @@ -1,4 +1,4 @@ # Version for target of current development cycle TS_MAJOR=5 -TS_MINOR=16 -TS_RELEASE=0 +TS_MINOR=18 +TS_RELEASE=1 diff --git a/buildTools/LICENSE.txt.in b/buildTools/LICENSE.txt.in index 35147afd..578b2923 100644 --- a/buildTools/LICENSE.txt.in +++ b/buildTools/LICENSE.txt.in @@ -1,18 +1,13 @@ -@CMAKE_PROJECT_NAME@ -- @PROJECT_DESCRIPTION@ +This end-user license agreement contains 4 separate and distinct licenses: (1) Torrent Suite™ Software Version 5.18 Open Source License (pgs. 1-32), (2) Service & Support Telemetry Module Software Version 2.0.1 End User License Agreement (pgs. 32 - 47), (3) Ion Chef™ Instrument Software Version 5.18 License Agreement (pgs. 47 - 182), and (4) Ion GeneStudio™ S5 V5.18 License Agreement (pgs. 182 - 236). -This document contains 2 separate and distinct licenses: (1) Torrent Suite(tm) Software Version 5.16 Open Source License -and (2) Service & Support Telemetry Module Software Version 2.0.1 End User License Agreement. - -(1) Torrent Suite(tm) Software Version 5.16 -======================================== - -Torrent Suite(tm) Software v5.16: This software provides for the analysis and storage of data received from -the Ion GeneStudio S5 Sequencer or the Ion GeneStudio S5 XL Sequencer, the Ion GeneStudio S5 Prime -or the Ion GeneStudio S5 Plus. +(1) Torrent Suite™ Software Version 5.18 +===================================================================== +Torrent Suite™ Software v5.18: This software provides for the analysis and storage of data received from the Ion Personal Genome Machine™ (PGM™) Sequencer, the Ion Proton™ Sequencer, the Ion S5TM Sequencer, the Ion S5TM XL Sequencer, or the Ion GeneStudio™ S5 Prime. +The Ion Chef™ System provides automated, high-throughput template preparation and chip loading for use with an Ion Personal Genome Machine™ PGMTM Sequencer, Ion Proton™ Sequencer, Ion S5™ Sequencer, Ion S5™ XL Sequencer, or the Ion GeneStudio™ S5 Prime. -January 27, 2021 +May 26th, 2022 -Copyright (C) 2011 - 2021 Life Technologies Corporation +Copyright © 2011 - 2022 Life Technologies Corporation All Rights Reserved. This program is free software; you can redistribute it and/or modify it @@ -29,17 +24,12 @@ with this program (see Section 2 below); if not, write to the Free Software Foun 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. You can also find the GPL version 2 on the GNU web site: https://www.gnu.org/licenses/gpl-2.0.html - -1. Third Party Software Notices and Licenses ===================================================================== - -This software uses third party software components from several sources. Portions of these software components are -copyrighted and licensed by their respective owners as indicated below. Various licenses require distribution of -source code or if a link is used to point the end-user to a source-code repository, and the source code is not -available at such site, the distributor must, for a time determined by license, offer to provide source code. -In such cases, please contact your Life Technologies representative. As well, various licenses require that the -end-user receive a copy of the license or certain notices. Such licenses and notices may be found below. -In order to use this software, the end-user must abide by the terms and conditions of these third party licenses. + 1. Third Party Software Notices and Licenses +===================================================================== + +This software uses third party software components from several sources. Portions of these software components are copyrighted and licensed by their respective owners as indicated below. Various licenses require distribution of source code or if a link is used to point the end-user to a source-code repository, and the source code is not available at such site, the distributor must, for a time determined by license, offer to provide source code. In such cases, please contact your Life Technologies representative. As well, various licenses require that the end-user receive a copy of the license or certain notices. Such licenses and notices may be found below. In order to use this software, the end-user must abide by the terms and conditions of these third party licenses. + Armadillo ------------------------------------------------------------- @@ -49,622 +39,238 @@ Apache License Version 2.0, January 2004 http://www.apache.org/licenses/ -TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION - -1. Definitions. - - "License" shall mean the terms and conditions for use, reproduction, - and distribution as defined by Sections 1 through 9 of this document. - - "Licensor" shall mean the copyright owner or entity authorized by - the copyright owner that is granting the License. - - "Legal Entity" shall mean the union of the acting entity and all - other entities that control, are controlled by, or are under common - control with that entity. For the purposes of this definition, - "control" means (i) the power, direct or indirect, to cause the - direction or management of such entity, whether by contract or - otherwise, or (ii) ownership of fifty percent (50%) or more of the - outstanding shares, or (iii) beneficial ownership of such entity. - - "You" (or "Your") shall mean an individual or Legal Entity - exercising permissions granted by this License. - - "Source" form shall mean the preferred form for making modifications, - including but not limited to software source code, documentation - source, and configuration files. - - "Object" form shall mean any form resulting from mechanical - transformation or translation of a Source form, including but - not limited to compiled object code, generated documentation, - and conversions to other media types. - - "Work" shall mean the work of authorship, whether in Source or - Object form, made available under the License, as indicated by a - copyright notice that is included in or attached to the work - (an example is provided in the Appendix below). - - "Derivative Works" shall mean any work, whether in Source or Object - form, that is based on (or derived from) the Work and for which the - editorial revisions, annotations, elaborations, or other modifications - represent, as a whole, an original work of authorship. For the purposes - of this License, Derivative Works shall not include works that remain - separable from, or merely link (or bind by name) to the interfaces of, - the Work and Derivative Works thereof. - - "Contribution" shall mean any work of authorship, including - the original version of the Work and any modifications or additions - to that Work or Derivative Works thereof, that is intentionally - submitted to Licensor for inclusion in the Work by the copyright owner - or by an individual or Legal Entity authorized to submit on behalf of - the copyright owner. For the purposes of this definition, "submitted" - means any form of electronic, verbal, or written communication sent - to the Licensor or its representatives, including but not limited to - communication on electronic mailing lists, source code control systems, - and issue tracking systems that are managed by, or on behalf of, the - Licensor for the purpose of discussing and improving the Work, but - excluding communication that is conspicuously marked or otherwise - designated in writing by the copyright owner as "Not a Contribution." - - "Contributor" shall mean Licensor and any individual or Legal Entity - on behalf of whom a Contribution has been received by Licensor and - subsequently incorporated within the Work. - -2. Grant of Copyright License. Subject to the terms and conditions of - this License, each Contributor hereby grants to You a perpetual, - worldwide, non-exclusive, no-charge, royalty-free, irrevocable - copyright license to reproduce, prepare Derivative Works of, - publicly display, publicly perform, sublicense, and distribute the - Work and such Derivative Works in Source or Object form. - -3. Grant of Patent License. Subject to the terms and conditions of - this License, each Contributor hereby grants to You a perpetual, - worldwide, non-exclusive, no-charge, royalty-free, irrevocable - (except as stated in this section) patent license to make, have made, - use, offer to sell, sell, import, and otherwise transfer the Work, - where such license applies only to those patent claims licensable - by such Contributor that are necessarily infringed by their - Contribution(s) alone or by combination of their Contribution(s) - with the Work to which such Contribution(s) was submitted. If You - institute patent litigation against any entity (including a - cross-claim or counterclaim in a lawsuit) alleging that the Work - or a Contribution incorporated within the Work constitutes direct - or contributory patent infringement, then any patent licenses - granted to You under this License for that Work shall terminate - as of the date such litigation is filed. - -4. Redistribution. You may reproduce and distribute copies of the - Work or Derivative Works thereof in any medium, with or without - modifications, and in Source or Object form, provided that You - meet the following conditions: - - (a) You must give any other recipients of the Work or - Derivative Works a copy of this License; and - - (b) You must cause any modified files to carry prominent notices - stating that You changed the files; and - - (c) You must retain, in the Source form of any Derivative Works - that You distribute, all copyright, patent, trademark, and - attribution notices from the Source form of the Work, - excluding those notices that do not pertain to any part of - the Derivative Works; and - - (d) If the Work includes a "NOTICE" text file as part of its - distribution, then any Derivative Works that You distribute must - include a readable copy of the attribution notices contained - within such NOTICE file, excluding those notices that do not - pertain to any part of the Derivative Works, in at least one - of the following places: within a NOTICE text file distributed - as part of the Derivative Works; within the Source form or - documentation, if provided along with the Derivative Works; or, - within a display generated by the Derivative Works, if and - wherever such third-party notices normally appear. The contents - of the NOTICE file are for informational purposes only and - do not modify the License. You may add Your own attribution - notices within Derivative Works that You distribute, alongside - or as an addendum to the NOTICE text from the Work, provided - that such additional attribution notices cannot be construed - as modifying the License. - - You may add Your own copyright statement to Your modifications and - may provide additional or different license terms and conditions - for use, reproduction, or distribution of Your modifications, or - for any such Derivative Works as a whole, provided Your use, - reproduction, and distribution of the Work otherwise complies with - the conditions stated in this License. - -5. Submission of Contributions. Unless You explicitly state otherwise, - any Contribution intentionally submitted for inclusion in the Work - by You to the Licensor shall be under the terms and conditions of - this License, without any additional terms or conditions. - Notwithstanding the above, nothing herein shall supersede or modify - the terms of any separate license agreement you may have executed - with Licensor regarding such Contributions. - -6. Trademarks. This License does not grant permission to use the trade - names, trademarks, service marks, or product names of the Licensor, - except as required for reasonable and customary use in describing the - origin of the Work and reproducing the content of the NOTICE file. - -7. Disclaimer of Warranty. Unless required by applicable law or - agreed to in writing, Licensor provides the Work (and each - Contributor provides its Contributions) on an "AS IS" BASIS, - WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or - implied, including, without limitation, any warranties or conditions - of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A - PARTICULAR PURPOSE. You are solely responsible for determining the - appropriateness of using or redistributing the Work and assume any - risks associated with Your exercise of permissions under this License. - -8. Limitation of Liability. In no event and under no legal theory, - whether in tort (including negligence), contract, or otherwise, - unless required by applicable law (such as deliberate and grossly - negligent acts) or agreed to in writing, shall any Contributor be - liable to You for damages, including any direct, indirect, special, - incidental, or consequential damages of any character arising as a - result of this License or out of the use or inability to use the - Work (including but not limited to damages for loss of goodwill, - work stoppage, computer failure or malfunction, or any and all - other commercial damages or losses), even if such Contributor - has been advised of the possibility of such damages. - -9. Accepting Warranty or Additional Liability. While redistributing - the Work or Derivative Works thereof, You may choose to offer, - and charge a fee for, acceptance of support, warranty, indemnity, - or other liability obligations and/or rights consistent with this - License. However, in accepting such obligations, You may act only - on Your own behalf and on Your sole responsibility, not on behalf - of any other Contributor, and only if You agree to indemnify, - defend, and hold each Contributor harmless for any liability - incurred by, or claims asserted against, such Contributor by reason - of your accepting any such warranty or additional liability. - - -END OF TERMS AND CONDITIONS - -APPENDIX: How to apply the Apache License to your work. - -To apply the Apache License to your work, attach the following -boilerplate notice, with the fields enclosed by brackets "[]" -replaced with your own identifying information. (Don't include -the brackets!) The text should be enclosed in the appropriate -comment syntax for the file format. We also recommend that a -file or class name and description of purpose be included on the -same "printed page" as the copyright notice for easier -identification within third-party archives. - -Copyright [yyyy] [name of copyright owner] - -Licensed under the Apache License, Version 2.0 (the "License"); -you may not use this file except in compliance with the License. -You may obtain a copy of the License at - -http://www.apache.org/licenses/LICENSE-2.0 - -Unless required by applicable law or agreed to in writing, software -distributed under the License is distributed on an "AS IS" BASIS, -WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -See the License for the specific language governing permissions and -limitations under the License. - - -Mozilla Public License Version 2.0 -------------------------------------------------------------- - -1. Definitions -------------------------------------------------------------- - -1.1. "Contributor" - means each individual or legal entity that creates, contributes to - the creation of, or owns Covered Software. -1.2. "Contributor Version" - means the combination of the Contributions of others (if any) used - by a Contributor and that particular Contributor's Contribution. - -1.3. "Contribution" - means Covered Software of a particular Contributor. - -1.4. "Covered Software" - means Source Code Form to which the initial Contributor has attached - the notice in Exhibit A, the Executable Form of such Source Code - Form, and Modifications of such Source Code Form, in each case - including portions thereof. - -1.5. "Incompatible With Secondary Licenses" - means - - (a) that the initial Contributor has attached the notice described - in Exhibit B to the Covered Software; or - - (b) that the Covered Software was made available under the terms of - version 1.1 or earlier of the License, but not also under the - terms of a Secondary License. - -1.6. "Executable Form" - means any form of the work other than Source Code Form. - -1.7. "Larger Work" - means a work that combines Covered Software with other material, in - a separate file or files, that is not Covered Software. - -1.8. "License" - means this document. - -1.9. "Licensable" - means having the right to grant, to the maximum extent possible, - whether at the time of the initial grant or subsequently, any and - all of the rights conveyed by this License. - -1.10. "Modifications" - means any of the following: - - (a) any file in Source Code Form that results from an addition to, - deletion from, or modification of the contents of Covered - Software; or - - (b) any new file in Source Code Form that contains any Covered - Software. - -1.11. "Patent Claims" of a Contributor - means any patent claim(s), including without limitation, method, - process, and apparatus claims, in any patent Licensable by such - Contributor that would be infringed, but for the grant of the - License, by the making, using, selling, offering for sale, having - made, import, or transfer of either its Contributions or its - Contributor Version. - -1.12. "Secondary License" - means either the GNU General Public License, Version 2.0, the GNU - Lesser General Public License, Version 2.1, the GNU Affero General - Public License, Version 3.0, or any later versions of those - licenses. - -1.13. "Source Code Form" - means the form of the work preferred for making modifications. - -1.14. "You" (or "Your") - means an individual or a legal entity exercising rights under this - License. For legal entities, "You" includes any entity that - controls, is controlled by, or is under common control with You. For - purposes of this definition, "control" means (a) the power, direct - or indirect, to cause the direction or management of such entity, - whether by contract or otherwise, or (b) ownership of more than - fifty percent (50%) of the outstanding shares or beneficial - ownership of such entity. - -2. License Grants and Conditions -------------------------------------------------------------- - -2.1. Grants - -Each Contributor hereby grants You a world-wide, royalty-free, -non-exclusive license: - -(a) under intellectual property rights (other than patent or trademark) - Licensable by such Contributor to use, reproduce, make available, - modify, display, perform, distribute, and otherwise exploit its - Contributions, either on an unmodified basis, with Modifications, or - as part of a Larger Work; and - -(b) under Patent Claims of such Contributor to make, use, sell, offer - for sale, have made, import, and otherwise transfer either its - Contributions or its Contributor Version. - -2.2. Effective Date - -The licenses granted in Section 2.1 with respect to any Contribution -become effective for each Contribution on the date the Contributor first -distributes such Contribution. - -2.3. Limitations on Grant Scope - -The licenses granted in this Section 2 are the only rights granted under -this License. No additional rights or licenses will be implied from the -distribution or licensing of Covered Software under this License. -Notwithstanding Section 2.1(b) above, no patent license is granted by a -Contributor: - -(a) for any code that a Contributor has removed from Covered Software; - or - -(b) for infringements caused by: (i) Your and any other third party's - modifications of Covered Software, or (ii) the combination of its - Contributions with other software (except as part of its Contributor - Version); or - -(c) under Patent Claims infringed by Covered Software in the absence of - its Contributions. - -This License does not grant any rights in the trademarks, service marks, -or logos of any Contributor (except as may be necessary to comply with -the notice requirements in Section 3.4). - -2.4. Subsequent Licenses - -No Contributor makes additional grants as a result of Your choice to -distribute the Covered Software under a subsequent version of this -License (see Section 10.2) or under the terms of a Secondary License (if -permitted under the terms of Section 3.3). - -2.5. Representation - -Each Contributor represents that the Contributor believes its -Contributions are its original creation(s) or it has sufficient rights -to grant the rights to its Contributions conveyed by this License. - -2.6. Fair Use - -This License is not intended to limit any rights You have under -applicable copyright doctrines of fair use, fair dealing, or other -equivalents. - -2.7. Conditions - -Sections 3.1, 3.2, 3.3, and 3.4 are conditions of the licenses granted -in Section 2.1. - -3. Responsibilities -------------------------------------------------------------- - -3.1. Distribution of Source Form - -All distribution of Covered Software in Source Code Form, including any -Modifications that You create or to which You contribute, must be under -the terms of this License. You must inform recipients that the Source -Code Form of the Covered Software is governed by the terms of this -License, and how they can obtain a copy of this License. You may not -attempt to alter or restrict the recipients' rights in the Source Code -Form. - -3.2. Distribution of Executable Form - -If You distribute Covered Software in Executable Form then: - -(a) such Covered Software must also be made available in Source Code - Form, as described in Section 3.1, and You must inform recipients of - the Executable Form how they can obtain a copy of such Source Code - Form by reasonable means in a timely manner, at a charge no more - than the cost of distribution to the recipient; and - -(b) You may distribute such Executable Form under the terms of this - License, or sublicense it under different terms, provided that the - license for the Executable Form does not attempt to limit or alter - the recipients' rights in the Source Code Form under this License. - -3.3. Distribution of a Larger Work - -You may create and distribute a Larger Work under terms of Your choice, -provided that You also comply with the requirements of this License for -the Covered Software. If the Larger Work is a combination of Covered -Software with a work governed by one or more Secondary Licenses, and the -Covered Software is not Incompatible With Secondary Licenses, this -License permits You to additionally distribute such Covered Software -under the terms of such Secondary License(s), so that the recipient of -the Larger Work may, at their option, further distribute the Covered -Software under the terms of either this License or such Secondary -License(s). - -3.4. Notices - -You may not remove or alter the substance of any license notices -(including copyright notices, patent notices, disclaimers of warranty, -or limitations of liability) contained within the Source Code Form of -the Covered Software, except that You may alter any license notices to -the extent required to remedy known factual inaccuracies. - -3.5. Application of Additional Terms - -You may choose to offer, and to charge a fee for, warranty, support, -indemnity or liability obligations to one or more recipients of Covered -Software. However, You may do so only on Your own behalf, and not on -behalf of any Contributor. You must make it absolutely clear that any -such warranty, support, indemnity, or liability obligation is offered by -You alone, and You hereby agree to indemnify every Contributor for any -liability incurred by such Contributor as a result of warranty, support, -indemnity or liability terms You offer. You may include additional -disclaimers of warranty and limitations of liability specific to any -jurisdiction. - -4. Inability to Comply Due to Statute or Regulation ---------------------------------------------------- - -If it is impossible for You to comply with any of the terms of this -License with respect to some or all of the Covered Software due to -statute, judicial order, or regulation then You must: (a) comply with -the terms of this License to the maximum extent possible; and (b) -describe the limitations and the code they affect. Such description must -be placed in a text file included with all distributions of the Covered -Software under this License. Except to the extent prohibited by statute -or regulation, such description must be sufficiently detailed for a -recipient of ordinary skill to be able to understand it. - -5. Termination -------------------------------------------------------------- - -5.1. The rights granted under this License will terminate automatically -if You fail to comply with any of its terms. However, if You become -compliant, then the rights granted under this License from a particular -Contributor are reinstated (a) provisionally, unless and until such -Contributor explicitly and finally terminates Your grants, and (b) on an -ongoing basis, if such Contributor fails to notify You of the -non-compliance by some reasonable means prior to 60 days after You have -come back into compliance. Moreover, Your grants from a particular -Contributor are reinstated on an ongoing basis if such Contributor -notifies You of the non-compliance by some reasonable means, this is the -first time You have received notice of non-compliance with this License -from such Contributor, and You become compliant prior to 30 days after -Your receipt of the notice. - -5.2. If You initiate litigation against any entity by asserting a patent -infringement claim (excluding declaratory judgment actions, -counter-claims, and cross-claims) alleging that a Contributor Version -directly or indirectly infringes any patent, then the rights granted to -You by any and all Contributors for the Covered Software under Section -2.1 of this License shall terminate. - -5.3. In the event of termination under Sections 5.1 or 5.2 above, all -end user license agreements (excluding distributors and resellers) which -have been validly granted by You or Your distributors under this License -prior to termination shall survive termination. - - - -6. Disclaimer of Warranty -------------------------------------------------------------- - -Covered Software is provided under this License on an "as is" basis, without -warranty of any kind, either expressed, implied, or statutory, including, -without limitation, warranties that the Covered Software is free of defects, -merchantable, fit for a particular purpose or non-infringing. The entire risk -as to the quality and performance of the Covered Software is with You. Should -any Covered Software prove defective in any respect, You (not any Contributor) -assume the cost of any necessary servicing, repair, or correction. This -disclaimer of warranty constitutes an essential part of this License. No use of -any Covered Software is authorized under this License except under this -disclaimer. - - -7. Limitation of Liability -------------------------------------------------------------- - -Under no circumstances and under no legal theory, whether tort (including -negligence), contract, or otherwise, shall any Contributor, or anyone who -distributes Covered Software as permitted above, be liable to You for any -direct, indirect, special, incidental, or consequential damages of any -character including, without limitation, damages for lost profits, loss of -goodwill, work stoppage, computer failure or malfunction, or any and all other -commercial damages or losses, even if such party shall have been informed of -the possibility of such damages. This limitation of liability shall not apply -to liability for death or personal injury resulting from such party's -negligence to the extent applicable law prohibits such limitation. Some -jurisdictions do not allow the exclusion or limitation of incidental or -consequential damages, so this exclusion and limitation may not apply to You. - - -8. Litigation -------------------------------------------------------------- - -Any litigation relating to this License may be brought only in the -courts of a jurisdiction where the defendant maintains its principal -place of business and such litigation shall be governed by laws of that -jurisdiction, without reference to its conflict-of-law provisions. -Nothing in this Section shall prevent a party's ability to bring -cross-claims or counter-claims. - -9. Miscellaneous -------------------------------------------------------------- - -This License represents the complete agreement concerning the subject -matter hereof. If any provision of this License is held to be -unenforceable, such provision shall be reformed only to the extent -necessary to make it enforceable. Any law or regulation which provides -that the language of a contract shall be construed against the drafter -shall not be used to construe this License against a Contributor. - -10. Versions of the License -------------------------------------------------------------- - -10.1. New Versions - -Mozilla Foundation is the license steward. Except as provided in Section -10.3, no one other than the license steward has the right to modify or -publish new versions of this License. Each version will be given a -distinguishing version number. - -10.2. Effect of New Versions - -You may distribute the Covered Software under the terms of the version -of the License under which You originally received the Covered Software, -or under the terms of any subsequent version published by the license -steward. - -10.3. Modified Versions - -If you create software not governed by this License, and you want to -create a new license for such software, you may create and use a -modified version of this License if you rename the license and remove -any references to the name of the license steward (except to note that -such modified license differs from this License). - -10.4. Distributing Source Code Form that is Incompatible With Secondary -Licenses - -If You choose to distribute Source Code Form that is Incompatible With -Secondary Licenses under the terms of this version of the License, the -notice described in Exhibit B of this License must be attached. - -Exhibit A - Source Code Form License Notice -------------------------------------------------------------- - -This Source Code Form is subject to the terms of the Mozilla Public -License, v. 2.0. If a copy of the MPL was not distributed with this -file, You can obtain one at http://mozilla.org/MPL/2.0/. - -If it is not possible or desirable to put the notice in a particular -file, then You may include the notice in a location (such as a LICENSE -file in a relevant directory) where a recipient would be likely to look -for such a notice. - -You may add additional accurate notices of copyright ownership. - -Exhibit B - "Incompatible With Secondary Licenses" Notice -------------------------------------------------------------- - -This Source Code Form is "Incompatible With Secondary Licenses", as -defined by the Mozilla Public License, v. 2.0. - - -HTS Lib and Samtools -------------------------------------------------------------- - -The MIT/Expat License -Copyright (C) 2008-2014 Genome Research Ltd. - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: -The above copyright notice and this permission notice shall be included in -all copies or substantial portions of the Software. -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL -THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING -FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER -DEALINGS IN THE SOFTWARE. - - -VCF Lib -------------------------------------------------------------- - + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. Definitions. + + "License" shall mean the terms and conditions for use, reproduction, + and distribution as defined by Sections 1 through 9 of this document. + + "Licensor" shall mean the copyright owner or entity authorized by + the copyright owner that is granting the License. + + "Legal Entity" shall mean the union of the acting entity and all + other entities that control, are controlled by, or are under common + control with that entity. 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In no event and under no legal theory, + whether in tort (including negligence), contract, or otherwise, + unless required by applicable law (such as deliberate and grossly + negligent acts) or agreed to in writing, shall any Contributor be + liable to You for damages, including any direct, indirect, special, + incidental, or consequential damages of any character arising as a + result of this License or out of the use or inability to use the + Work (including but not limited to damages for loss of goodwill, + work stoppage, computer failure or malfunction, or any and all + other commercial damages or losses), even if such Contributor + has been advised of the possibility of such damages. + + 9. Accepting Warranty or Additional Liability. While redistributing + the Work or Derivative Works thereof, You may choose to offer, + and charge a fee for, acceptance of support, warranty, indemnity, + or other liability obligations and/or rights consistent with this + License. However, in accepting such obligations, You may act only + on Your own behalf and on Your sole responsibility, not on behalf + of any other Contributor, and only if You agree to indemnify, + defend, and hold each Contributor harmless for any liability + incurred by, or claims asserted against, such Contributor by reason + of your accepting any such warranty or additional liability. + + +HTS Lib +Samtools + + + + The MIT/Expat License +Copyright © 2008-2014 Genome Research Ltd. + + Permission is hereby granted, free of charge, to any person obtaining a copy + of this software and associated documentation files (the "Software"), to deal + in the Software without restriction, including without limitation the rights + to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + copies of the Software, and to permit persons to whom the Software is + furnished to do so, subject to the following conditions: + + The above copyright notice and this permission notice shall be included in + all copies or substantial portions of the Software. + + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL + THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER + DEALINGS IN THE SOFTWARE. + + + +## VCF Lib The MIT License (see text above) -Copyright (c) 2012 Erik Garrison -Blas and Lapack -------------------------------------------------------------- -Copyright (c) 1992-2013 The University of Tennessee and The University of Tennessee Research Foundation. All rights reserved. +Copyright © 2012 Erik Garrison -Copyright (c) 2000-2013 The University of California Berkeley. All rights reserved. +Blas -Copyright (c) 2006-2013 The University of Colorado Denver. All rights reserved. +Lapack + +Copyright © 1992-2013 The University of Tennessee and The University + of Tennessee Research Foundation. All rights + reserved. +Copyright © 2000-2013 The University of California Berkeley. All + rights reserved. +Copyright © 2006-2013 The University of Colorado Denver. All rights + reserved. 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The copyright holders provide no reassurances that the source code provided does not infringe any patent, copyright, or any other @@ -685,793 +291,608 @@ THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -Django -------------------------------------------------------------- -Copyright (c) Django Software Foundation and individual contributors. All rights reserved. - -Redistribution and use in source and binary forms, with or without modification, -are permitted provided that the following conditions are met: - -1. Redistributions of source code must retain the above copyright notice, - this list of conditions and the following disclaimer. -2. 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By downloading, installing, copying, or otherwise using the SOFTWARE, You (as defined below) agree to be bound by the terms of this Agreement. If You do not agree to the terms of this Agreement, do not download the SOFTWARE. Recitals Use of NVIDIA's SOFTWARE requires three elements: the SOFTWARE, an NVIDIA GPU or application processor ("NVIDIA Hardware"), and a computer system. The SOFTWARE is protected by copyright laws and international copyright treaties, as well as other intellectual property laws and treaties. The SOFTWARE is not sold, and instead is only licensed for Your use, strictly in accordance with this Agreement. The NVIDIA Hardware is protected by various patents, and is sold, but this Agreement does not cover the sale or use of such hardware, since it may not necessarily be sold as a package with the SOFTWARE. This Agreement sets forth the terms and conditions of the SOFTWARE only. - -1.1. Definitions - - 1.1.1. 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Further Redistribution Rights Subject to the terms and conditions of the Agreement, Licensee may authorize Customers to further redistribute the Redistributable SOFTWARE that such Customers receive as part of the Licensee Application, solely in binary form, provided, however, that Licensee shall require in their standard software license agreements with Customers that all such redistributions must be made pursuant to a license agreement that has the effect of protecting the SOFTWARE and the rights of NVIDIA whose terms and conditions are at least as restrictive as those in the applicable Licensee software license agreement covering the Licensee Application. For avoidance of doubt, termination of this Agreement shall not affect rights previously granted by Licensee to its Customers under this Agreement to the extent validly granted to Customers under Section 1.2.1.1. - - 1.2.1.4. Linux/FreeBSD Exception Notwithstanding the foregoing terms of Section 1.2.1.2, Section 1.2.1.1 and Section 1.2.1.3, SOFTWARE designed exclusively for use on the Linux or FreeBSD operating systems, or other operating systems derived from the source code to these operating systems, may be copied and redistributed, provided that the binary files thereof are not modified in any way (except for unzipping of compressed files). - - 1.2.1.5. Additional Licensing Obligations Licensee acknowledges and agrees that its use of certain third party components included with the SOFTWARE may be subject to additional licensing terms and conditions as set forth or referenced in Attachment B of this Agreement. - - 1.2.1.6. Limitations No Reverse Engineering If the SOFTWARE is provided in binary form, Licensee may not reverse engineer, decompile, or disassemble the SOFTWARE, nor attempt in any other manner to obtain the source code. No Separation of Components The SOFTWARE is licensed as a single product. Except as authorized in this Agreement, Software component parts of the Software may not be separated for use on more than one computer, nor otherwise used separately from the other parts. No Rental Licensee may not rent or lease the SOFTWARE to someone else. -No Modifications -If the SOFTWARE is provided in source form, Licensee may not modify or create derivative works of the SOFTWARE. - -1.3. Term and Termination This Agreement will continue in effect for two (2) years ("Initial Term") after Your initial download and use of the SOFTWARE, subject to the exclusive right of NVIDIA to terminate as provided herein. The term of this Agreement will automatically renew for successive one (1) year renewal terms after the Initial Term, unless either party provides to the other party at least three (3) months prior written notice of termination before the end of the applicable renewal term. This Agreement will automatically terminate if Licensee fails to comply with any of the terms and conditions hereof. In such event, Licensee must destroy all copies of the SOFTWARE and all of its component parts. Defensive Suspension If Licensee commences or participates in any legal proceeding against NVIDIA, then NVIDIA may, in its sole discretion, suspend or terminate all license grants and any other rights provided under this Agreement during the pendency of such legal proceedings. - -1.4. Copyright All rights, title, interest and copyrights in and to the SOFTWARE (including but not limited to all images, photographs, animations, video, audio, music, text, and other information incorporated into the SOFTWARE), the accompanying printed materials, and any copies of the SOFTWARE, are owned by NVIDIA, or its suppliers. The SOFTWARE is protected by copyright laws and international treaty provisions. 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The United Nations Convention on Contracts for the International Sale of Goods is specifically disclaimed. The courts of Santa Clara County, California shall have exclusive jurisdiction and venue over any dispute arising out of or relating to this Agreement. - -1.6. Disclaimer of Warranties and Limitations on Liability - - 1.6.1. No Warranties TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, THE SOFTWARE IS PROVIDED "AS IS" AND NVIDIA AND ITS SUPPLIERS DISCLAIM ALL WARRANTIES, EITHER EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR NONINFRINGEMENT. - - 1.6.2. No Liability for Consequential Damages TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL NVIDIA OR ITS SUPPLIERS BE LIABLE FOR ANY SPECIAL, INCIDENTAL, INDIRECT, OR CONSEQUENTIAL DAMAGES WHATSOEVER (INCLUDING, WITHOUT LIMITATION, DAMAGES FOR LOSS OF BUSINESS PROFITS, BUSINESS INTERRUPTION, LOSS OF BUSINESS INFORMATION, OR ANY OTHER PECUNIARY LOSS) ARISING OUT OF THE USE OF OR INABILITY TO USE THE SOFTWARE, EVEN IF NVIDIA HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. - - 1.6.3. No Support . NVIDIA has no obligation to support or to provide any updates of the Software. - -1.7. Miscellaneous - - 1.7.1. Feedback Notwithstanding any Non-Disclosure Agreement executed by and between the parties, the parties agree that in the event Licensee or NVIDIA provides Feedback (as defined below) to the other party on how to design, implement, or improve the SOFTWARE or Licensee's product(s) for use with the SOFTWARE, the following terms and conditions apply the Feedback: - - 1.7.1.1. Exchange of Feedback Both parties agree that neither party has an obligation to give the other -party any suggestions, comments or other feedback, whether verbally or in written or source code form, relating to (i) the SOFTWARE; (ii) Licensee's products; (iii) Licensee's use of the SOFTWARE; or (iv) optimization/interoperability of Licensee's product with the SOFTWARE (collectively defined as "Feedback"). In the event either party provides Feedback to the other party, the party receiving the Feedback may use any Feedback that the other party voluntarily provides to improve the (i) SOFTWARE or other related NVIDIA technologies, respectively for the benefit of NVIDIA; or (ii) Licensee's product or other related Licensee technologies, respectively for the benefit of Licensee. Accordingly, if either party provides Feedback to the other party, both parties agree that the other party and its respective licensees may freely use, reproduce, license, distribute, and otherwise commercialize the Feedback in the (i) SOFTWARE or other related technologies; or (ii) Licensee's products or other related technologies, respectively, without the payment of any royalties or fees. - - 1.7.1.2. Residual Rights Licensee agrees that NVIDIA shall be free to use any general knowledge, skills and experience, (including, but not limited to, ideas, concepts, know-how, or techniques) ("Residuals"), contained in the (i) Feedback provided by Licensee to NVIDIA; (ii) Licensee's products shared or disclosed to NVIDIA in connection with the Feedback; or (c) Licensee's confidential information voluntarily provided to NVIDIA in connection with the Feedback, which are retained in the memories of NVIDIA's employees, agents, or contractors who have had access to such Residuals. Subject to the terms and conditions of this Agreement, NVIDIA's employees, agents, or contractors shall not be prevented from using Residuals as part of such employee's, agent's or contractor's general knowledge, skills, experience, talent, and/or expertise. NVIDIA shall not have any obligation to limit or restrict the assignment of such employees, agents or contractors or to pay royalties for any work resulting from the use of Residuals. - - 1.7.1.3. Disclaimer of Warranty FEEDBACK FROM EITHER PARTY IS PROVIDED FOR THE OTHER PARTY'S USE "AS IS" AND BOTH PARTIES DISCLAIM ALL WARRANTIES, EXPRESS, IMPLIED AND STATUTORY INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR NONINFRINGEMENT. BOTH PARTIES DO NOT REPRESENT OR WARRANT THAT THE FEEDBACK WILL MEET THE OTHER PARTY'S REQUIREMENTS OR THAT THE OPERATION OR IMPLEMENTATION OF THE FEEDBACK WILL BE UNINTERRUPTED OR ERROR-FREE. - 1.7.1.4. No Liability for Consequential Damages TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL EITHER PARTY OR ITS SUPPLIERS BE LIABLE FOR ANY SPECIAL, INCIDENTAL, INDIRECT, OR CONSEQUENTIAL DAMAGES WHATSOEVER (INCLUDING, WITHOUT LIMITATION, DAMAGES FOR LOSS OF BUSINESS PROFITS, BUSINESS INTERRUPTION, LOSS OF BUSINESS INFORMATION, OR ANY OTHER PECUNIARY LOSS) ARISING OUT OF THE USE OF OR INABILITY TO USE THE FEEDBACK, EVEN IF THE OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. - - 1.7.2. Freedom of Action Licensee agrees that this Agreement is nonexclusive and NVIDIA may currently or in the future be developing software, other technology or confidential information internally, or receiving confidential information from other parties that maybe similar to the Feedback and Licensee's confidential information (as provided in Section 1.7.1.2 above), which may be provided to NVIDIA in connection with Feedback by Licensee. 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This Agreement is the final, complete and exclusive agreement between the parties relating to the subject matter hereof, and supersedes all prior or contemporaneous understandings and agreements relating to such subject matter, whether oral or written. This Agreement may only be modified in writing signed by an authorized officer of NVIDIA. Licensee agrees that it will not ship, transfer or export the SOFTWARE into any country, or use the SOFTWARE in any manner, prohibited by the United States Bureau of Industry and Security or any export laws, restrictions or regulations. The parties agree that the following sections of the Agreement will survive the termination of the License: Section 1.2.1.4, Section 1.4, Section 1.5, Section 1.6, and Section 1.7. - -1.8. 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Automatic Licensing of Downstream Recipients. + Each time you convey a covered work, the recipient automatically receives a license from + the original licensors, to run, modify and propagate that work, subject to this License. + You are not responsible for enforcing compliance by third parties with this License. + An "entity transaction" is a transaction transferring control of an organization, or + substantially all assets of one, or subdividing an organization, or merging organizations. 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"Knowingly relying" + means you have actual knowledge that, but for the patent license, your conveying the + covered work in a country, or your recipient's use of the covered work in a country, + would infringe one or more identifiable patents in that country that you have reason to + believe are valid. + If, pursuant to or in connection with a single transaction or arrangement, you convey, or + propagate by procuring conveyance of, a covered work, and grant a patent license to + some of the parties receiving the covered work authorizing them to use, propagate, + modify or convey a specific copy of the covered work, then the patent license you grant + is automatically extended to all recipients of the covered work and works based on it. + A patent license is "discriminatory" if it does not include within the scope of its coverage, + prohibits the exercise of, or is conditioned on the non-exercise of one or more of the + rights that are specifically granted under this License. You may not convey a covered + work if you are a party to an arrangement with a third party that is in the business of + distributing software, under which you make payment to the third party based on the + extent of your activity of conveying the work, and under which the third party grants, to + any of the parties who would receive the covered work from you, a discriminatory patent + license (a) in connection with copies of the covered work conveyed by you (or copies + made from those copies), or (b) primarily for and in connection with specific products or + compilations that contain the covered work, unless you entered into that arrangement, or + that patent license was granted, prior to 28 March 2007. + Nothing in this License shall be construed as excluding or limiting any implied license or + other defenses to infringement that may otherwise be available to you under applicable + patent law. + 12. No Surrender of Others' Freedom. + If conditions are imposed on you (whether by court order, agreement or otherwise) that + contradict the conditions of this License, they do not excuse you from the conditions of + this License. If you cannot convey a covered work so as to satisfy simultaneously your + obligations under this License and any other pertinent obligations, then as a consequence + you may not convey it at all. For example, if you agree to terms that obligate you to + collect a royalty for further conveying from those to whom you convey the Program, the + only way you could satisfy both those terms and this License would be to refrain entirely + from conveying the Program. + 13. Use with the GNU Affero General Public License. + Notwithstanding any other provision of this License, you have permission to link or + combine any covered work with a work licensed under version 3 of the GNU Affero + General Public License into a single combined work, and to convey the resulting work. + The terms of this License will continue to apply to the part which is the covered work, but + the special requirements of the GNU Affero General Public License, section 13, + concerning interaction through a network will apply to the combination as such. + 14. Revised Versions of this License. + The Free Software Foundation may publish revised and/or new versions of the GNU + General Public License from time to time. Such new versions will be similar in spirit to the + present version, but may differ in detail to address new problems or concerns. + Each version is given a distinguishing version number. If the Program specifies that a + certain numbered version of the GNU General Public License "or any later version" + applies to it, you have the option of following the terms and conditions either of that + numbered version or of any later version published by the Free Software Foundation. If + the Program does not specify a version number of the GNU General Public License, you + may choose any version ever published by the Free Software Foundation. + If the Program specifies that a proxy can decide which future versions of the GNU + General Public License can be used, that proxy's public statement of acceptance of a + version permanently authorizes you to choose that version for the Program. + Later license versions may give you additional or different permissions. However, no + additional obligations are imposed on any author or copyright holder as a result of your + choosing to follow a later version. + 15. Disclaimer of Warranty. + THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT + PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN + WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE + THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER + EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR + PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF + THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, + YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR + CORRECTION. + 16. Limitation of Liability. + IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN + WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO + MODIFIES AND/OR CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE + LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, + INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE + OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO + LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES + SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM + TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR + OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH + DAMAGES. + 17. Interpretation of Sections 15 and 16. + If the disclaimer of warranty and limitation of liability provided above cannot be given + local legal effect according to their terms, reviewing courts shall apply local law that most + closely approximates an absolute waiver of all civil liability in connection with the + Program, unless a warranty or assumption of liability accompanies a copy of the Program + in return for a fee. -15. BECAUSE THE LIBRARY IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE LIBRARY, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE LIBRARY "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE LIBRARY IS WITH YOU. SHOULD THE LIBRARY PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. -16. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE LIBRARY AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE LIBRARY (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE LIBRARY TO OPERATE WITH ANY OTHER SOFTWARE), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. OEM Plupload -------------------------------------------------------------------------- -GNU General Public License + GNU General Public License Version 2, June 1991 -Copyright (C) 1989, 1991 Free Software Foundation, Inc., - -51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA + Copyright © 1989, 1991 Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA See Section 2 below for text of GPL v2.0 license. Font awesome -------------------------------------------------------------------------- The Font Awesome font is licensed under the SIL OFL 1.1: This Font Software is licensed under the SIL Open Font License, Version 1.1. +This license is copied below, and is also available with a FAQ at: +http://scripts.sil.org/OFL + -This license is copied below, and is also available with a FAQ at: http://scripts.sil.org/OFL ------------------------------------------------------------ SIL OPEN FONT LICENSE Version 1.1 - 26 February 2007 ----------------------------------------------------------- @@ -1567,992 +988,406 @@ Font Awesome CSS, LESS, and Sass files are licensed under the MIT License: The MIT License -Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated -documentation files (the "Software"), to deal in the Software without restriction, including without limitation -the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, -and to permit persons to whom the Software is furnished to do so, subject to the following conditions: - +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED -TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL -THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, -TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. - - -2. GNU General Public License version 2 (GPL v2) +===================================================================== + 2. GNU General Public License version 2 (GPL v2) ===================================================================== GNU GENERAL PUBLIC LICENSE -Version 2, June 1991 -Copyright (C) 1989, 1991 Free Software Foundation, Inc. +Version 2, June 1991 + +Copyright © 1989, 1991 Free Software Foundation, Inc. 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. -Preamble +###Preamble The licenses for most software are designed to take away your freedom to share and change it. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change free software--to make sure the software is free for all its users. This General Public License applies to most of the Free Software Foundation's software and to any other program whose authors commit to using it. (Some other Free Software Foundation software is covered by the GNU Lesser General Public License instead.) You can apply it to your programs, too. - When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for this service if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs; and that you know you can do these things. - To protect your rights, we need to make restrictions that forbid anyone to deny you these rights or to ask you to surrender the rights. These restrictions translate to certain responsibilities for you if you distribute copies of the software, or if you modify it. - For example, if you distribute copies of such a program, whether gratis or for a fee, you must give the recipients all the rights that you have. You must make sure that they, too, receive or can get the source code. And you must show them these terms so they know their rights. - We protect your rights with two steps: (1) copyright the software, and (2) offer you this license which gives you legal permission to copy, distribute and/or modify the software. - Also, for each author's protection and ours, we want to make certain that everyone understands that there is no warranty for this free software. If the software is modified by someone else and passed on, we want its recipients to know that what they have is not the original, so that any problems introduced by others will not reflect on the original authors' reputations. - Finally, any free program is threatened constantly by software patents. We wish to avoid the danger that redistributors of a free program will individually obtain patent licenses, in effect making the program proprietary. To prevent this, we have made it clear that any patent must be licensed for everyone's free use or not licensed at all. - The precise terms and conditions for copying, distribution and modification follow. - TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION -------------------------------------------------------------- 0. This License applies to any program or other work which contains a notice placed by the copyright holder saying it may be distributed under the terms of this General Public License. The "Program", below, refers to any such program or work, and a "work based on the Program" means either the Program or any derivative work under copyright law: that is to say, a work containing the Program or a portion of it, either verbatim or with modifications and/or translated into another language. (Hereinafter, translation is included without limitation in the term "modification".) Each licensee is addressed as "you". Activities other than copying, distribution and modification are not covered by this License; they are outside its scope. The act of running the Program is not restricted, and the output from the Program is covered only if its contents constitute a work based on the Program (independent of having been made by running the Program). Whether that is true depends on what the Program does. - 1. You may copy and distribute verbatim copies of the Program's source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty; keep intact all the notices that refer to this License and to the absence of any warranty; and give any other recipients of the Program a copy of this License along with the Program. You may charge a fee for the physical act of transferring a copy, and you may at your option offer warranty protection in exchange for a fee. - 2. You may modify your copy or copies of the Program or any portion of it, thus forming a work based on the Program, and copy and distribute such modifications or work under the terms of Section 1 above, provided that you also meet all of these conditions: - - a) You must cause the modified files to carry prominent notices stating that you changed the files and the date of any change. - b) You must cause any work that you distribute or publish, that in whole or in part contains or is derived from the Program or any part thereof, to be licensed as a whole at no charge to all third parties under the terms of this License. - c) If the modified program normally reads commands interactively when run, you must cause it, when started running for such interactive use in the most ordinary way, to print or display an announcement including an appropriate copyright notice and a notice that there is no warranty (or else, saying that you provide a warranty) and that users may redistribute the program under these conditions, and telling the user how to view a copy of this License. (Exception: if the Program itself is interactive but does not normally print such an announcement, your work based on the Program is not required to print an announcement.) - - These requirements apply to the modified work as a whole. If identifiable sections of that work are not derived from the Program, and can be reasonably considered independent and separate works in themselves, then this License, and its terms, do not apply to those sections when you distribute them as separate works. But when you distribute the same sections as part of a whole which is a work based on the Program, the distribution of the whole must be on the terms of this License, whose permissions for other licensees extend to the entire whole, and thus to each and every part regardless of who wrote it. - - Thus, it is not the intent of this section to claim rights or contest your rights to work written entirely by you; rather, the intent is to exercise the right to control the distribution of derivative or collective works based on the Program. - - In addition, mere aggregation of another work not based on the Program with the Program (or with a work based on the Program) on a volume of a storage or distribution medium does not bring the other work under the scope of this License. - +a) You must cause the modified files to carry prominent notices stating that you changed the files and the date of any change. +b) You must cause any work that you distribute or publish, that in whole or in part contains or is derived from the Program or any part thereof, to be licensed as a whole at no charge to all third parties under the terms of this License. +c) If the modified program normally reads commands interactively when run, you must cause it, when started running for such interactive use in the most ordinary way, to print or display an announcement including an appropriate copyright notice and a notice that there is no warranty (or else, saying that you provide a warranty) and that users may redistribute the program under these conditions, and telling the user how to view a copy of this License. (Exception: if the Program itself is interactive but does not normally print such an announcement, your work based on the Program is not required to print an announcement.) +These requirements apply to the modified work as a whole. If identifiable sections of that work are not derived from the Program, and can be reasonably considered independent and separate works in themselves, then this License, and its terms, do not apply to those sections when you distribute them as separate works. But when you distribute the same sections as part of a whole which is a work based on the Program, the distribution of the whole must be on the terms of this License, whose permissions for other licensees extend to the entire whole, and thus to each and every part regardless of who wrote it. +Thus, it is not the intent of this section to claim rights or contest your rights to work written entirely by you; rather, the intent is to exercise the right to control the distribution of derivative or collective works based on the Program. +In addition, mere aggregation of another work not based on the Program with the Program (or with a work based on the Program) on a volume of a storage or distribution medium does not bring the other work under the scope of this License. 3. You may copy and distribute the Program (or a work based on it, under Section 2) in object code or executable form under the terms of Sections 1 and 2 above provided that you also do one of the following: - - a) Accompany it with the complete corresponding machine-readable source code, which must be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, - b) Accompany it with a written offer, valid for at least three years, to give any third party, for a charge no more than your cost of physically performing source distribution, a complete machine-readable copy of the corresponding source code, to be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, - c) Accompany it with the information you received as to the offer to distribute corresponding source code. (This alternative is allowed only for noncommercial distribution and only if you received the program in object code or executable form with such an offer, in accord with Subsection b above.) +a) Accompany it with the complete corresponding machine-readable source code, which must be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, +b) Accompany it with a written offer, valid for at least three years, to give any third party, for a charge no more than your cost of physically performing source distribution, a complete machine-readable copy of the corresponding source code, to be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, +c) Accompany it with the information you received as to the offer to distribute corresponding source code. (This alternative is allowed only for noncommercial distribution and only if you received the program in object code or executable form with such an offer, in accord with Subsection b above.) The source code for a work means the preferred form of the work for making modifications to it. For an executable work, complete source code means all the source code for all modules it contains, plus any associated interface definition files, plus the scripts used to control compilation and installation of the executable. However, as a special exception, the source code distributed need not include anything that is normally distributed (in either source or binary form) with the major components (compiler, kernel, and so on) of the operating system on which the executable runs, unless that component itself accompanies the executable. If distribution of executable or object code is made by offering access to copy from a designated place, then offering equivalent access to copy the source code from the same place counts as distribution of the source code, even though third parties are not compelled to copy the source along with the object code. - 4. You may not copy, modify, sublicense, or distribute the Program except as expressly provided under this License. Any attempt otherwise to copy, modify, sublicense or distribute the Program is void, and will automatically terminate your rights under this License. However, parties who have received copies, or rights, from you under this License will not have their licenses terminated so long as such parties remain in full compliance. - 5. You are not required to accept this License, since you have not signed it. However, nothing else grants you permission to modify or distribute the Program or its derivative works. These actions are prohibited by law if you do not accept this License. Therefore, by modifying or distributing the Program (or any work based on the Program), you indicate your acceptance of this License to do so, and all its terms and conditions for copying, distributing or modifying the Program or works based on it. - 6. Each time you redistribute the Program (or any work based on the Program), the recipient automatically receives a license from the original licensor to copy, distribute or modify the Program subject to these terms and conditions. You may not impose any further restrictions on the recipients' exercise of the rights granted herein. You are not responsible for enforcing compliance by third parties to this License. - 7. If, as a consequence of a court judgment or allegation of patent infringement or for any other reason (not limited to patent issues), conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot distribute so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not distribute the Program at all. For example, if a patent license would not permit royalty-free redistribution of the Program by all those who receive copies directly or indirectly through you, then the only way you could satisfy both it and this License would be to refrain entirely from distribution of the Program. If any portion of this section is held invalid or unenforceable under any particular circumstance, the balance of the section is intended to apply and the section as a whole is intended to apply in other circumstances. - - It is not the purpose of this section to induce you to infringe any patents or other property right claims or to contest validity of any such claims; this section has the sole purpose of protecting the integrity of the free software distribution system, which is implemented by public license practices. Many people have made generous contributions to the wide range of software distributed through that system in reliance on consistent application of that system; it is up to the author/donor to decide if he or she is willing to distribute software through any other system and a licensee cannot impose that choice. +It is not the purpose of this section to induce you to infringe any patents or other property right claims or to contest validity of any such claims; this section has the sole purpose of protecting the integrity of the free software distribution system, which is implemented by public license practices. Many people have made generous contributions to the wide range of software distributed through that system in reliance on consistent application of that system; it is up to the author/donor to decide if he or she is willing to distribute software through any other system and a licensee cannot impose that choice. This section is intended to make thoroughly clear what is believed to be a consequence of the rest of this License. - 8. If the distribution and/or use of the Program is restricted in certain countries either by patents or by copyrighted interfaces, the original copyright holder who places the Program under this License may add an explicit geographical distribution limitation excluding those countries, so that distribution is permitted only in or among countries not thus excluded. In such case, this License incorporates the limitation as if written in the body of this License. - 9. The Free Software Foundation may publish revised and/or new versions of the General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. Each version is given a distinguishing version number. If the Program specifies a version number of this License which applies to it and "any later version", you have the option of following the terms and conditions either of that version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of this License, you may choose any version ever published by the Free Software Foundation. - 10. If you wish to incorporate parts of the Program into other free programs whose distribution conditions are different, write to the author to ask for permission. For software which is copyrighted by the Free Software Foundation, write to the Free Software Foundation; we sometimes make exceptions for this. Our decision will be guided by the two goals of preserving the free status of all derivatives of our free software and of promoting the sharing and reuse of software generally. NO WARRANTY - 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. - 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. +###End of (1) Torrent Suite™ Software Version 5.18 Open Source License - - - -**(2) BEGINS:** +**************************************************** + (2) BEGINS: +================================================================================ LIFE TECHNOLOGIES CORPORATION END USER LICENSE AGREEMENT +## FOR SERVICE & SUPPORT TELEMETRY MODULE SOFTWARE VERSION 2.0.1 -FOR SERVICE & SUPPORT TELEMETRY MODULE Software VERSION 2.0.1 - -NOTICE TO USER: PLEASE READ THIS DOCUMENT CAREFULLY. THIS IS THE -CONTRACT BETWEEN YOU AND LIFE TECHNOLOGIES CORPORATION ("LIFE -TECHNOLOGIES") REGARDING THIS SOFTWARE PRODUCT. THIS AGREEMENT CONTAINS -WARRANTY AND LIABILITY DISCLAIMERS AND LIMITATIONS. YOUR INSTALLATION -AND/OR USE OF THIS LIFE TECHNOLOGIES SOFTWARE IS SUBJECT TO THE TERMS -AND CONDITIONS CONTAINED IN THIS END USER SOFTWARE LICENSE AGREEMENT, -AND YOU WILL BE BOUND BY THESE TERMS AND CONDITIONS IF YOU INSTALL -AND/OR USE THE SOFTWARE. - -IF YOU DO NOT AGREE TO THESE TERMS AND CONDITIONS, YOU SHOULD PROMPTLY -RETURN THIS SOFTWARE, TOGETHER WITH ALL PACKAGING, TO LIFE TECHNOLOGIES -AND YOUR PURCHASE PRICE WILL BE REFUNDED. - -This Life Technologies End User License Agreement accompanies a Life -Technologies software product ("Software") and related explanatory -materials ("Documentation"). The term "Software" also includes any -upgrades, modified versions, updates, additions and copies of the -Software licensed to you by Life Technologies. The term "License" or -"Agreement" means this End User Software License Agreement. The term -"you" or "Licensee" means the purchaser or user of this license to the -Software. This Agreement includes herein by reference any additional use -restrictions or Limited Use Label Licenses listed in or on user manuals, -labeling, product inserts, technical notes, literature (including but -not limited to Documentation) and/or splash screens related to this -Software ("Supplemental Terms"). To the extent such Supplemental Terms -are more restrictive than those contained herein, the more restrictive -usage terms shall control. - -This Software may use third-party software components from several -sources. Portions of these software components are copyrighted and -licensed by their respective owners. Various components require -distribution of source code or if a URL is used to point the end-user to -a source-code repository, and the source code is not available at such -site, the distributor must, for a time determined by the license, offer -to provide the source code. In such cases, please contact your Life -Technologies representative. As well, various licenses require that the -end-user receive a copy of the license. Such licenses, if any, may be -found in Appendix 1 below. In order to use this Software, the end-user -must abide by the terms and conditions of these third-party licenses. +NOTICE TO USER: PLEASE READ THIS DOCUMENT CAREFULLY. THIS IS THE CONTRACT BETWEEN YOU AND LIFE TECHNOLOGIES CORPORATION ("LIFE TECHNOLOGIES") REGARDING THIS SOFTWARE PRODUCT. THIS AGREEMENT CONTAINS WARRANTY AND LIABILITY DISCLAIMERS AND LIMITATIONS. YOUR INSTALLATION AND/OR USE OF THIS LIFE TECHNOLOGIES SOFTWARE IS SUBJECT TO THE TERMS AND CONDITIONS CONTAINED IN THIS END USER SOFTWARE LICENSE AGREEMENT, AND YOU WILL BE BOUND BY THESE TERMS AND CONDITIONS IF YOU INSTALL AND/OR USE THE SOFTWARE. +IF YOU DO NOT AGREE TO THESE TERMS AND CONDITIONS, YOU SHOULD PROMPTLY RETURN THIS SOFTWARE, TOGETHER WITH ALL PACKAGING, TO LIFE TECHNOLOGIES AND YOUR PURCHASE PRICE WILL BE REFUNDED. +This Life Technologies End User License Agreement accompanies a Life Technologies software product ("Software") and related explanatory materials ("Documentation"). The term "Software" also includes any upgrades, modified versions, updates, additions and copies of the Software licensed to you by Life Technologies. The term "License" or "Agreement" means this End User Software License Agreement. The term "you" or "Licensee" means the purchaser or user of this license to the Software. This Agreement includes herein by reference any additional use restrictions or Limited Use Label Licenses listed in or on user manuals, labeling, product inserts, technical notes, literature (including but not limited to Documentation) and/or splash screens related to this Software ("Supplemental Terms"). To the extent such Supplemental Terms are more restrictive than those contained herein, the more restrictive usage terms shall control. +This Software may use third-party software components from several sources. Portions of these software components are copyrighted and licensed by their respective owners. Various components require distribution of source code or if a URL is used to point the end-user to a source-code repository, and the source code is not available at such site, the distributor must, for a time determined by the license, offer to provide the source code. In such cases, please contact your Life Technologies representative. As well, various licenses require that the end-user receive a copy of the license. Such licenses, if any, may be found in Appendix 1 below. In order to use this Software, the end-user must abide by the terms and conditions of these third-party licenses. TITLE -Title, ownership rights and intellectual property rights in and to the -Software and Documentation shall at all times remain with Life -Technologies and its subsidiaries, and their suppliers. All rights not -specifically granted by this License, including Federal and -international copyrights, are reserved by Life Technologies or their -respective owners. +Title, ownership rights and intellectual property rights in and to the Software and Documentation shall at all times remain with Life Technologies and its subsidiaries, and their suppliers. All rights not specifically granted by this License, including Federal and international copyrights, are reserved by Life Technologies or their respective owners. COPYRIGHT -The Software, including its structure, organization, code, user -interface and associated Documentation, is a proprietary product of Life -Technologies or its suppliers, and is protected by international laws of -copyright. The law provides for civil and criminal penalties for anyone -in violation of the laws of copyright. +The Software, including its structure, organization, code, user interface and associated Documentation, is a proprietary product of Life Technologies or its suppliers, and is protected by international laws of copyright. The law provides for civil and criminal penalties for anyone in violation of the laws of copyright. LICENSE USE OF THE SOFTWARE -Subject to the terms and conditions of this Agreement, Life Technologies -grants the purchaser of this product a non-exclusive, non-transferable -license, with no rights to sublicense, to install and/or use the -Software only in object code (machine readable) format and only on -single computers owned or controlled by you (or in a single network, if -your Software is designated as a network version) for the sole purpose -of managing, analyzing, viewing, editing, reporting and/or printing data -provided by Life Technologies or generated by Life Technologies -instruments for research use only. - -If the software uses registration codes, access to the number of -licenses copies of Software is controlled by a registration code. For -example, if you have a registration code that enables you to use three -copies of Software simultaneously, you cannot install Software on more -than three separate computers. - -You may make one copy of the Software in machine-readable form solely -for backup or archival purposes. You must reproduce on any such copy all -copyright notices and any other proprietary legends found on the -original. You may not make any other copies of the Software. +Subject to the terms and conditions of this Agreement, Life Technologies grants the purchaser of this product a non-exclusive, non-transferable license, with no rights to sublicense, to install and/or use the Software only in object code (machine readable) format and only on single computers owned or controlled by you (or in a single network, if your Software is designated as a network version) for the sole purpose of managing, analyzing, viewing, editing, reporting and/or printing data provided by Life Technologies or generated by Life Technologies instruments for research use only. +If the software uses registration codes, access to the number of licenses copies of Software is controlled by a registration code. For example, if you have a registration code that enables you to use three copies of Software simultaneously, you cannot install Software on more than three separate computers. +You may make one copy of the Software in machine-readable form solely for backup or archival purposes. You must reproduce on any such copy all copyright notices and any other proprietary legends found on the original. You may not make any other copies of the Software. RESTRICTIONS -Unless permitted by applicable law, and in such cases only to the extent -permitted by such law: - -1. You shall not copy, transfer (except temporarily in the event of a - computer malfunction), rent, modify, distribute, electronically - transmit, lend, lease, use, create derivative works based on the - Software or merge the Software, or the associated Documentation, in - whole or in part, whether alone or combined with any other products, - except as expressly permitted in this Agreement. - -2. You shall not reverse assemble, decompile, discover the source code - or otherwise reverse engineer the Software. - -3. You shall not remove any proprietary, copyright, trade secret or - warning legend from the Software or any Documentation. +Unless permitted by applicable law, and in such cases only to the extent permitted by such law: -4. You agree to comply fully with all export laws and restrictions and - regulations of the United States or applicable foreign agencies or - authorities. You agree that you will not export or reexport, - directly or indirectly, the Software and the Documentation into any - country prohibited by the United States Export Administration Act - and the regulations thereunder or other applicable United States - law. - -5. You may not use the Software or Documentation for the benefit of any - third party by means of an outsourcing or service bureau - relationship or for any similar commercial time-sharing or - third-party training use. - -6. You agree to use Software, and data generated by Software, for the - sole purpose of review and analysis of data generated by Life - Technologies instruments. +1. You shall not copy, transfer (except temporarily in the event of a computer malfunction), rent, modify, distribute, electronically transmit, lend, lease, use, create derivative works based on the Software or merge the Software, or the associated Documentation, in whole or in part, whether alone or combined with any other products, except as expressly permitted in this Agreement. +2. You shall not reverse assemble, decompile, discover the source code or otherwise reverse engineer the Software. +3. You shall not remove any proprietary, copyright, trade secret or warning legend from the Software or any Documentation. +4. You agree to comply fully with all export laws and restrictions and regulations of the United States or applicable foreign agencies or authorities. You agree that you will not export or reexport, directly or indirectly, the Software and the Documentation into any country prohibited by the United States Export Administration Act and the regulations thereunder or other applicable United States law. +5. You may not use the Software or Documentation for the benefit of any third party by means of an outsourcing or service bureau relationship or for any similar commercial time-sharing or third-party training use. +6. You agree to use Software, and data generated by Software, for the sole purpose of review and analysis of data generated by Life Technologies instruments. TRIAL -If this license is granted on a trial basis, you are hereby notified -that license management software may be included to automatically cause -the Software to cease functioning at the end of the trial period (and in -any case you agree to discontinue usage at the end of the trial period -or at the express written request of Life Technologies). +If this license is granted on a trial basis, you are hereby notified that license management software may be included to automatically cause the Software to cease functioning at the end of the trial period (and in any case you agree to discontinue usage at the end of the trial period or at the express written request of Life Technologies). TERMINATION -You may terminate this Agreement by discontinuing use of the Software, -removing all copies from your computers and storage media, and returning -the Software and Documentation, and all copies thereof, to Life -Technologies. Life Technologies may terminate this Agreement if you fail -to comply with all of its terms, in which case you agree to discontinue -using the Software, remove all copies from your computers and storage -media, and return the Software and Documentation, and all copies -thereof, to Life Technologies. +You may terminate this Agreement by discontinuing use of the Software, removing all copies from your computers and storage media, and returning the Software and Documentation, and all copies thereof, to Life Technologies. Life Technologies may terminate this Agreement if you fail to comply with all of its terms, in which case you agree to discontinue using the Software, remove all copies from your computers and storage media, and return the Software and Documentation, and all copies thereof, to Life Technologies. U.S. GOVERNMENT END USERS -The Software is a "commercial item," as that term is defined in 48 -C.F.R. 2.101 (Oct. 1995), consisting of "commercial computer software" -and "commercial computer software documentation," as such terms are used -in 48 C.F.R. 12.212 (Sept. 1995). Consistent with 48 C.F.R. 12.212 and -48 C.F.R. 227.7202-1 through 227.7202-4 (June 1995), all U.S. Government -End Users acquire the Software with only those rights set forth herein. +The Software is a "commercial item," as that term is defined in 48 C.F.R. 2.101 (Oct. 1995), consisting of "commercial computer software" and "commercial computer software documentation," as such terms are used in 48 C.F.R. 12.212 (Sept. 1995). Consistent with 48 C.F.R. 12.212 and 48 C.F.R. 227.7202-1 through 227.7202-4 (June 1995), all U.S. Government End Users acquire the Software with only those rights set forth herein. EUROPEAN UNION END USERS -If this Software is used within a country of the European Union, nothing -in this Agreement shall be construed as restricting any rights available -under Directive 2009/24/EC of the European Parliament and of the Council -of 23 April 2009 on the legal protection of computer programs. - -YOU ACKNOWLEDGE THAT LIFE TECHNOLOGIES HAS NO CONTROL OVER THE SPECIFIC -CONDITIONS UNDER WHICH YOU USE THE SOFTWARE. LICENSOR CANNOT AND DOES -NOT WARRANT THE PERFORMANCE OF THE SOFTWARE OR ANY PARTICULAR RESULTS -THAT MAY BE OBTAINED BY THE USE OF THE SOFTWARE. THE SOFTWARE DOES NOT -REPLACE YOUR OBLIGATION TO EXERCISE YOUR INDEPENDENT JUDGMENT IN USING -THE SOFTWARE. The warranties, if any, made by Life Technologies may be -voided by abuse or misuse of the Software. - +If this Software is used within a country of the European Union, nothing in this Agreement shall be construed as restricting any rights available under Directive 2009/24/EC of the European Parliament and of the Council of 23 April 2009 on the legal protection of computer programs. +YOU ACKNOWLEDGE THAT LIFE TECHNOLOGIES HAS NO CONTROL OVER THE SPECIFIC CONDITIONS UNDER WHICH YOU USE THE SOFTWARE. LICENSOR CANNOT AND DOES NOT WARRANT THE PERFORMANCE OF THE SOFTWARE OR ANY PARTICULAR RESULTS THAT MAY BE OBTAINED BY THE USE OF THE SOFTWARE. THE SOFTWARE DOES NOT REPLACE YOUR OBLIGATION TO EXERCISE YOUR INDEPENDENT JUDGMENT IN USING THE SOFTWARE. The warranties, if any, made by Life Technologies may be voided by abuse or misuse of the Software. LIMITATION OF LIABILITY - -IN NO EVENT SHALL LIFE TECHNOLOGIES OR ITS SUPPLIERS BE RESPONSIBLE OR -LIABLE, WHETHER IN CONTRACT, TORT, WARRANTY OR UNDER ANY STATUTE -(INCLUDING WITHOUT LIMITATION ANY TRADE PRACTICE, UNFAIR COMPETITION OR -OTHER STATUTE OF SIMILAR IMPORT) OR ON ANY OTHER BASIS FOR DAMAGES -ARISING FROM PERSONAL INJURY OR DEATH OR SPECIAL, INDIRECT, INCIDENTAL, -MULTIPLE, PUNITIVE, OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE -POSSESSION OR USE OF, OR THE INABILITY TO USE, THE SOFTWARE, THE -GENERATED DATA OR DOCUMENTATION, EVEN IF LIFE TECHNOLOGIES IS ADVISED IN -ADVANCE OF THE POSSIBILITY OF SUCH DAMAGES, INCLUDING WITHOUT LIMITATION -DAMAGES OR EXPENSES ARISING FROM OR RELATED TO, OR ALLEGED TO HAVE -ARISEN FROM OR BE RELATED TO, LOSS OF USE, LOSS OF DATA, DOWNTIME, OR -FOR LOSS OF REVENUE, PROFITS, GOODWILL OR BUSINESS OR OTHER FINANCIAL -LOSS. IN ANY CASE, THE ENTIRE LIABILITY OF LIFE TECHNOLOGIES AND ITS -SUPPLIERS UNDER THIS LICENSE, OR ARISING OUT OF THE USE OF THE SOFTWARE -OR DOCUMENTATION OR GENERATED DATA, SHALL NOT EXCEED, IN THE AGGREGATE, -THE PURCHASE PRICE OF THE PRODUCT. - -SOME STATES, COUNTRIES OR JURISDICTIONS LIMIT THE SCOPE OF OR PRECLUDE -LIMITATIONS OR EXCLUSION OF REMEDIES OR DAMAGES, OR OF LIABILITY, SUCH -AS LIABILITY FOR GROSS NEGLIGENCE OR WILLFUL MISCONDUCT, AS OR TO THE -EXTENT SET FORTH ABOVE, OR DO NOT ALLOW IMPLIED WARRANTIES TO BE -EXCLUDED. IN SUCH STATES, COUNTRIES OR JURISDICTIONS, THE LIMITATION OR -EXCLUSION OF WARRANTIES, REMEDIES, DAMAGES OR LIABILITY SET FORTH ABOVE -MAY NOT APPLY TO YOU. HOWEVER, ALTHOUGH THEY SHALL NOT APPLY TO THE -EXTENT PROHIBITED BY LAW, THEY SHALL APPLY TO THE FULLEST EXTENT -PERMITTED BY LAW. YOU MAY ALSO HAVE OTHER RIGHTS THAT VARY BY STATE, -COUNTRY OR OTHER JURISDICTION. +IN NO EVENT SHALL LIFE TECHNOLOGIES OR ITS SUPPLIERS BE RESPONSIBLE OR LIABLE, WHETHER IN CONTRACT, TORT, WARRANTY OR UNDER ANY STATUTE (INCLUDING WITHOUT LIMITATION ANY TRADE PRACTICE, UNFAIR COMPETITION OR OTHER STATUTE OF SIMILAR IMPORT) OR ON ANY OTHER BASIS FOR DAMAGES ARISING FROM PERSONAL INJURY OR DEATH OR SPECIAL, INDIRECT, INCIDENTAL, MULTIPLE, PUNITIVE, OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE POSSESSION OR USE OF, OR THE INABILITY TO USE, THE SOFTWARE, THE GENERATED DATA OR DOCUMENTATION, EVEN IF LIFE TECHNOLOGIES IS ADVISED IN ADVANCE OF THE POSSIBILITY OF SUCH DAMAGES, INCLUDING WITHOUT LIMITATION DAMAGES OR EXPENSES ARISING FROM OR RELATED TO, OR ALLEGED TO HAVE ARISEN FROM OR BE RELATED TO, LOSS OF USE, LOSS OF DATA, DOWNTIME, OR FOR LOSS OF REVENUE, PROFITS, GOODWILL OR BUSINESS OR OTHER FINANCIAL LOSS. IN ANY CASE, THE ENTIRE LIABILITY OF LIFE TECHNOLOGIES AND ITS SUPPLIERS UNDER THIS LICENSE, OR ARISING OUT OF THE USE OF THE SOFTWARE OR DOCUMENTATION OR GENERATED DATA, SHALL NOT EXCEED, IN THE AGGREGATE, THE PURCHASE PRICE OF THE PRODUCT. +SOME STATES, COUNTRIES OR JURISDICTIONS LIMIT THE SCOPE OF OR PRECLUDE LIMITATIONS OR EXCLUSION OF REMEDIES OR DAMAGES, OR OF LIABILITY, SUCH AS LIABILITY FOR GROSS NEGLIGENCE OR WILLFUL MISCONDUCT, AS OR TO THE EXTENT SET FORTH ABOVE, OR DO NOT ALLOW IMPLIED WARRANTIES TO BE EXCLUDED. IN SUCH STATES, COUNTRIES OR JURISDICTIONS, THE LIMITATION OR EXCLUSION OF WARRANTIES, REMEDIES, DAMAGES OR LIABILITY SET FORTH ABOVE MAY NOT APPLY TO YOU. HOWEVER, ALTHOUGH THEY SHALL NOT APPLY TO THE EXTENT PROHIBITED BY LAW, THEY SHALL APPLY TO THE FULLEST EXTENT PERMITTED BY LAW. YOU MAY ALSO HAVE OTHER RIGHTS THAT VARY BY STATE, COUNTRY OR OTHER JURISDICTION. CONFIDENTIALITY -You agree to protect Life Technologies Confidential Information with the -same degree of care used to protect your own confidential information -(but in no event less than a reasonable standard of care), and not to -use or disclose any portion of such Confidential Information to third -parties, except as expressly authorized in this Agreement. You -acknowledge that the Software, including its content, structure, -organization and design constitute proprietary and valuable trade -secrets (and other intellectual property rights) of Life Technology -and/or its licensors. The term "Confidential Information" means, -collectively, non-public information that Life Technologies (and its -licensors) provide and reasonably consider to be of a confidential, -proprietary or trade secret nature, including but not limited to (i) the -Software, and (ii) confidential elements of the Software and Life -Technologies (and its licensors) technology and know-how, whether in -tangible or intangible form, whether designated as confidential or not, -and whether or not stored, compiled or memorialized physically, -electronically, graphically, photographically, or in writing. -Confidential Information does not include any information which you can -demonstrate by credible evidence: (a) is, as of the time of its -disclosure, or thereafter becomes part of the public domain through no -fault of yours; (b) was rightfully known to you prior to the time of its -disclosure, or to have been independently developed by you without use -of Confidential Information; and/or (c) is subsequently learned from a -third party not under a confidentiality obligation with respect to such -Confidential Information. Confidential Information that is required to -be disclosed by you pursuant to a duly authorized subpoena, court order, -or government authority shall continue to be Confidential Information -for all other purposes and you agree, prior to disclosing pursuant to a -subpoena, court order, or government authority, to provide prompt -written notice and assistance to Life Technologies prior to such -disclosure, so that Life Technologies may seek a protective order or -other appropriate remedy to protect against disclosure. +You agree to protect Life Technologies Confidential Information with the same degree of care used to protect your own confidential information (but in no event less than a reasonable standard of care), and not to use or disclose any portion of such Confidential Information to third parties, except as expressly authorized in this Agreement. You acknowledge that the Software, including its content, structure, organization and design constitute proprietary and valuable trade secrets (and other intellectual property rights) of Life Technology and/or its licensors. The term "Confidential Information" means, collectively, non-public information that Life Technologies (and its licensors) provide and reasonably consider to be of a confidential, proprietary or trade secret nature, including but not limited to (i) the Software, and (ii) confidential elements of the Software and Life Technologies (and its licensors) technology and know-how, whether in tangible or intangible form, whether designated as confidential or not, and whether or not stored, compiled or memorialized physically, electronically, graphically, photographically, or in writing. Confidential Information does not include any information which you can demonstrate by credible evidence: (a) is, as of the time of its disclosure, or thereafter becomes part of the public domain through no fault of yours; (b) was rightfully known to you prior to the time of its disclosure, or to have been independently developed by you without use of Confidential Information; and/or © is subsequently learned from a third party not under a confidentiality obligation with respect to such Confidential Information. Confidential Information that is required to be disclosed by you pursuant to a duly authorized subpoena, court order, or government authority shall continue to be Confidential Information for all other purposes and you agree, prior to disclosing pursuant to a subpoena, court order, or government authority, to provide prompt written notice and assistance to Life Technologies prior to such disclosure, so that Life Technologies may seek a protective order or other appropriate remedy to protect against disclosure. SOFTWARE IMPROVEMENTS -You acknowledge and agree that any ideas, enhancements, modifications, -and the like disclosed by you to Life Technologies with respect to the -Software ("Software Improvements and Feedback") will be the property of -Life Technologies. You agree to assign, and hereby assign, all right, -title, and interest worldwide in the Software Improvements and Feedback -to Life Technologies and agree to assist Life Technologies, at Life -Technologies' expense, in perfecting and enforcing Life Technologies -rights thereto and ownership thereof. You acknowledge and agree that -Life Technologies may use such Software Improvements and Feedback for -its business purposes without restriction. +You acknowledge and agree that any ideas, enhancements, modifications, and the like disclosed by you to Life Technologies with respect to the Software ("Software Improvements and Feedback") will be the property of Life Technologies. You agree to assign, and hereby assign, all right, title, and interest worldwide in the Software Improvements and Feedback to Life Technologies and agree to assist Life Technologies, at Life Technologies' expense, in perfecting and enforcing Life Technologies rights thereto and ownership thereof. You acknowledge and agree that Life Technologies may use such Software Improvements and Feedback for its business purposes without restriction. GENERAL -This Agreement shall be governed by laws of the State of California, -exclusive of its conflict of laws provisions. This Agreement shall not -be governed by the United Nations Convention on Contracts for the -International Sale of Goods. This Agreement contains the complete -agreement between the parties with respect to the subject matter hereof, -and supersedes all prior or contemporaneous agreements or -understandings, whether oral or written. If any provision of this -Agreement is held by a court of competent jurisdiction to be contrary to -law, that provision will be enforced to the maximum extent permissible -and the remaining provisions of this Agreement will remain in full force -and effect. The controlling language of this Agreement, and any -proceedings relating to this Agreement, shall be English. You agree to -bear any and all costs of translation, if necessary. The headings to the -sections of this Agreement are used for convenience only and shall have -no substantive meaning. All questions concerning this Agreement shall be -directed to: Life Technologies Corporation, 5781 Van Allen Way, -Carlsbad, CA 92008, Attention: Legal Department. - -Unpublished rights reserved under the copyright laws of the United -States. Life Technologies Corporation, 5781 Van Allen Way, Carlsbad, CA -92008. - -Life Technologies is a trademark of Life Technologies Corporation or its -subsidiaries in the U.S. and certain other countries. - +This Agreement shall be governed by laws of the State of California, exclusive of its conflict of laws provisions. This Agreement shall not be governed by the United Nations Convention on Contracts for the International Sale of Goods. This Agreement contains the complete agreement between the parties with respect to the subject matter hereof, and supersedes all prior or contemporaneous agreements or understandings, whether oral or written. If any provision of this Agreement is held by a court of competent jurisdiction to be contrary to law, that provision will be enforced to the maximum extent permissible and the remaining provisions of this Agreement will remain in full force and effect. The controlling language of this Agreement, and any proceedings relating to this Agreement, shall be English. You agree to bear any and all costs of translation, if necessary. The headings to the sections of this Agreement are used for convenience only and shall have no substantive meaning. All questions concerning this Agreement shall be directed to: Life Technologies Corporation, 5781 Van Allen Way, Carlsbad, CA 92008, Attention: Legal Department. +Unpublished rights reserved under the copyright laws of the United States. Life Technologies Corporation, 5781 Van Allen Way, Carlsbad, CA 92008. +Life Technologies is a trademark of Life Technologies Corporation or its subsidiaries in the U.S. and certain other countries. All other trademarks are the sole property of their respective owners. -February 28, 2019 +July 15, 2020 Appendix 1 Life Technologies Corporation Third Party Copyright Notices and Licenses + SERVICE & SUPPORT TELEMETRY MODULE SOFTWARE VERSION 2.0.1 +This software uses third party software components from several sources. Portions of these software components are copyrighted and licensed by their respective owners as indicated below. Various licenses require distribution of source code or if a link is used to point the end-user to a source-code repository, and the source code is not available at such site, the distributor must, for a time determined by license, offer to provide source code. In such cases, please contact your Life Technologies representative. As well, various licenses require that the end-user receive a copy of the license or certain notices. Such licenses and notices may be found in this appendix. -SERVICE & SUPPORT TELEMETRY MODULE SOFTWARE VERSION 2.0.1 - -This software uses third party software components from several sources. -Portions of these software components are copyrighted and licensed by -their respective owners as indicated below. Various licenses require -distribution of source code or if a link is used to point the end-user -to a source-code repository, and the source code is not available at -such site, the distributor must, for a time determined by license, offer -to provide source code. In such cases, please contact your Life -Technologies representative. As well, various licenses require that the -end-user receive a copy of the license or certain notices. Such licenses -and notices may be found in this appendix. - -**Asn1crypto Copyright (c) 2015-2018 Will Bond** +Asn1crypto Copyright © 2015-2018 Will Bond +Six Copyright © 2010-2018 Benjamin Peterson -**Six Copyright (c) 2010-2018 Benjamin Peterson** - **The MIT License** - - Permission is hereby granted, free of charge, to any person obtaining a copy of - this software and associated documentation files (the "Software"), to deal in - the Software without restriction, including without limitation the rights to - use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies - of the Software, and to permit persons to whom the Software is furnished to do - so, subject to the following conditions: +The MIT License - The above copyright notice and this permission notice shall be included in all - copies or substantial portions of the Software. +Permission is hereby granted, free of charge, to any person obtaining a copy of + this software and associated documentation files (the "Software"), to deal in + the Software without restriction, including without limitation the rights to + use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies + of the Software, and to permit persons to whom the Software is furnished to do + so, subject to the following conditions: - THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE - SOFTWARE. + The above copyright notice and this permission notice shall be included in all + copies or substantial portions of the Software. + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE + SOFTWARE. -**Boto3** +Boto3 -**Botocore** +Botocore -**Pelix** +Pelix -**S3transfer** +S3transfer Apache License -============== -### Version 2.0, January 2004 +Version 2.0, January 2004 TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION -1\. Definitions. - -"License" shall mean the terms and conditions for use, reproduction, and -distribution as defined by Sections 1 through 9 of this document. - -"Licensor" shall mean the copyright owner or entity authorized by the -copyright owner that is granting the License. - -"Legal Entity" shall mean the union of the acting entity and all other -entities that control, are controlled by, or are under common control -with that entity. For the purposes of this definition, "control" means -(i) the power, direct or indirect, to cause the direction or management -of such entity, whether by contract or otherwise, or (ii) ownership of -fifty percent (50%) or more of the outstanding shares, or (iii) -beneficial ownership of such entity. - -"You" (or "Your") shall mean an individual or Legal Entity exercising -permissions granted by this License. - -"Source" form shall mean the preferred form for making modifications, -including but not limited to software source code, documentation source, -and configuration files. - -"Object" form shall mean any form resulting from mechanical -transformation or translation of a Source form, including but not -limited to compiled object code, generated documentation, and -conversions to other media types. - -"Work" shall mean the work of authorship, whether in Source or Object -form, made available under the License, as indicated by a copyright -notice that is included in or attached to the work (an example is -provided in the Appendix below). - -"Derivative Works" shall mean any work, whether in Source or Object -form, that is based on (or derived from) the Work and for which the -editorial revisions, annotations, elaborations, or other modifications -represent, as a whole, an original work of authorship. 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This License Agreement does not grant permission to use PSF - trademarks or trade name in a trademark sense to endorse or promote - products or services of Licensee, or any third party. - - 8. By copying, installing or otherwise using Python, Licensee - agrees to be bound by the terms and conditions of this License - Agreement. - - -**Paho** +1. Definitions. +"License" shall mean the terms and conditions for use, reproduction, and distribution as defined by Sections 1 through 9 of this document. +"Licensor" shall mean the copyright owner or entity authorized by the copyright owner that is granting the License. +"Legal Entity" shall mean the union of the acting entity and all other entities that control, are controlled by, or are under common control with that entity. For the purposes of this definition, "control" means (i) the power, direct or indirect, to cause the direction or management of such entity, whether by contract or otherwise, or (ii) ownership of fifty percent (50%) or more of the outstanding shares, or (iii) beneficial ownership of such entity. +"You" (or "Your") shall mean an individual or Legal Entity exercising permissions granted by this License. +"Source" form shall mean the preferred form for making modifications, including but not limited to software source code, documentation source, and configuration files. +"Object" form shall mean any form resulting from mechanical transformation or translation of a Source form, including but not limited to compiled object code, generated documentation, and conversions to other media types. +"Work" shall mean the work of authorship, whether in Source or Object form, made available under the License, as indicated by a copyright notice that is included in or attached to the work (an example is provided in the Appendix below). +"Derivative Works" shall mean any work, whether in Source or Object form, that is based on (or derived from) the Work and for which the editorial revisions, annotations, elaborations, or other modifications represent, as a whole, an original work of authorship. For the purposes of this License, Derivative Works shall not include works that remain separable from, or merely link (or bind by name) to the interfaces of, the Work and Derivative Works thereof. +"Contribution" shall mean any work of authorship, including the original version of the Work and any modifications or additions to that Work or Derivative Works thereof, that is intentionally submitted to Licensor for inclusion in the Work by the copyright owner or by an individual or Legal Entity authorized to submit on behalf of the copyright owner. For the purposes of this definition, "submitted" means any form of electronic, verbal, or written communication sent to the Licensor or its representatives, including but not limited to communication on electronic mailing lists, source code control systems, and issue tracking systems that are managed by, or on behalf of, the Licensor for the purpose of discussing and improving the Work, but excluding communication that is conspicuously marked or otherwise designated in writing by the copyright owner as "Not a Contribution." +"Contributor" shall mean Licensor and any individual or Legal Entity on behalf of whom a Contribution has been received by Licensor and subsequently incorporated within the Work. +2. Grant of Copyright License. Subject to the terms and conditions of this License, each Contributor hereby grants to You a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable copyright license to reproduce, prepare Derivative Works of, publicly display, publicly perform, sublicense, and distribute the Work and such Derivative Works in Source or Object form. +3. Grant of Patent License. Subject to the terms and conditions of this License, each Contributor hereby grants to You a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable (except as stated in this section) patent license to make, have made, use, offer to sell, sell, import, and otherwise transfer the Work, where such license applies only to those patent claims licensable by such Contributor that are necessarily infringed by their Contribution(s) alone or by combination of their Contribution(s) with the Work to which such Contribution(s) was submitted. If You institute patent litigation against any entity (including a cross-claim or counterclaim in a lawsuit) alleging that the Work or a Contribution incorporated within the Work constitutes direct or contributory patent infringement, then any patent licenses granted to You under this License for that Work shall terminate as of the date such litigation is filed. +4. Redistribution. You may reproduce and distribute copies of the Work or Derivative Works thereof in any medium, with or without modifications, and in Source or Object form, provided that You meet the following conditions: +1. You must give any other recipients of the Work or Derivative Works a copy of this License; and +2. You must cause any modified files to carry prominent notices stating that You changed the files; and +3. You must retain, in the Source form of any Derivative Works that You distribute, all copyright, patent, trademark, and attribution notices from the Source form of the Work, excluding those notices that do not pertain to any part of the Derivative Works; and +4. If the Work includes a "NOTICE" text file as part of its distribution, then any Derivative Works that You distribute must include a readable copy of the attribution notices contained within such NOTICE file, excluding those notices that do not pertain to any part of the Derivative Works, in at least one of the following places: within a NOTICE text file distributed as part of the Derivative Works; within the Source form or documentation, if provided along with the Derivative Works; or, within a display generated by the Derivative Works, if and wherever such third-party notices normally appear. The contents of the NOTICE file are for informational purposes only and do not modify the License. You may add Your own attribution notices within Derivative Works that You distribute, alongside or as an addendum to the NOTICE text from the Work, provided that such additional attribution notices cannot be construed as modifying the License. +You may add Your own copyright statement to Your modifications and may provide additional or different license terms and conditions for use, reproduction, or distribution of Your modifications, or for any such Derivative Works as a whole, provided Your use, reproduction, and distribution of the Work otherwise complies with the conditions stated in this License. +5. Submission of Contributions. Unless You explicitly state otherwise, any Contribution intentionally submitted for inclusion in the Work by You to the Licensor shall be under the terms and conditions of this License, without any additional terms or conditions. Notwithstanding the above, nothing herein shall supersede or modify the terms of any separate license agreement you may have executed with Licensor regarding such Contributions. +6. Trademarks. This License does not grant permission to use the trade names, trademarks, service marks, or product names of the Licensor, except as required for reasonable and customary use in describing the origin of the Work and reproducing the content of the NOTICE file. +7. Disclaimer of Warranty. Unless required by applicable law or agreed to in writing, Licensor provides the Work (and each Contributor provides its Contributions) on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied, including, without limitation, any warranties or conditions of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A PARTICULAR PURPOSE. You are solely responsible for determining the appropriateness of using or redistributing the Work and assume any risks associated with Your exercise of permissions under this License. +8. Limitation of Liability. In no event and under no legal theory, whether in tort (including negligence), contract, or otherwise, unless required by applicable law (such as deliberate and grossly negligent acts) or agreed to in writing, shall any Contributor be liable to You for damages, including any direct, indirect, special, incidental, or consequential damages of any character arising as a result of this License or out of the use or inability to use the Work (including but not limited to damages for loss of goodwill, work stoppage, computer failure or malfunction, or any and all other commercial damages or losses), even if such Contributor has been advised of the possibility of such damages. +9. Accepting Warranty or Additional Liability. While redistributing the Work or Derivative Works thereof, You may choose to offer, and charge a fee for, acceptance of support, warranty, indemnity, or other liability obligations and/or rights consistent with this License. However, in accepting such obligations, You may act only on Your own behalf and on Your sole responsibility, not on behalf of any other Contributor, and only if You agree to indemnify, defend, and hold each Contributor harmless for any liability incurred by, or claims asserted against, such Contributor by reason of your accepting any such warranty or additional liability. + +Concurrent + +The Python Software Foundation License Version 2 + + 1. This LICENSE AGREEMENT is between the Python Software Foundation + ("PSF"), and the Individual or Organization ("Licensee") accessing and + otherwise using this software ("Python") in source or binary form and + its associated documentation. + + 2. Subject to the terms and conditions of this License Agreement, PSF + hereby grants Licensee a nonexclusive, royalty-free, world-wide + license to reproduce, analyze, test, perform and/or display publicly, + prepare derivative works, distribute, and otherwise use Python + alone or in any derivative version, provided, however, that PSF's + License Agreement and PSF's notice of copyright, i.e., "Copyright © + 2001, 2002, 2003, 2004, 2005, 2006 Python Software Foundation; All Rights + Reserved" are retained in Python alone or in any derivative version + prepared by Licensee. + + 3. In the event Licensee prepares a derivative work that is based on + or incorporates Python or any part thereof, and wants to make + the derivative work available to others as provided herein, then + Licensee hereby agrees to include in any such work a brief summary of + the changes made to Python. + + 4. PSF is making Python available to Licensee on an "AS IS" + basis. PSF MAKES NO REPRESENTATIONS OR WARRANTIES, EXPRESS OR + IMPLIED. BY WAY OF EXAMPLE, BUT NOT LIMITATION, PSF MAKES NO AND + DISCLAIMS ANY REPRESENTATION OR WARRANTY OF MERCHANTABILITY OR FITNESS + FOR ANY PARTICULAR PURPOSE OR THAT THE USE OF PYTHON WILL NOT + INFRINGE ANY THIRD PARTY RIGHTS. + + 5. PSF SHALL NOT BE LIABLE TO LICENSEE OR ANY OTHER USERS OF PYTHON + FOR ANY INCIDENTAL, SPECIAL, OR CONSEQUENTIAL DAMAGES OR LOSS AS + A RESULT OF MODIFYING, DISTRIBUTING, OR OTHERWISE USING PYTHON, + OR ANY DERIVATIVE THEREOF, EVEN IF ADVISED OF THE POSSIBILITY THEREOF. + + 6. This License Agreement will automatically terminate upon a material + breach of its terms and conditions. + + 7. Nothing in this License Agreement shall be deemed to create any + relationship of agency, partnership, or joint venture between PSF and + Licensee. This License Agreement does not grant permission to use PSF + trademarks or trade name in a trademark sense to endorse or promote + products or services of Licensee, or any third party. + + 8. By copying, installing or otherwise using Python, Licensee + agrees to be bound by the terms and conditions of this License + Agreement. + +Paho Eclipse Distribution License - v 1.0 -==================================== -**Copyright (c) 2007, Eclipse Foundation, Inc. and its licensors.** +Copyright © 2007, Eclipse Foundation, Inc. and its licensors. All rights reserved. -Redistribution and use in source and binary forms, with or without -modification, are permitted provided that the following conditions are -met: +Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: -- Redistributions of source code must retain the above copyright - notice, this list of conditions and the following disclaimer. +* Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. +* Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. +* Neither the name of the Eclipse Foundation, Inc. nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. 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IN NO EVENT SHALL THE COPYRIGHT OWNER -OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, -EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, -PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR -PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF -LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING -NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +THE ACCOMPANYING PROGRAM IS PROVIDED UNDER THE TERMS OF THIS ECLIPSE PUBLIC LICENSE ("AGREEMENT"). ANY USE, REPRODUCTION OR DISTRIBUTION OF THE PROGRAM CONSTITUTES RECIPIENT'S ACCEPTANCE OF THIS AGREEMENT. -**AND** +1. DEFINITIONS -Eclipse Public License - v 1.0 -============================== -THE ACCOMPANYING PROGRAM IS PROVIDED UNDER THE TERMS OF THIS ECLIPSE -PUBLIC LICENSE ("AGREEMENT"). 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Contributions do not include additions to the Program which: (i) are separate modules of software distributed in conjunction with the Program under their own license agreement, and (ii) are not derivative works of the Program. +"Contributor" means any person or entity that distributes the Program. +"Licensed Patents " mean patent claims licensable by a Contributor which are necessarily infringed by the use or sale of its Contribution alone or when combined with the Program. +"Program" means the Contributions distributed in accordance with this Agreement. +"Recipient" means anyone who receives the Program under this Agreement, including all Contributors. -ii)additions to the Program; +2. GRANT OF RIGHTS -where such changes and/or additions to the Program originate from and -are distributed by that particular Contributor. 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This patent license shall apply to the combination of the Contribution and the Program if, at the time the Contribution is added by the Contributor, such addition of the Contribution causes such combination to be covered by the Licensed Patents. The patent license shall not apply to any other combinations which include the Contribution. No hardware per se is licensed hereunder. -"Program" means the Contributions distributed in accordance with this -Agreement. + c) Recipient understands that although each Contributor grants the licenses to its Contributions set forth herein, no assurances are provided by any Contributor that the Program does not infringe the patent or other intellectual property rights of any other entity. Each Contributor disclaims any liability to Recipient for claims brought by any other entity based on infringement of intellectual property rights or otherwise. As a condition to exercising the rights and licenses granted hereunder, each Recipient hereby assumes sole responsibility to secure any other intellectual property rights needed, if any. For example, if a third party patent license is required to allow Recipient to distribute the Program, it is Recipient's responsibility to acquire that license before distributing the Program. +d) Each Contributor represents that to its knowledge it has sufficient copyright rights in its Contribution, if any, to grant the copyright license set forth in this Agreement. + +3. REQUIREMENTS + + A Contributor may choose to distribute the Program in object code form under its own license agreement, provided that: + + a) it complies with the terms and conditions of this Agreement; and -"Recipient" means anyone who receives the Program under this Agreement, -including all Contributors. - -**2. 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When the Program is made available in source code form: -a) it must be made available under this Agreement; and - -b) a copy of this Agreement must be included with each copy of the -Program. - -Contributors may not remove or alter any copyright notices contained -within the Program. - -Each Contributor must identify itself as the originator of its -Contribution, if any, in a manner that reasonably allows subsequent -Recipients to identify the originator of the Contribution. - -**4. COMMERCIAL DISTRIBUTION** - -Commercial distributors of software may accept certain responsibilities -with respect to end users, business partners and the like. While this -license is intended to facilitate the commercial use of the Program, the -Contributor who includes the Program in a commercial product offering -should do so in a manner which does not create potential liability for -other Contributors. Therefore, if a Contributor includes the Program in -a commercial product offering, such Contributor ("Commercial -Contributor") hereby agrees to defend and indemnify every other -Contributor ("Indemnified Contributor") against any losses, damages and -costs (collectively "Losses") arising from claims, lawsuits and other -legal actions brought by a third party against the Indemnified -Contributor to the extent caused by the acts or omissions of such -Commercial Contributor in connection with its distribution of the -Program in a commercial product offering. The obligations in this -section do not apply to any claims or Losses relating to any actual or -alleged intellectual property infringement. In order to qualify, an -Indemnified Contributor must: a) promptly notify the Commercial -Contributor in writing of such claim, and b) allow the Commercial -Contributor to control, and cooperate with the Commercial Contributor -in, the defense and any related settlement negotiations. The Indemnified -Contributor may participate in any such claim at its own expense. - -For example, a Contributor might include the Program in a commercial -product offering, Product X. That Contributor is then a Commercial -Contributor. If that Commercial Contributor then makes performance -claims, or offers warranties related to Product X, those performance -claims and warranties are such Commercial Contributor's responsibility -alone. Under this section, the Commercial Contributor would have to -defend claims against the other Contributors related to those -performance claims and warranties, and if a court requires any other -Contributor to pay any damages as a result, the Commercial Contributor -must pay those damages. - -**5. NO WARRANTY** - -EXCEPT AS EXPRESSLY SET FORTH IN THIS AGREEMENT, THE PROGRAM IS PROVIDED -ON AN "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, -EITHER EXPRESS OR IMPLIED INCLUDING, WITHOUT LIMITATION, ANY WARRANTIES -OR CONDITIONS OF TITLE, NON-INFRINGEMENT, MERCHANTABILITY OR FITNESS FOR -A PARTICULAR PURPOSE. Each Recipient is solely responsible for -determining the appropriateness of using and distributing the Program -and assumes all risks associated with its exercise of rights under this -Agreement , including but not limited to the risks and costs of program -errors, compliance with applicable laws, damage to or loss of data, -programs or equipment, and unavailability or interruption of operations. - -**6. DISCLAIMER OF LIABILITY** - -EXCEPT AS EXPRESSLY SET FORTH IN THIS AGREEMENT, NEITHER RECIPIENT NOR -ANY CONTRIBUTORS SHALL HAVE ANY LIABILITY FOR ANY DIRECT, INDIRECT, -INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING -WITHOUT LIMITATION LOST PROFITS), HOWEVER CAUSED AND ON ANY THEORY OF -LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING -NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OR -DISTRIBUTION OF THE PROGRAM OR THE EXERCISE OF ANY RIGHTS GRANTED -HEREUNDER, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. - -**7. GENERAL** - -If any provision of this Agreement is invalid or unenforceable under -applicable law, it shall not affect the validity or enforceability of -the remainder of the terms of this Agreement, and without further action -by the parties hereto, such provision shall be reformed to the minimum -extent necessary to make such provision valid and enforceable. - -If Recipient institutes patent litigation against any entity (including -a cross-claim or counterclaim in a lawsuit) alleging that the Program -itself (excluding combinations of the Program with other software or -hardware) infringes such Recipient's patent(s), then such Recipient's -rights granted under Section 2(b) shall terminate as of the date such -litigation is filed. - -All Recipient's rights under this Agreement shall terminate if it fails -to comply with any of the material terms or conditions of this Agreement -and does not cure such failure in a reasonable period of time after -becoming aware of such noncompliance. If all Recipient's rights under -this Agreement terminate, Recipient agrees to cease use and distribution -of the Program as soon as reasonably practicable. However, Recipient's -obligations under this Agreement and any licenses granted by Recipient -relating to the Program shall continue and survive. - -Everyone is permitted to copy and distribute copies of this Agreement, -but in order to avoid inconsistency the Agreement is copyrighted and may -only be modified in the following manner. The Agreement Steward reserves -the right to publish new versions (including revisions) of this -Agreement from time to time. No one other than the Agreement Steward has -the right to modify this Agreement. The Eclipse Foundation is the -initial Agreement Steward. The Eclipse Foundation may assign the -responsibility to serve as the Agreement Steward to a suitable separate -entity. Each new version of the Agreement will be given a distinguishing -version number. The Program (including Contributions) may always be -distributed subject to the version of the Agreement under which it was -received. In addition, after a new version of the Agreement is -published, Contributor may elect to distribute the Program (including -its Contributions) under the new version. Except as expressly stated in -Sections 2(a) and 2(b) above, Recipient receives no rights or licenses -to the intellectual property of any Contributor under this Agreement, -whether expressly, by implication, estoppel or otherwise. All rights in -the Program not expressly granted under this Agreement are reserved. - -This Agreement is governed by the laws of the State of New York and the -intellectual property laws of the United States of America. No party to -this Agreement will bring a legal action under this Agreement more than -one year after the cause of action arose. Each party waives its rights -to a jury trial in any resulting litigation. - -**Docutils** - -Public Domain Dedication -======================== - -The persons who have associated their work with this project (the -"Dedicator": David Goodger and the many contributors to the Docutils -project) hereby dedicate the entire copyright, less -the [exceptions](http://docutils.sourceforge.net/COPYING.html#exceptions) listed -below, in the work of authorship known as "Docutils" identified below -(the "Work") to the public domain. - -The primary repository for the Work is the Internet World Wide Web site -<>. The Work consists of the -files within the "docutils" module of the Docutils project Subversion -repository (Internet host docutils.svn.sourceforge.net, filesystem path -/svnroot/docutils), whose Internet web interface is located at -<>. Files -dedicated to the public domain may be identified by the inclusion, near -the beginning of each file, of a declaration of the form: - -Copyright: This document/module/DTD/stylesheet/file/etc. has been placed in the public domain. - -Dedicator makes this dedication for the benefit of the public at large -and to the detriment of Dedicator's heirs and successors. Dedicator -intends this dedication to be an overt act of relinquishment in -perpetuity of all present and future rights under copyright law, whether -vested or contingent, in the Work. Dedicator understands that such -relinquishment of all rights includes the relinquishment of all rights -to enforce (by lawsuit or otherwise) those copyrights in the Work. - -Dedicator recognizes that, once placed in the public domain, the Work -may be freely reproduced, distributed, transmitted, used, modified, -built upon, or otherwise exploited by anyone for any purpose, commercial -or non-commercial, and in any way, including by methods that have not -yet been invented or conceived. - -**Dateutil** - -Copyright (c) 2003-2011 - Gustavo Niemeyer <gustavo@niemeyer.net> - -Copyright (c) 2012-2014 - Tomi Pievilainen -<tomi.pievilainen@iki.fi> - -Copyright (c) 2014 - Yaron de Leeuw <me@jarondl.net> + a) it must be made available under this Agreement; and -All rights reserved. + b) a copy of this Agreement must be included with each copy of the Program. + Contributors may not remove or alter any copyright notices contained within the Program. + Each Contributor must identify itself as the originator of its Contribution, if any, in a manner that reasonably allows subsequent Recipients to identify the originator of the Contribution. -Redistribution and use in source and binary forms, with or without +4. COMMERCIAL DISTRIBUTION -modification, are permitted provided that the following conditions are -met: + Commercial distributors of software may accept certain responsibilities with respect to end users, business partners and the like. While this license is intended to facilitate the commercial use of the Program, the Contributor who includes the Program in a commercial product offering should do so in a manner which does not create potential liability for other Contributors. Therefore, if a Contributor includes the Program in a commercial product offering, such Contributor ("Commercial Contributor") hereby agrees to defend and indemnify every other Contributor ("Indemnified Contributor") against any losses, damages and costs (collectively "Losses") arising from claims, lawsuits and other legal actions brought by a third party against the Indemnified Contributor to the extent caused by the acts or omissions of such Commercial Contributor in connection with its distribution of the Program in a commercial product offering. The obligations in this section do not apply to any claims or Losses relating to any actual or alleged intellectual property infringement. In order to qualify, an Indemnified Contributor must: a) promptly notify the Commercial Contributor in writing of such claim, and b) allow the Commercial Contributor to control, and cooperate with the Commercial Contributor in, the defense and any related settlement negotiations. The Indemnified Contributor may participate in any such claim at its own expense. + For example, a Contributor might include the Program in a commercial product offering, Product X. That Contributor is then a Commercial Contributor. If that Commercial Contributor then makes performance claims, or offers warranties related to Product X, those performance claims and warranties are such Commercial Contributor's responsibility alone. Under this section, the Commercial Contributor would have to defend claims against the other Contributors related to those performance claims and warranties, and if a court requires any other Contributor to pay any damages as a result, the Commercial Contributor must pay those damages. -* Redistributions of source code must retain the above copyright -notice,this list of conditions and the following disclaimer. +5. NO WARRANTY -* Redistributions in binary form must reproduce the above copyright -notice, this list of conditions and the following disclaimer in the -documentation and/or other materials provided with the distribution. + EXCEPT AS EXPRESSLY SET FORTH IN THIS AGREEMENT, THE PROGRAM IS PROVIDED ON AN "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, EITHER EXPRESS OR IMPLIED INCLUDING, WITHOUT LIMITATION, ANY WARRANTIES OR CONDITIONS OF TITLE, NON-INFRINGEMENT, MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. Each Recipient is solely responsible for determining the appropriateness of using and distributing the Program and assumes all risks associated with its exercise of rights under this Agreement , including but not limited to the risks and costs of program errors, compliance with applicable laws, damage to or loss of data, programs or equipment, and unavailability or interruption of operations. -* Neither the name of the copyright holder nor the names of its -contributors may be used to endorse or promote products derived from -this software without specific prior written permission. +6. DISCLAIMER OF LIABILITY -THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS + EXCEPT AS EXPRESSLY SET FORTH IN THIS AGREEMENT, NEITHER RECIPIENT NOR ANY CONTRIBUTORS SHALL HAVE ANY LIABILITY FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING WITHOUT LIMITATION LOST PROFITS), HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OR DISTRIBUTION OF THE PROGRAM OR THE EXERCISE OF ANY RIGHTS GRANTED HEREUNDER, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. + +7. GENERAL + + If any provision of this Agreement is invalid or unenforceable under applicable law, it shall not affect the validity or enforceability of the remainder of the terms of this Agreement, and without further action by the parties hereto, such provision shall be reformed to the minimum extent necessary to make such provision valid and enforceable. + + If Recipient institutes patent litigation against any entity (including a cross-claim or counterclaim in a lawsuit) alleging that the Program itself (excluding combinations of the Program with other software or hardware) infringes such Recipient's patent(s), then such Recipient's rights granted under Section 2(b) shall terminate as of the date such litigation is filed. + + All Recipient's rights under this Agreement shall terminate if it fails to comply with any of the material terms or conditions of this Agreement and does not cure such failure in a reasonable period of time after becoming aware of such noncompliance. If all Recipient's rights under this Agreement terminate, Recipient agrees to cease use and distribution of the Program as soon as reasonably practicable. However, Recipient's obligations under this Agreement and any licenses granted by Recipient relating to the Program shall continue and survive. +Everyone is permitted to copy and distribute copies of this Agreement, but in order to avoid inconsistency the Agreement is copyrighted and may only be modified in the following manner. The Agreement Steward reserves the right to publish new versions (including revisions) of this Agreement from time to time. No one other than the Agreement Steward has the right to modify this Agreement. The Eclipse Foundation is the initial Agreement Steward. The Eclipse Foundation may assign the responsibility to serve as the Agreement Steward to a suitable separate entity. Each new version of the Agreement will be given a distinguishing version number. The Program (including Contributions) may always be distributed subject to the version of the Agreement under which it was received. In addition, after a new version of the Agreement is published, Contributor may elect to distribute the Program (including its Contributions) under the new version. Except as expressly stated in Sections 2(a) and 2(b) above, Recipient receives no rights or licenses to the intellectual property of any Contributor under this Agreement, whether expressly, by implication, estoppel or otherwise. All rights in the Program not expressly granted under this Agreement are reserved. + + This Agreement is governed by the laws of the State of New York and the intellectual property laws of the United States of America. No party to this Agreement will bring a legal action under this Agreement more than one year after the cause of action arose. Each party waives its rights to a jury trial in any resulting litigation. + +## Docutils + + Public Domain Dedication + + The persons who have associated their work with this project (the "Dedicator": David Goodger and the many contributors to the Docutils project) hereby dedicate the entire copyright, less the exceptions listed below, in the work of authorship known as "Docutils" identified below (the "Work") to the public domain. + + The primary repository for the Work is the Internet World Wide Web site . The Work consists of the files within the "docutils" module of the Docutils project Subversion repository (Internet host docutils.svn.sourceforge.net, filesystem path /svnroot/docutils), whose Internet web interface is located at . Files dedicated to the public domain may be identified by the inclusion, near the beginning of each file, of a declaration of the form: + + Copyright: This document/module/DTD/stylesheet/file/etc. has been + placed in the public domain. + + Dedicator makes this dedication for the benefit of the public at large and to the detriment of Dedicator's heirs and successors. Dedicator intends this dedication to be an overt act of relinquishment in perpetuity of all present and future rights under copyright law, whether vested or contingent, in the Work. Dedicator understands that such relinquishment of all rights includes the relinquishment of all rights to enforce (by lawsuit or otherwise) those copyrights in the Work. + + Dedicator recognizes that, once placed in the public domain, the Work may be freely reproduced, distributed, transmitted, used, modified, built upon, or otherwise exploited by anyone for any purpose, commercial or non-commercial, and in any way, including by methods that have not yet been invented or conceived. + +## Dateutil + + Copyright © 2003-2011 - Gustavo Niemeyer + + Copyright © 2012-2014 - Tomi Pievilainen + + Copyright © 2014 - Yaron de Leeuw + + All rights reserved. + + Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + * Redistributions of source code must retain the above copyright notice, + this list of conditions and the following disclaimer. + * Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + * Neither the name of the copyright holder nor the names of its + contributors may be used to endorse or promote products derived from + this software without specific prior written permission. + + THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR -A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT -OWNER OR +A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR @@ -2561,9 +1396,9 @@ LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -**Enum** +## Enum -Copyright (c) 2013, Ethan Furman. +Copyright © 2013, Ethan Furman. All rights reserved. @@ -2571,36 +1406,35 @@ Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: -Redistributions of source code must retain the above -copyright notice, this list of conditions and the -following disclaimer. - -Redistributions in binary form must reproduce the above -copyright notice, this list of conditions and the following -disclaimer in the documentation and/or other materials -provided with the distribution. - -Neither the name Ethan Furman nor the names of any -contributors may be used to endorse or promote products -derived from this software without specific prior written -permission. - -THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS -IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, -THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR -PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS -BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR + Redistributions of source code must retain the above + copyright notice, this list of conditions and the + following disclaimer. + + Redistributions in binary form must reproduce the above + copyright notice, this list of conditions and the following + disclaimer in the documentation and/or other materials + provided with the distribution. + + Neither the name Ethan Furman nor the names of any + contributors may be used to endorse or promote products + derived from this software without specific prior written + permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE +LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) -ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF -THE POSSIBILITY OF SUCH DAMAGE. +ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE +POSSIBILITY OF SUCH DAMAGE. -**Jmespath** +## Jmespath -Copyright (c) 2013 Amazon.com, Inc. or its affiliates. All Rights -Reserved +Copyright © 2013 Amazon.com, Inc. or its affiliates. All Rights Reserved Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the @@ -2614,67 +1448,4785 @@ The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS -OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT +OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABIL- +ITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. -**Oscrypto** +## Oscrypto -Copyright (c) 2015-2018 Will Bond <will@wbond.net> +Copyright © 2015-2018 Will Bond -Permission is hereby granted, free of charge, to any person obtaining a -copy of this software and associated documentation files (the "Software"), to -deal in the Software without restriction, including without limitation the -rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies - -of the Software, and to permit persons to whom the Software is furnished -to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included -in all copies or substantial portions of the Software. +Permission is hereby granted, free of charge, to any person obtaining a copy of +this software and associated documentation files (the "Software"), to deal in +the Software without restriction, including without limitation the rights to +use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies +of the Software, and to permit persons to whom the Software is furnished to do +so, subject to the following conditions: -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS -OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL -THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING -FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS -IN THE SOFTWARE. +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. -**Pubsub** +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. -Copyright (c) since 2006, Oliver Schoenborn +## Pubsub +Copyright © since 2006, Oliver Schoenborn All rights reserved. Redistribution and use in source and binary forms, with or without -modification, are permitted provided that the following conditions are -met: +modification, are permitted provided that the following conditions are met: -1. Redistributions of source code must retain the above copyright -notice, this -list of conditions and the following disclaimer. +1. Redistributions of source code must retain the above copyright notice, this + list of conditions and the following disclaimer. +2. Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR +ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES +(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; +LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND +ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +###END OF (2) SERVICE & SUPPORT TELEMETRY MODULE SOFTWARE VERSION 2.0.1 END USER LICENSE AGREEMENT +**************************************************** +(3) BEGINS: +======================================== + + +LIFE TECHNOLOGIES CORPORATION + +END USER LICENSE AGREEMENT and LIMITED PRODUCT WARRANTY + +FOR ION CHEF™ INSTRUMENT SOFTWARE VERSION 5.18 INSTRUMENT OPERATING SOFTWARE + +NOTICE TO USER: PLEASE READ THIS DOCUMENT CAREFULLY. THIS IS THE CONTRACT BETWEEN YOU AND LIFE TECHNOLOGIES CORPORATION ("LIFE TECHNOLOGIES") REGARDING THE OPERATING SOFTWARE FOR YOUR LIFE TECHNOLOGIES WORKSTATION OR OTHER INSTRUMENT AND BUNDLED SOFTWARE INSTALLED WITH YOUR OPERATING SOFTWARE. THIS AGREEMENT CONTAINS WARRANTY AND LIABILITY DISCLAIMERS AND LIMITATIONS. YOUR INSTALLATION AND USE OF THIS LIFE TECHNOLOGIES SOFTWARE IS SUBJECT TO THE TERMS AND CONDITIONS CONTAINED IN THIS END USER SOFTWARE LICENSE AGREEMENT, AND YOU WILL BE BOUND BY THESE TERMS AND CONDITIONS IF YOU INSTALL AND USE THE SOFTWARE. + +IF YOU DO NOT AGREE TO THESE TERMS AND CONDITIONS, YOU SHOULD PROMPTLY RETURN THIS SOFTWARE, TOGETHER WITH ALL PACKAGING, TO LIFE TECHNOLOGIES AND YOUR PURCHASE PRICE WILL BE REFUNDED. +This Life Technologies End User License Agreement accompanies a Life Technologies software product ("Software") and related explanatory materials ("Documentation"). The term "Software" also includes any upgrades, modified versions, updates, additions and copies of the Software licensed to you by Life Technologies. The term "License" or "Agreement" means this End User Software License Agreement. The term "you" or "Licensee" means the purchaser or user of this license to the Software. This Agreement includes herein by reference any additional use restrictions or Limited Use Label Licenses listed in or on user manuals, labeling, product inserts, technical notes, literature (including but not limited to Documentation) and/or splash screens related to this Software ("Supplemental Terms"). To the extent such Supplemental Terms are more restrictive than those contained herein, the more restrictive usage terms shall control. +This Software may use third-party software components from several sources. Portions of these software components are copyrighted and licensed by their respective owners. Various components require distribution of source code or if a URL is used to point the end-user to a source-code repository, and the source code is not available at such site, the distributor must, for a time determined by the license, offer to provide the source code. In such cases, please contact your Life Technologies representative. As well, various licenses require that the end-user receive a copy of the license. Such licenses, if any, may be found in Appendix 1 below. In order to use this Software, the end-user must abide by the terms and conditions of these third-party licenses. + +TITLE + +Title, ownership rights and intellectual property rights in and to the Software and Documentation shall at all times remain with Life Technologies and its subsidiaries, and their suppliers. 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You shall not copy, transfer (except temporarily in the event of a computer malfunction), rent, modify, distribute, electronically transmit, lend, lease, use, create derivative works based on the Software or merge the Software, or the associated Documentation, in whole or in part, whether alone or combined with any other products, except as expressly permitted in this Agreement. +2. You shall not reverse assemble, decompile, discover the source code or otherwise reverse engineer the Software. +3. You shall not remove any proprietary, copyright, trade secret or warning legend from the Software or any Documentation. +4. You agree to comply fully with all export laws and restrictions and regulations of the United States or applicable foreign agencies or authorities. You agree that you will not export or reexport, directly or indirectly, the Software and the Documentation into any country prohibited by the United States Export Administration Act and the regulations thereunder or other applicable United States law. +5. You may not use the Software or Documentation for the benefit of any third party by means of an outsourcing or service bureau relationship or for any similar commercial time-sharing or third-party training use. +6. You shall not sell, rent, transfer, resell for profit, or distribute this license or the Software, or any part thereof or any interest therein, unless the next user agrees to comply with the terms of this End User License Agreement. + +VERIFICATION + +At the written request of Life Technologies, not more frequently than annually, you shall furnish Life Technologies with a signed certification verifying that the Software is being used pursuant to the provisions of this License. + +TRIAL + +If this license is granted on a trial basis, you are hereby notified that license management software may be included to automatically cause the Software to cease functioning at the end of the trial period (and in any case you agree to discontinue usage at the end of the trial period or at the express written request of Life Technologies). + +TERMINATION + +You may terminate this Agreement by discontinuing use of the Software, removing all copies from your computers and storage media, and returning the Software and Documentation, and all copies thereof, to Life Technologies. Life Technologies may terminate this Agreement if you fail to comply with all of its terms, in which case you agree to discontinue using the Software, remove all copies from your computers and storage media, and return the Software and Documentation, and all copies thereof, to Life Technologies. + +U.S. GOVERNMENT END USERS + +The Software is a "commercial item," as that term is defined in 48 C.F.R. 2.101 (Oct. 1995), consisting of "commercial computer software" and "commercial computer software documentation," as such terms are used in 48 C.F.R. 12.212 (Sept. 1995). Consistent with 48 C.F.R. 12.212 and 48 C.F.R. 227.7202-1 through 227.7202-4 (June 1995), all U.S. Government End Users acquire the Software with only those rights set forth herein. + +EUROPEAN UNION END USERS + +If this Software is used within a country of the European Union, nothing in this Agreement shall be construed as restricting any rights available under Directive 2009/24/EC of the European Parliament and of the Council of 23 April 2009 on the legal protection of computer programs. + +LIMITED WARRANTY AND LIMITATION OF REMEDIES + +Limited Warranty. Life Technologies warrants that, except for Software provided on a trial basis, for a period of ninety days from the beginning of the applicable warranty period (as described below) the Software will, under normal use and as unmodified, function substantially in accordance with the functions and features described in the Documentation delivered with the Software when properly installed, and that for a period of ninety days from the beginning of the applicable warranty period (as described below) the tapes, CDs, diskettes or other media bearing the Software will be free of defects in materials and workmanship under normal use. +The above warranties do not apply to defects resulting from misuse, neglect, or accident, including without limitation: operation outside of the environmental or use specifications, or not in conformance with the instructions for any instrument system, software, or accessories; improper or inadequate maintenance by the user; installation of software or interfacing, or use in combination with software or products not supplied or authorized by Life Technologies; and modification or repair of the products not authorized by Life Technologies. +Warranty Period Commencement Date. 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You may not impose any further restrictions on the recipients' exercise of the rights granted herein. +You are not responsible for enforcing compliance by third parties to this License. + + +7. If, as a consequence of a court judgment or allegation of patent infringement or for any other reason (not limited to patent issues), conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot distribute so as to satisfy simultaneously your obligations under this +License and any other pertinent obligations, then as a consequence you +may not distribute the Program at all. For example, if a patent +license would not permit royalty-free redistribution of the Program by all those who receive copies directly or indirectly through you, then the only way you could satisfy both it and this License would be to refrain entirely from distribution of the Program. + + + If any portion of this section is held invalid or unenforceable under any particular circumstance, the balance of the section is intended to apply and the section as a whole is intended to apply in other circumstances. + + + It is not the purpose of this section to induce you to infringe any patents or other property right claims or to contest validity of any such claims; this section has the sole purpose of protecting the integrity of the free software distribution system, which is implemented by public license practices. Many people have made generous contributions to the wide range of software distributed through that system in reliance on consistent application of that system; it is up to the author/donor to decide if he or she is willing +to distribute software through any other system and a licensee cannot impose that choice. + + + This section is intended to make thoroughly clear what is believed to be a consequence of the rest of this License. + +8. If the distribution and/or use of the Program is restricted in certain countries either by patents or by copyrighted interfaces, the original copyright holder who places the Program under this License may add an explicit geographical distribution limitation excluding those countries, so that distribution is permitted only in or among countries not thus excluded. In such case, this License incorporates the limitation as if written in the body of this License. + + +9. The Free Software Foundation may publish revised and/or new versions of the General Public License from time to time. Such new versions will +be similar in spirit to the present version, but may differ in detail to address new problems or concerns. + + + Each version is given a distinguishing version number. If the Program specifies a version number of this License which applies to it and "any later version", you have the option of following the terms and conditions either of that version or of any later version published by the Free +Software Foundation. If the Program does not specify a version number of +this License, you may choose any version ever published by the Free Software +Foundation. + + +10. If you wish to incorporate parts of the Program into other free programs whose distribution conditions are different, write to the author to ask for permission. For software which is copyrighted by the Free +Software Foundation, write to the Free Software Foundation; we sometimes make exceptions for this. Our decision will be guided by the two goals +of preserving the free status of all derivatives of our free software and of promoting the sharing and reuse of software generally. + + + NO WARRANTY + + +11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED +OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, +REPAIR OR CORRECTION. + + +12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, +INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING +OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY +YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER +PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. + + +END OF TERMS AND CONDITIONS + +Mozilla Public License, v. 2.0 + +DHCP + +Mozilla Public License +Version 2.0 + +1. Definitions + + 1.1. "Contributor" +means each individual or legal entity that creates, contributes to the creation of, or owns Covered +Software. + + + 1.2. "Contributor Version" +means the combination of the Contributions of others (if any) used by a Contributor and that particular +Contributor's Contribution. + + + 1.3. "Contribution" +means Covered Software of a particular Contributor. + + + 1.4. "Covered Software" +means Source Code Form to which the initial Contributor has attached the notice in Exhibit A, the Executable Form of such Source Code Form, and Modifications of such Source Code Form, in each case including portions thereof. + + + 1.5. "Incompatible With Secondary Licenses" +means +that the initial Contributor has attached the notice described in Exhibit B to the Covered Software; or that the Covered Software was made available under the terms of version 1.1 or earlier of the License, +but not also under the terms of a Secondary License. + + + 1.6. "Executable Form" +means any form of the work other than Source Code Form. + + + 1.7. "Larger Work" +means a work that combines Covered Software with other material, in a separate file or files, that is not +Covered Software. + + + 1.8. "License" +means this document. + + + 1.9. "Licensable" +means having the right to grant, to the maximum extent possible, whether at the time of the initial grant or subsequently, any and all of the rights conveyed by this License. + + + 1.10. "Modifications" +means any of the following: + + any file in Source Code Form that results from an addition to, deletion from, or modification of the +contents of Covered Software; or + + + any new file in Source Code Form that contains any Covered Software. + + + 1.11. "Patent Claims" of a Contributor +means any patent claim(s), including without limitation, method, process, and apparatus claims, in any patent Licensable by such Contributor that would be infringed, but for the grant of the License, by the making, using, selling, offering for sale, having made, import, or transfer of either its Contributions or its Contributor Version. + + + 1.12. "Secondary License" +means either the GNU General Public License, Version 2.0, the GNU Lesser General Public License, Version 2.1, the GNU Affero General Public License, Version 3.0, or any later versions of those licenses. + + + 1.13. "Source Code Form" +means the form of the work preferred for making modifications. + + + 1.14. "You" (or "Your") +means an individual or a legal entity exercising rights under this License. For legal entities, "You" includes any entity that controls, is controlled by, or is under common control with You. For purposes of this definition, "control" means (a) the power, direct or indirect, to cause the direction or management of such entity, whether by contract or otherwise, or (b) ownership of more than fifty percent (50%) of the outstanding shares or beneficial ownership of such entity. + + +2. License Grants and Conditions + + 2.1. Grants + + Each Contributor hereby grants You a world-wide, royalty-free, non-exclusive license: + under intellectual property rights (other than patent or trademark) Licensable by such Contributor to use, reproduce, make available, modify, display, perform, distribute, and otherwise exploit its Contributions, either on an unmodified basis, with Modifications, or as part of a Larger Work; and under Patent Claims of such Contributor to make, use, sell, offer for sale, have made, import, and otherwise transfer either its Contributions or its Contributor Version. + + + 2.2. Effective Date + + The licenses granted in Section 2.1 with respect to any Contribution become effective for each +Contribution on the date the Contributor first distributes such Contribution. + + + 2.3. Limitations on Grant Scope + + The licenses granted in this Section 2 are the only rights granted under this License. No additional rights or licenses will be implied from the distribution or licensing of Covered Software under this License. Notwithstanding Section 2.1(b) above, no patent license is granted by a Contributor: +for any code that a Contributor has removed from Covered Software; or for infringements caused by: (i) Your and any other third party's modifications of Covered Software, or (ii) the combination of its Contributions with other software (except as part of its Contributor Version); or +under Patent Claims infringed by Covered Software in the absence of its Contributions. +T. his License does not grant any rights in the trademarks, service marks, or logos of any Contributor +(except as may be necessary to comply with the notice requirements in Section 3.4). + + + 2.4. Subsequent Licenses + + No Contributor makes additional grants as a result of Your choice to distribute the Covered Software under a subsequent version of this License (see Section 10.2) or under the terms of a Secondary License (if permitted under the terms of Section 3.3). + + + 2.5. Representation + + Each Contributor represents that the Contributor believes its Contributions are its original creation(s) or it has sufficient rights to grant the rights to its Contributions conveyed by this License. + + + 2.6. Fair Use + + This License is not intended to limit any rights You have under applicable copyright doctrines of fair use, fair dealing, or other equivalents. + + + 2.7. Conditions + + Sections 3.1, 3.2, 3.3, and 3.4 are conditions of the licenses granted in Section 2.1. + + +3. Responsibilities + + + 3.1. Distribution of Source Form + + All distribution of Covered Software in Source Code Form, including any Modifications that You create or to which You contribute, must be under the terms of this License. You must inform recipients that the Source Code Form of the Covered Software is governed by the terms of this License, and how they can obtain a copy of this License. You may not attempt to alter or restrict the recipients' rights in the Source Code Form. + + 3.2. Distribution of Executable Form + + If You distribute Covered Software in Executable Form then: + such Covered Software must also be made available in Source Code Form, as described in Section 3.1, and You must inform recipients of the Executable Form how they can obtain a copy of such Source Code Form by reasonable means in a timely manner, at a charge no more than the cost of distribution to the recipient; and +You may distribute such Executable Form under the terms of this License, or sublicense it under different terms, provided that the license for the Executable Form does not attempt to limit or alter the recipients' rights in the Source Code Form under this License. + + 3.3. Distribution of a Larger Work + + You may create and distribute a Larger Work under terms of Your choice, provided that You also comply with the requirements of this License for the Covered Software. If the Larger Work is a combination of Covered Software with a work governed by one or more Secondary Licenses, and the Covered Software is not Incompatible With Secondary Licenses, this License permits You to additionally distribute such Covered Software under the terms of such Secondary License(s), so that the recipient of the Larger Work may, at their option, further distribute the Covered Software under the terms of either this License or such Secondary License(s). + + + 3.4. Notices + + You may not remove or alter the substance of any license notices (including copyright notices, patent notices, disclaimers of warranty, or limitations of liability) contained within the Source Code Form of the Covered Software, except that You may alter any license notices to the extent required to remedy known factual inaccuracies. + + + 3.5. Application of Additional Terms + + You may choose to offer, and to charge a fee for, warranty, support, indemnity or liability obligations +to one or more recipients of Covered Software. However, You may do so only on Your own behalf, and not on behalf of any Contributor. You must make it absolutely clear that any such warranty, support, indemnity, or liability obligation is offered by You alone, and You hereby agree to indemnify every Contributor for any liability incurred by such Contributor as a result of warranty, support, indemnity or liability terms You offer. You may include additional disclaimers of warranty and limitations of +liability specific to any jurisdiction. + + +4. Inability to Comply Due to Statute or Regulation + + + If it is impossible for You to comply with any of the terms of this License with respect to some or all of the Covered Software due to statute, judicial order, or regulation then You must: (a) comply with the terms of this License to the maximum extent possible; and (b) describe the limitations and the code they affect. Such description must be placed in a text file included with all distributions of the Covered Software under this License. Except to the extent prohibited by statute or regulation, such description must be sufficiently detailed for a recipient of ordinary skill to be able to understand it. + + +5. Termination + + + 5.1. The rights granted under this License will terminate automatically if You fail to comply with any of its terms. However, if You become compliant, then the rights granted under this License from a particular Contributor are reinstated (a) provisionally, unless and until such Contributor explicitly and finally terminates Your grants, and (b) on an ongoing basis, if such Contributor fails to notify You of the non-compliance by some reasonable means prior to 60 days after You have come back into compliance. Moreover, Your grants from a particular Contributor are reinstated on an ongoing basis if such Contributor notifies You of the non-compliance by some reasonable means, this is the first time +You have received notice of non-compliance with this License from such Contributor, and You become compliant prior to 30 days after Your receipt of the notice. + + + 5.2. If You initiate litigation against any entity by asserting a patent infringement claim (excluding declaratory judgment actions, counter-claims, and cross-claims) alleging that a Contributor Version directly or indirectly infringes any patent, then the rights granted to You by any and all Contributors for the Covered Software under Section 2.1 of this License shall terminate. + + + 5.3. In the event of termination under Sections 5.1 or 5.2 above, all end user license agreements (excluding distributors and resellers) which have been validly granted by You or Your distributors under this License prior to termination shall survive termination. + + +6. Disclaimer of Warranty + + Covered Software is provided under this License on an "as is" basis, without warranty of any kind, either expressed, implied, or statutory, including, without limitation, warranties that the Covered Software is free of defects, merchantable, fit for a particular purpose or non-infringing. The entire risk as to the quality and performance of the Covered Software is with You. Should any Covered Software prove defective in any respect, You (not any Contributor) assume the cost of any necessary servicing, repair, or correction. This disclaimer of warranty constitutes an essential part of this License. No use of any Covered Software is authorized under this License except under this disclaimer. + + +7. Limitation of Liability + + Under no circumstances and under no legal theory, whether tort (including negligence), contract, or otherwise, shall any Contributor, or anyone who distributes Covered Software as permitted above, be liable to You for any direct, indirect, special, incidental, or consequential damages of any character including, without limitation, damages for lost profits, loss of goodwill, work stoppage, computer failure or malfunction, or any and all other commercial damages or losses, even if such party shall have been informed of the possibility of such damages. This limitation of liability shall not apply to liability +for death or personal injury resulting from such party's negligence to the extent applicable law prohibits such limitation. Some jurisdictions do not allow the exclusion or limitation of incidental or consequential damages, so this exclusion and limitation may not apply to You. + + +8. Litigation + + Any litigation relating to this License may be brought only in the courts of a jurisdiction where the defendant maintains its principal place of business and such litigation shall be governed by laws of that jurisdiction, without reference to its conflict-of-law provisions. Nothing in this Section shall prevent a party's ability to bring cross-claims or counter-claims. + + +9. Miscellaneous + + This License represents the complete agreement concerning the subject matter hereof. If any provision of this License is held to be unenforceable, such provision shall be reformed only to the extent necessary to make it enforceable. Any law or regulation which provides that the language of a contract shall be construed against the drafter shall not be used to construe this License against a Contributor. + +10. Versions of the License + + + 10.1. New Versions + + Mozilla Foundation is the license steward. Except as provided in Section 10.3, no one other than the license steward has the right to modify or publish new versions of this License. Each version will be given a distinguishing version number. + + + 10.2. Effect of New Versions + + You may distribute the Covered Software under the terms of the version of the License under which You originally received the Covered Software, or under the terms of any subsequent version published by the license steward. + + + 10.3. Modified Versions + + If you create software not governed by this License, and you want to create a new license for such software, you may create and use a modified version of this License if you rename the license and remove any references to the name of the license steward (except to note that such modified license differs from this License). + + + 10.4. Distributing Source Code Form that is Incompatible With Secondary Licenses + + If You choose to distribute Source Code Form that is Incompatible With Secondary Licenses under the terms of this version of the License, the notice described in Exhibit B of this License must be attached. + + + Exhibit A - Source Code Form License Notice + + This Source Code Form is subject to the terms of the Mozilla Public License, v. 2.0. If a copy of the +MPL was not distributed with this file, You can obtain one at https://mozilla.org/MPL/2.0/. + + + If it is not possible or desirable to put the notice in a particular file, then You may include the notice in +a location (such as a LICENSE file in a relevant directory) where a recipient would be likely to look for such a notice. +You may add additional accurate notices of copyright ownership. Exhibit B - "Incompatible With Secondary Licenses" Notice +This Source Code Form is "Incompatible With Secondary Licenses", as defined by the Mozilla Public +License, v. 2.0. + + + + +## Private PTC CUSTOMER AGREEMENT Axeda Agent Embedded +======================================================================= + +PTC CUSTOMER AGREEMENT + +THIS PTC CUSTOMER AGREEMENT ("AGREEMENT") IS A LEGAL AGREEMENT BETWEEN THE INDIVIDUAL, OR +THE COMPANY OR OTHER ORGANIZATION ON WHOSE BEHALF SUCH INDIVIDUAL ACCEPTS THIS AGREEMENT, +THAT EITHER (A) CLICKS THE "I ACCEPT" BUTTON BELOW OR (B) INSTALLS, ACCESSES, +OR USES ANY +SOFTWARE OR DOCUMENTATION FROM PTC ("CUSTOMER"), AND PTC INC. OR, IF THE PURCHASE WAS MADE IN +A COUNTRY SPECIFIED ON SCHEDULE A TO THIS AGREEMENT, THE PTC AFFILIATE SPECIFIED ON SCHEDULE A +(AS APPLICABLE, "PTC"). +PLEASE READ THE TERMS AND CONDITIONS OF THIS AGREEMENT CAREFULLY BEFORE ACCEPTING THIS +AGREEMENT. BY CLICKING ON THE "I ACCEPT" BUTTON BELOW OR BY INSTALLING, ACCESSING, OR USING +ANY SOFTWARE OR DOCUMENTATION FROM PTC, CUSTOMER HEREBY AGREES TO BE BOUND BY THIS +AGREEMENT AND REPRESENTS THAT IT IS AUTHORIZED TO DO SO. +IF YOU DO NOT AGREE TO ALL OF THE TERMS OF THIS AGREEMENT OR IF YOU DO NOT HAVE AUTHORITY TO +BIND THE COMPANY OR OTHER ORGANIZATION ON WHOSE BEHALF YOU ARE ACCEPTING THIS AGREEMENT, +CLICK THE "I DECLINE" BUTTON AND RETURN TO PTC THE SOFTWARE AND DOCUMENTATION PRODUCTS +PROVIDED TOGETHER WITH THIS AGREEMENT IN ACCORDANCE WITH THE INSTRUCTIONS PROVIDED WHEN +YOU CLICK THE "I DECLINE" BUTTON. NOTE THAT FAILURE TO COMPLY WITH SUCH INSTRUCTIONS WITHIN +THE TIME PERIOD SPECIFIED WILL VOID ANY RIGHT YOU WOULD OTHERWISE HAVE HAD FOR A REFUND OF +ANY FEES PAID. EACH ORDER FOR LICENSED PRODUCTS MAY NOT BE CANCELLED ONCE THIS AGREEMENT +HAS BEEN ACCEPTED. +IF CUSTOMER DID NOT OBTAIN THE LICENSED PRODUCT FROM PTC DIRECTLY, FROM AN AUTHORIZED PTC +DISTRIBUTOR OR RESELLER OR FROM THE PTC ONLINE STORE (AT WWW.PTC.COM), CUSTOMER IS USING AN +ILLEGALLY OBTAINED UNLICENSED VERSION OF THE APPLICABLE LICENSED PRODUCT. PTC REGARDS +SOFTWARE PIRACY AS THE CRIME IT IS AND PURSUES (BOTH CIVILLY AND CRIMINALLY) THOSE WHO TAKE +PART IN THESE ACTIVITIES. AS PART OF THESE EFFORTS, PTC UTILIZES DATA MONITORING AND SCOURING +TECHNOLOGIES TO OBTAIN AND TRANSMIT TO PTC DATA ON USERS OF ILLEGAL COPIES OF LICENSED +PRODUCTS. IF CUSTOMER IS USING AN ILLEGAL COPY OF SOFTWARE, CEASE USING THE ILLEGAL VERSION +AND CONTACT PTC TO OBTAIN A LEGALLY LICENSED COPY. BY USING THIS SOFTWARE, YOU CONSENT TO THE +COLLECTION, USE, AND TRANSFER OF PERSONAL DATA (INCLUDING TO THE UNITED STATES) FOR THE +PURPOSES OF IDENTIFYING USERS OF ILLEGAL COPIES OF OUR SOFTWARE. SUCH CONSENT SHALL BE BINDING +ON ANY USERS OF THIS SOFTWARE, INCLUDING USERS OTHER THAN YOU. +IN ORDER TO UNDERSTAND THE PREFERENCES OF OUR SOFTWARE USERS, PTC USES DATA MONITORING +TECHNOLOGIES TO OBTAIN AND TRANSMIT DATA ON SYSTEM USE AND PERFORMANCE AND FOR GATHERING +USER DATA AND USE METRICS ON USERS OF OUR SOFTWARE. WE WILL SHARE THIS DATA WITHIN PTC, ITS +AFFILIATED COMPANIES AND OUR BUSINESS PARTNERS, INCLUDING WITHIN THE UNITED STATES AND +ELSEWHERE FOR TECHNICAL AND MARKETING PURPOSES AND WILL ENDEAVOR TO ENSURE THAT ANY SUCH +DATA TRANSFERRED IS APPROPRIATELY PROTECTED. OUR COMMERCIAL LICENSES PERMIT USERS TO OPT OUT OF THIS DATA COLLECTION AND OUR STUDENT/EDUCATIONAL VERSIONS ONLY COLLECT DATA ON +SYSTEM USE AND PERFORMANCE. OUR FREE AND TRIAL VERSIONS OF SOFTWARE DO NOT ALLOW USERS TO +OPT-OUT OF THIS DATA COLLECTION, INCLUDING USER DATA. +IF YOU ARE USING PTC SOFTWARE, VISITING A PTC WEBSITE OR COMMUNICATING ELECTRONICALLY WITH US +FROM A COUNTRY OTHER THAN THE UNITED STATES, VARIOUS COMMUNICATIONS WILL NECESSARILY +RESULT IN A TRANSFER OF THIS INFORMATION ACROSS INTERNATIONAL BOUNDARIES. +IF YOU DO NOT CONSENT TO THE COLLECTION AND/OR TRANSMISSION (INCLUDING TO THE UNITED STATES) +OF YOUR DATA AS DESCRIBED ABOVE, DO NOT DOWNLOAD OR USE PTC SOFTWARE. BY (I) USING FREE OR +TRIAL SOFTWARE OR (II) NOT OPTING-OUT OF THE COLLECTION OF CERTAIN PERSONAL DATA AS YOU ARE +ABLE TO WITH PTC COMMERCIAL SOFTWARE, YOU CONSENT TO PTC'S COLLECTION, USE, AND TRANSFER OF +YOUR PERSONAL DATA (INCLUDING TO THE UNITED STATES). +CAPITALIZED TERMS NOT DEFINED IN THE TEXT BELOW ARE DEFINED IN SCHEDULE B AT THE END OF THIS +AGREEMENT. +SCHEDULE A TO THIS AGREEMENT CONTAINS ADDITIONAL (OR ALTERNATIVE) TERMS APPLICABLE TO +SPECIFIC GEOGRAPHIES. + + + +### PTC Clickwrap Customer Agreement - Rev. 12/14 + +1. License. + + 1.1 License Grant. Subject to the terms and conditions of this Agreement, PTC hereby grants to Customer a non-exclusive, revocable, non-transferable license, without any right to sub-license, to install and use the Licensed +Products identified in the Quote +during the applicable License Term, solely for Customer's internal business purposes and solely in accordance with the applicable +usage and license-type restrictions identified in the Quote and in the Licensing Basis Webpage +("License"). Notwithstanding the foregoing: + + (a) If the Licensed Product is being provided by PTC on an "evaluation" or "trial" basis, such License will be instead to +install and use the Licensed Product solely to evaluate such Licensed Products, and Customer agrees not to use the +Licensed Product in any commercial applications or for productive purposes. + + (b) If the Licensed Software is Educational Software, Customer must be enrolled in, or employed by, an accredited, academic +institution, and shall use the Licensed Software solely for educational purposes in a degree-granting program. If Customer +does not meet one of these qualifications, Customer has no rights under this Agreement. Without limitation, non educational research or funded educational research conducted using the facilities of an academic institution or under an +academic name does not qualify as "educational purposes" and use of Educational Software for such purposes represents a +violation of the terms of this Agreement. + + © If the Licensed Software is sold on a "demo and test" or "non-production" basis (or similar designation), such Licensed +Software may not be used in a production environment. + + 1.2 Designated Country/Computers/Networks. Subject to Section 1.3, Customer may only install and operate Licensed Products on +the applicable Designated Computers or Designated Networks on computer systems and networks situated in the applicable +Designated Country. Customer may, from time to time, change the Designated Computer, Designated +Network, and/or the +Designated Country in which Customer seeks to install or operate a Licensed Product, provided that in each case (i) Customer shall +give prior written notice to PTC of any such change, and (ii) upon moving the Licensed Products to a different Designated Country, +Customer shall pay all applicable Uplift Fees. Notwithstanding the foregoing, Registered Users need not be located in the +Designated Country when accessing a Registered User Product. + + 1.3 Global/Restricted Global Licenses. If a Concurrent User Licensed Product is licensed by PTC on a +"Global" or "Restricted +Global" basis, Section 1.2 shall not apply to such Licensed Products and the following provisions shall apply instead: + + (i) Global Licenses. Subject to the other requirements of this Agreement, a Global License allows the +Customer to install, +operate and use such Licensed Product at any Customer site(s) throughout the world. + + (ii) Restricted Global Licenses. Subject to the other requirements of this Agreement, a Restricted +Global License allows the +Customer to install, operate and use such Licensed Product at any Customer site(s) located in the +Designated Country +and/or in any Permitted Country. "Permitted Countries" means China, India, Russia, the Czech +Republic, Poland, +Hungary, Malaysia, South Africa, Israel, Mexico, Brazil, Argentina, and Romania. + + 1.4 Additional Restrictions on Use. Customer shall not permit any persons who are not Permitted Users to access or use the +Licensed Products. Customer shall not and shall not permit any third party(ies) to: + + (i) modify or create any derivative work of any part of the Licensed Products; + + (ii) rent, lease, or loan the Licensed Products; + + (iii) use the Licensed Products, or permit them to be used, for third-party training, to deliver software implementation or +consulting services to any third parties, or for commercial time-sharing or service bureau use; + + + (iv) disassemble, decompile or reverse engineer the Licensed Products or the file format of the Licensed +Products, or otherwise +attempt to gain access to the source code or file format of the Licensed Products, except as expressly permitted in +Schedule A, if applicable; + + + (v) sell, license, sublicense, loan, assign, or otherwise transfer (whether by sale, exchange, gift, operation of law, or +otherwise) to any third party the Licensed Products, any copy thereof, or any License or other rights thereto, in whole or in +part, without in each case obtaining PTC's prior written consent, except to the extent that any of the foregoing are +explicitly authorized in the Quote and/or the Licensing Basis Webpage; + + (vi) alter, remove, or obscure any copyright, trade secret, patent, trademark, logo, proprietary and/or other legal notices on or +in any copies of the Licensed Products; and + + (vii) copy or otherwise reproduce the Licensed Products in whole or in part, except (a) as may be required for their installation +into computer memory for the purpose of executing the Licensed Products in accordance with this +Section 1, and/or (b) to +make a reasonable number of copies solely for back-up purposes (provided that any such permitted copies shall be the +property of PTC, and Customer shall reproduce thereon all PTC copyright, trade secret, patent, trademark, logo, +proprietary and/or other legal notices contained in the original copy of the Licensed Product obtained from PTC). +If Customer uses any unlicensed or unauthorized copies of any PTC software, Customer agrees that, +without limiting PTC's right to +terminate this Agreement for breach in accordance with Section 7 and without limiting any other remedies to which PTC may be entitled, Customer will pay to PTC the PTC then-current list price for all such unlicensed software, in addition to any fines or +penalties that may be imposed by law. + + 1.5 Additional Restrictions on Use Applicable to Concurrent User Products. If the Licensed Product is a +Concurrent User Product, +the following provisions apply: + + (i) The number of Permitted Users accessing or operating a Concurrent User Product at any point in time may not exceed the +number of Licenses in effect at such time for that particular Licensed Product. + + (ii) Except with respect to Integrity and Implementer Products, only Permitted Users physically located in the Designated +Country may access, operate and/or use the Licensed Products. Permitted Users who are not employees of Customer may +use the Licensed Products while physically located at Customer's site only. + + (iii) Where a Concurrent User Product is Licensed on a "fixed," "locked" or "node-locked" basis, or the +Licensed Product is +licensed as a "Designated Computer" product, such Licensed Product is licensed to operate solely on the Designated +Computer on which it is installed. + + 1.6 Additional Restrictions on Use Applicable to Registered User Products. A License is required for each individual who accesses +a Registered User product or the data contained therein, whether directly or through a web portal or other mechanism for "batching" +or otherwise achieving indirect access to the Licensed Product or such data. Generic or shared log-ins are not permitted. Customer +may add and/or substitute from time to time new Registered Users as long as the aggregate number of +Registered Users does not +exceed at any point in time the number of Licenses in effect at such time for that particular Licensed +Product and, provided further, +that if a person who was previously a Registered User returns to Registered User status, a new License fee must be paid to PTC at +PTC's then current rates. + + 1.7 Additional Restrictions on Use Applicable to Designated Server Products. Each Designated Server product may only be used on +the computer server that is designated by the Customer in connection with the initial installation of such product and that has one +unique instance of the applicable installed product application. In the event a computer server is partitioned in any manner +(physically, logically or otherwise), the reference in the preceding sentence to "computer server" shall mean each partition of such +server, and such Designated Server product may only be used on one of such partitions. Customer may, from time to time, change +the Designated Server(s) for a Designated Server Product, and/or the location thereof, provided that in each case (a) Customer shall +give prior written notice to PTC of any such change, and (b) upon transferring the Designated Server +Products to a different +Designated Country, Customer pays all applicable Uplift Fees. + + 1.8 Third Party Components and Bundled Third Party Products. Certain of the Licensed Products may contain third party software +components for which additional terms apply ("Third Party Components"). The current additional terms are set forth on the Schedule +of Third Party Terms available in the legal policies and guidelines section of http://www.ptc.com. Separately, third party software +products that PTC resells and/or bundles for distribution with the Licensed Products are licensed to +Customer directly by the +manufacturer of such third party software products ("Bundled Third Party Products"). Such Bundled +Third Party Products are also +described on the Schedule of Third Party Terms. Customer agrees that its use of Third Party +Components and/or Bundled Third +Party Products is subject to the terms of the Schedule of Third Party Terms. New Releases containing +Third Party Components or +Bundled Third Party Products may be subject to additional or different third party terms, of which PTC +shall notify the Customer at +the time such New Releases are delivered to the Customer. + + 1.9 Upgrades: If the Licensed Software was licensed as an upgrade from a previous version, Customer must first be licensed for the +Licensed Software identified by PTC as eligible for the upgrade and Customer must be active on +Support Services for such software. +After installing the upgrade, Licensed Software licensed as an upgrade replaces and/or supplements the product that formed the basis +of Customer's eligibility for the upgrade and Customer may no longer use the original Licensed +Software that formed the basis for +Customer's upgrade eligibility. + +2. Compliance. + + 2.1 License Usage Assessments. To confirm Customer's compliance with the terms and conditions hereof, Customer agrees that +PTC may perform a usage assessment with respect to Customer's use of the Licensed Products. Customer agrees to provide PTC +access to Customer's facilities and computer systems, and cooperation from Customer's employees and consultants, as reasonably +requested by PTC in order to perform such assessment, all during normal business hours, and after reasonable prior notice from PTC. +2.2 Reports. Upon written request from PTC, Customer agrees to provide to PTC an installation and/or usage report with respect to +the Licensed Products (and in the case of Registered User Products, such report shall include a list of all users for whom Customer +has issued a password or other unique identifier to enable such individual to use the Registered User +Product). Such report shall be +certified by an authorized representative of Customer as to its accuracy within ten (10) business days after receipt of any written +request from PTC. For any period in which Customer's use of the Licensed Products exceeds the number and/or the scope of the +Licenses in effect during such period for such Licensed Products, Customer agrees to pay for any such excess usage, including +applicable license and Support Services fees, and without limiting any other rights or remedies to which it is entitled, failure to pay +shall be grounds for termination in accordance with Section 7 hereof. + + +3. Intellectual Property. PTC and its licensors are the sole owners of the Licensed Products and of any copies of the Licensed +Products, and of all copyright, trade secret, patent, trademark and other intellectual or industrial property rights in and to the Licensed +Products. All copies of the Licensed Products, in whatever form provided by PTC or made by +Customer, shall remain the property of +PTC, and such copies shall be deemed to be on loan to Customer during the License Term. Customer acknowledges that the License +granted hereunder does not provide Customer with title to or ownership of the Licensed Products or any copies thereof, but only a +right of limited use consistent with the express terms and conditions of this Agreement. Customer shall have no rights to the source +code for the Licensed Products, and Customer agrees that only PTC shall have the right to maintain, enhance, or otherwise modify +the Licensed Products. + +4. Support Services; Warranty; Disclaimer of Warranties. +See Schedule A for a modified version of this Section 4 for Licensed Products licensed and used in +Germany, Austria or Switzerland. + + 4.1 Support Services. Upon PTC's acceptance of an order for Support Services or for Licensed +Products for which Usage License +Fees apply, PTC agrees that it or its designated service provider shall provide the applicable Support +Services in accordance with +Schedule C. + + 4.2 Warranty. PTC warrants to Customer that PTC is authorized to grant the License(s) and that, subject to Section 4.3, the +Licensed Products will be free from Errors for a period of ninety (90) days following PTC's initial shipment to Customer or +Customer's designee of such Licensed Products (the "Warranty Period"). + + 4.3 Warranty Exceptions. PTC shall have no warranty obligations hereunder with respect to any (i) +evaluation, "trial" or "express" +Licenses, (ii) New Releases, (iii) computer software provided to Customer in the course of PTC's delivery of Training Services, (iv) +Errors attributable to the use of the Licensed Product in an application or environment for which it was not designed or contemplated, +(v) Errors attributable to any modifications or customizations of the Licensed Products, (vi) Licensed +Products that are provided by +PTC free of charge to Customer, and/or (vii) Sun Software, Oracle Software and/or Bundled Third +Party Products. + + 4.4 Sole Remedy. PTC's and its licensors' entire liability and Customer's exclusive remedy for any breach by PTC of the warranty +given in Section 4.2 above shall be, at PTC's sole discretion, either to (a) replace the Licensed Product +(s) or (b) use diligent efforts to +repair the Error. PTC's obligations set forth in the preceding sentence shall apply only if notice of the +Error is received by PTC +within the Warranty Period and Customer supplies such additional information regarding the Error as +PTC may reasonably request. +If PTC does not replace the applicable Licensed Product(s) and/or does not repair the Error (either by providing a bug fix, a +workaround or otherwise) within a reasonable time after notice of the Error and associated information from Customer is received by +PTC, PTC will provide a refund of the license fees paid by Customer for the applicable Licensed +Product(s) upon return of such +Licensed Product(s) and any copies thereof. + + 4.5 No Additional Warranties. No third party, including any employee, partner, distributor (including any Reseller) or agent of PTC +or any of its resellers or sales agents, is authorized to give any representations, warranties or covenants greater or different than those +contained in this Agreement with respect to any Licensed Products or Services, except as specifically set forth in a written agreement +signed on behalf of Customer by an authorized officer and on behalf of PTC by its legal counsel or +Corporate Controller. + + 4.6 Disclaimer of Warranties. EXCEPT AS EXPRESSLY STATED IN SECTION 4, PTC DISCLAIMS (AND CUSTOMER +WAIVES) ALL WARRANTIES, WHETHER EXPRESS, IMPLIED, OR STATUTORY, WRITTEN OR ORAL, INCLUDING +ANY WARRANTY OF MERCHANTABILITY, SATISFACTORY QUALITY, FITNESS FOR A PARTICULAR PURPOSE, +NON-INFRINGEMENT, AND/OR ANY WARRANTY THAT CUSTOMER WILL ACHIEVE ANY PARTICULAR RETURN +ON INVESTMENT. THE LICENSED PRODUCTS ARE INTENDED TO BE USED BY TRAINED PROFESSIONALS AND +ARE NOT A SUBSTITUTE FOR PROFESSIONAL JUDGMENT, TESTING, SAFETY AND UTILITY. CUSTOMER IS +SOLELY RESPONSIBLE FOR ANY RESULTS OBTAINED FROM USING THE LICENSED +PRODUCTS, INCLUDING +THE ADEQUACY OF INDEPENDENT TESTING OF RELIABILITY AND ACCURACY OF ANY ITEM DESIGNED USING +LICENSED PRODUCTS. PTC does not warrant that the operation or other use of the Licensed +Products will be uninterrupted or +error free or will not cause damage or disruption to Customer's data, computers or networks. + +5. Indemnification; Infringement. + + 5.1 PTC's Obligation to Indemnify Customer. PTC, at its own expense, will defend any action brought against Customer based on a +claim that any Licensed Product infringes a United States, European Union or Japanese patent, copyright or trademark and, at its +option, will settle any such action or will pay any final judgment awarded against Customer, provided that: (a) PTC shall be notified +promptly in writing by Customer of any notice of any such claim; (b) PTC shall have the sole control of the defense of any action on +such claim and all negotiations for its settlement or compromise and shall bear the costs of the same +(save where one or more of the +exclusions in Section 5.3 applies); and © Customer shall cooperate fully at PTC's expense with PTC +in the defense, settlement or +compromise of such claim. This Section 5 states PTC's sole and exclusive liability, and Customer's sole remedy, for any and all +claims relating to infringement of any intellectual property right. + + 5.2 PTC's Right to Act to Prevent a Claim. If a claim described in Section 5.1 hereof occurs or, in +PTC's opinion, may occur, +Customer shall permit PTC, at PTC's option and expense to: (a) procure for Customer the right to continue using the Licensed +Product; (b) modify the Licensed Product so that it becomes non-infringing without materially impairing its functionality; or © +terminate the applicable Licenses, accept return of the Licensed Products and grant Customer a credit thereon. For Licenses purchased with a perpetual License Term, such credit shall be equal to the License fees paid by +Customer for such Licensed Product +depreciated on a straight-line, five year basis. For Licenses purchased on a term license or subscription basis, such credit shall be +equal to the prepaid license or subscription fees for the remainder of the License Term. + + 5.3 Exclusions from PTC's Obligation to Indemnify Customer. PTC shall have no liability to Customer under Section 5.1 hereof or +otherwise to the extent that any infringement or claim thereof is based upon: (a) use of the Licensed +Product in combination +with equipment or software not supplied hereunder where the Licensed Product itself would not be infringing; (b) use of the Licensed +Product in an application or environment for which it was not designed or not contemplated under this +Agreement; © use of other +than a current release of the Licensed Product(s) provided to Customer; (d) modification of the +Licensed Product by anyone other +than PTC or its employees or agents; or (e) any claims of infringement of any patent, copyright, trade secret, trademark or other +proprietary right in which Customer has an interest. + +6. Limitation of Liability. + + See Schedule A for a modified version of this Section 6 for Licensed Products licensed and used in +Germany, Austria or Switzerland. + + + 6.1 The warranty and indemnification provisions of Sections 4 and 5 hereof state the entire liability of +PTC, its subsidiaries and +affiliates, and each of their respective directors, officers, employees or agents, with respect to the +Licensed Products and Services, +including (without limitation) any liability for breach of warranty, or for infringement or alleged infringement of patent, copyrights, +trademarks, trade secrets and other intellectual or proprietary rights by the Licensed Products, or their use. + + 6.2 EXCEPT FOR PTC'S INDEMNIFICATION OBLIGATIONS IDENTIFIED IN SECTION 5.1 +ABOVE, THE MAXIMUM +LIABILITY OF PTC AND ITS LICENSORS ARISING OUT OF, OR RELATING TO, THE CREATION, LICENSE, +FUNCTIONING, USE OR SUPPLY OF THE LICENSED PRODUCTS OR THE PROVISION OF SERVICES OR OTHERWISE +RELATING TO THIS AGREEMENT, WHETHER BASED UPON WARRANTY, CONTRACT, TORT, OR OTHERWISE, +SHALL NOT, (I) FOR LICENSES PURCHASED ON A PERPETUAL BASIS, EXCEED THE FEES PAID BY CUSTOMER FOR +THE LICENSED PRODUCTS OR SERVICES THAT GAVE RISE TO THE CLAIM AND (II) FOR LICENSES PURCHASED +ON A TERM OR SUBSCRIPTION BASIS, EXCEED THE FEES PAID BY CUSTOMER IN THE TWELVE MONTH PERIOD +IMMEDIATELY PRECEDING THE EVENT GIVING RISE TO DAMAGES FOR THE LICENSED PRODUCTS OR SERVICES +THAT GAVE RISE TO THE CLAIM. + + 6.3 IN NO EVENT SHALL PTC, ITS LICENSORS, ITS AFFILIATES (INCLUDING ITS SUBSIDIARY COMPANIES), OR +ANY OF THEIR RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES OR AGENTS BE LIABLE FOR: (A) ANY LOSS OF +PROFIT, LOSS OF USE DAMAGES, LOSS OF GOODWILL, LOSS OF BUSINESS OPPORTUNITY, LOSS OF SALES, LOSS +OF REPUTATION OR LOSS OF ANTICIPATED SAVINGS; (B) ANY LOSS OR INACCURACY OF DATA OR BUSINESS +INFORMATION OR FAILURE OR INADEQUACY OF ANY SECURITY SYSTEM OR FEATURE; AND © SPECIAL, +INCIDENTAL, INDIRECT, PUNITIVE OR CONSEQUENTIAL LOSS OR DAMAGE +HOWSOEVER CAUSED; IN EACH +CASE EVEN IF PTC HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. + + 6.4 Customer agrees not to bring any suit or action against PTC, and/or its subsidiaries and affiliates, and/or any of their respective +directors, officers, employees or agents for any reason whatsoever more than one year after the cause of action arises. Customer +recognizes that fees paid by Customer for the Licensed Products and Services are based in part on the disclaimer of warranty and +limitation of liability provisions set forth herein and that, in the absence of Customer's agreement to such terms, the charges for the +Licensed Products would be significantly higher. The limitations and exclusions set forth in this Section +6 shall not apply to any +claim in respect of death or personal injury. + + +7. Term and Termination. + + 7.1 Events Causing Termination. This Agreement and all Licenses will terminate: + + (a) Automatically and without notice on the following events: (I) Customer's breach of any of clauses +(i) through (vii) of +Section 1.4 or Sections 3 or 8.4 hereof; (II) a receiver, trustee, liquidator, or such similar officer is appointed for Customer +or for any of Customer's properties or assets; (III) Customer makes a general assignment for the benefit of Customer's +creditors; (IV) Customer files a petition for its reorganization, dissolution or liquidation, or such a petition is filed against +Customer and is not dismissed within sixty (60) days thereafter; or (V) Customer ceases doing business or commence +dissolution or liquidation proceedings; or + + (b) Thirty (30) days after written notice from PTC specifying a breach (other than as listed in Section + + 7.1(a) above) of this +Agreement, including failure to make any payment due to either PTC or a Reseller in connection with the Licensed +Products in a timely manner, if that breach is not, within that thirty (30) day period, remedied to PTC's reasonable +satisfaction. + + 7.2 Effects of Expiration or Termination. Upon expiration of a given License Term and/or any expiration or termination of this +Agreement, Customer shall promptly pay all sums owed by Customer, return to PTC the original copies of all Licensed Products for +which the License Term has expired or has been terminated, destroy and/or delete all copies and backup copies thereof from Customer's computer libraries, storage facilities and/or hosting facilities, and certify in writing by an officer that Customer is in +compliance with the foregoing requirements and that such Licensed Products are no longer in +Customer's possession or in use. +7.3 Survival. Sections 2, 3, 4.6, 5, 6, 7.2, 7.3 and 8 shall survive expiration or termination of this +Agreement. + +8. General. + + 8.1 Governing Law and Jurisdiction. Unless otherwise stated in Schedule A, all disputes arising under, out of, or in any way +connected with this Agreement shall be governed by and construed in accordance with the laws of the +Commonwealth of +Massachusetts without reference to conflict of laws principles (and specifically excluding the Uniform +Computer Information +Transactions Act). The parties hereby expressly disclaim the application of the U.N. Convention for the +International Sale of Goods. +All disputes arising under, out of, or in any way connected with this Agreement shall be litigated exclusively in the state or federal +courts situated in the Commonwealth of Massachusetts, and in no other court or jurisdiction. Notwithstanding the foregoing or +anything to the contrary, PTC shall have the right to bring a claim in any court of competent jurisdiction to enforce any intellectual +property rights and/or protect any confidential information. Customer agrees that the state and federal courts situated in the +Commonwealth of Massachusetts shall have personal jurisdiction over its person, and Customer hereby irrevocably (i) submits to the +personal jurisdiction of said courts and (ii) consents to the service of process, pleadings, and notices in connection with any and all +actions initiated in said courts. The parties agree that a final judgment in any such action or proceeding shall be conclusive and +binding and may be enforced in any other jurisdiction. Each party waives its right to trial by jury in connection with any dispute +arising out of this Agreement. + + 8.2 Notices. Any notice or communication required or permitted under this Agreement shall be in writing. In the case of notice to +Customer, the notice shall be directed to the address set forth on the Customer's purchase order or to such other address as may be +provided to PTC in writing. In the case of notice to PTC, such notice shall be directed to PTC, 140 +Kendrick Street, Needham, MA +02494; Attn: Corporate Controller, with a copy to General Counsel. Any notice provided under this section shall be deemed to have +been received: (a) if given by hand, immediately; (b) if given by mail, five (5) business days after posting; © if given by express +courier service, the second business day following dispatch in the jurisdiction of the sender; or (d) if given by fax, upon receipt +thereof by the recipient's fax machine or as stated in the sender's transmission confirmation report as produced electronically by +sender's fax machine. + + 8.3 Assignment, Waiver, Modification. Customer may not assign, transfer, delegate or sublicense any +of Customer's rights or +obligations hereunder (including without limitation by operation of law or by sale of Customer assets, whether directly or by merger, +and a change in control of Customer shall be deemed to be an "assignment" for purposes of the foregoing) without PTC's prior +written consent, and any such attempted delegation, assignment, transfer or sublicense shall be void and a breach of this Agreement. +No waiver, consent, modification, amendment or change of the terms of this Agreement shall be binding unless in writing and signed +by PTC and Customer. PTC reserves the right to charge a transfer fee for any proposed assignment, transfer or sublicense of this +Agreement. + + 8.4 Compliance with Laws. Each party shall be responsible for its own compliance with applicable laws, regulations and other legal +requirements relating to the conduct of its business and this Agreement. Further Customer represents and warrants that it will use the +Licensed Products, as well as related technology and services, in full compliance with applicable laws and regulations. Customer +acknowledges and agrees that the Licensed Products and related technical data and services are subject to the export control laws and +regulations of the United States and any country in which the Licensed Products or related technical data or services are developed, +received, downloaded, used, or performed. Further, Customer understands and acknowledges that the release of software or +technology to a non-U.S. person within the United States or elsewhere abroad is deemed to be an export to the non-U.S. person's +home country or countries, and that the transfer of the Licensed Products or related technology to +Customer's employees, affiliates, +or any third party, may require a license from the United States Government and possibly other applicable authorities. Customer shall +be solely responsible for determining whether Customer's use or transfer of the Licensed Products or related technology or services +requires an export license or approval from U.S. or other authorities, and for securing all required authorizations. Customer hereby +warrants and represents that: (x) neither Customer nor any of Customer's directors, officers or affiliates is identified on the U.S. +Commerce Department's Denied Persons List, Entity List, or Unverified List, the U.S. State +Department's Nonproliferation +Sanctions List, the U.S. Treasury Department's List of Specially Designated Nationals and Blocked +Persons or any similar Export +Controls Division-Foreign Affairs and International Trade Canada listing that designates individuals or entities to which export +restrictions apply (collectively, the "Restricted Parties Lists"), (y) except as specifically authorized or licensed by the United States +Government and other applicable authorities, Customer will not sell, offer, transfer, deliver, release, either directly or indirectly, the +Licensed Products or related technology or services to any end-user: (A) that is either located in, a national of, or acting on behalf of +a country subject to U.S. economic embargoes, or (B) that have been designated as prohibited or restricted parties by the U.S. +Government, including but not limited to persons listed on the Restricted Parties Lists, or © engaged in activities related to the +design, development, stockpiling, or proliferation of nuclear, chemical, or biological weapons, or missiles or missile systems, or (D) +engaged in maritime nuclear propulsion activities. Customer represents and warrants that it will ensure that any person or entity to +which Customer has granted access to the Licensed Products or related technology or services has been made aware of, and will +comply with, this provision and U.S. and other applicable export control laws and regulations. Unless prohibited by applicable law +and without waiving sovereign immunity, Customer shall indemnify and hold harmless PTC and its employees against any damage, +loss, liability or expense (including attorneys' fees) that PTC may incur as a result of Customer's failure to comply with this Section + + 8.4. Such indemnification shall survive the expiration or termination of this Agreement. + + 8.5 Severability. It is intended that this Agreement shall not violate any applicable law and the unenforceability or invalidity of any +provision (other than the provisions obligating Customer to make payments to PTC) shall not affect the force and validity of the +remaining provisions and such provisions determined to be invalid shall be deemed severed from this +Agreement and, to the extent +possible, be replaced with terms which as closely as possible approximate the interest and economic intent of such invalid provisions. + + 8.6 Entire Agreement. This Agreement is the complete and exclusive statement of the contract between +PTC and Customer +with respect to the subject matter hereof. No waiver, consent, modification, amendment or change of this Agreement shall be binding +unless in writing and signed or otherwise expressly acknowledged by PTC and Customer. + + 8.7 Third Party Beneficiaries. It is agreed by the parties to this Agreement that PTC's third party licensors are intended +beneficiaries of this Agreement and have the right to rely upon and directly enforce its terms with respect to the products of such +licensors. + + 8.8 Marketing. Customer agrees that while this Agreement is in effect, PTC shall be authorized to identify Customer as a +customer/end-user of PTC software and services (as applicable) in public relations and marketing materials. + + 8.9 Government Licensees. If Customer is a United States Governmental entity, Customer agrees that the Licensed Products +are "commercial computer software" under the applicable federal acquisition regulations and are provided with the commercial +license rights and restrictions described elsewhere herein. If Customer is acquiring the Licensed +Product(s) under a United States +government contract, Customer agrees that Customer will include all necessary and applicable restricted rights legends on the +Licensed Products to protect PTC's proprietary rights under the FAR or other similar regulations of other federal agencies. Customer +agrees to always include such legends whenever the Licensed Products are, or are deemed to be, a deliverable under a government +contract. +Schedule A - Purchases from PTC Affiliates +If the Customer has obtained a License to any Licensed Products in one of the following countries, the entity granting the +License is specified below and, notwithstanding Section 8.1 of this Agreement, the governing law and jurisdiction shall be as set +forth below. +Country PTC Affiliate Licensing Entity Governing Law/Jurisdiction for +Disputes +Belgium, Netherlands, Luxembourg +Parametric Technology Nederland B.V. Netherlands +Austria, Germany Parametric Technology GmbH German Law*, Landgericht Munchen I, Germany +France Parametric Technology S.A. France Ireland PTC Software and Services (Ireland) Limited +Republic of Ireland +Italy Parametric Technology Italia S.r.L. Italy +Spain, Portugal Parametric Technology Espana, S.A. Spain +Switzerland Parametric Technology (Schweiz) AG German Law*, Landgericht Munchen I, Germany +United Kingdom Parametric Technology (UK) Limited United Kingdom +Remaining countries of the +European Union +PTC Software and Services (Ireland) Limited +Republic of Ireland Turkey, Kosovo, Serbia, Macedonia, Montenegro, Croatia, Bosnia and Herzegovina, and Albania +PTC Software and Services (Ireland) Limited +Republic of Ireland +The Russian Federation PTC International LLC Russian Law / International +Commercial Arbitration Court at the Chamber of Commerce and Industry of the Russian Federation in Moscow Belarus, Moldova, Ukraine, +Armenia, Georgia, Azerbaijan, Kazakhstan, Kyrgyzstan, Tajikistan, Turkmenistan, and Uzbekistan +PTC Software and Services (Ireland) Limited +Republic of Ireland +Norway, Sweden, and Denmark, Finland, Iceland, and the Faeroe Islands +PTC Sweden AB Sweden +Japan PTC Japan K.K. Japan / Tokyo District Court +Country PTC Affiliate Licensing Entity Governing Law/Jurisdiction for +Disputes +China Parametric Technology (Shanghai) Software Co., Ltd. +The People's Republic of China/China International Economic and Trade Arbitration Commission in Shanghai +Taiwan Parametric Technology Taiwan Limited Taiwan / Courts of Taipei, Taiwan +India Parametric Technology (India) Private +Limited +India +Korea Parametric Technology Korea Ltd. Republic of Korea +Other Asia Pacific Countries including Australia and New Zealand, but excluding China, Japan and Taiwan) +PTC Inc. Special Administrative Region of Hong +Kong / Hong Kong International +Arbitration Centre +Canada PTC (Canada) Inc. Ontario +Any other country PTC Inc., or such other affiliate of PTC as +PTC directs at the time of the order +Commonwealth of Massachusetts, +United States + +*Specific Provisions for Austria, Germany and Switzerland: +For Licensed Products licensed and used in Austria, Germany or Switzerland, the following provisions shall apply. The following +provisions shall have no applicability to any Licensed Products or Services purchased outside of +Austria, Germany or Switzerland. + +References to sections below are references to the applicable sections in the body of the Agreement. + +Section 1.4 (iv) above shall not apply to the extent that (i) the processes Customer undertakes are required to achieve +information necessary to achieve interoperability of an independently created computer program with other software +programs, (ii) the further requirements of Section 69e of the German Copyright Act are fulfilled and +(iii) PTC, upon +Customer's written request, has not made available the information required for this within a reasonable period. + +Sections 4.2 (Warranty), 4.4 (Sole Remedy), 4.5 (No Additional Warranties) and 4.6 (Disclaimer of +Warranties) are hereby +replaced by the following provisions: + +4.2 Warranty Period, Restarts and Investigation Duty. The limitation period for warranty claims shall be twelve (12) +months from delivery. Any replacement of the Licensed Product(s) and/or repair of Errors will not restart the warranty +period. The pre-requisite for the Customer's warranty claims (Mangelanspruche) is that: (i) the +Customer inspects the +Licensed Products according to Section 377 German Commercial Code, (ii) the defect is an Error as defined in this +Agreement, (iii) the Error already existed at the time of delivery and (iv) the Customer effects a proper notification of the +Error. Customer shall provide notifications of Errors to PTC in writing and Customer shall provide specific details of the +Error as deemed reasonable under the specific circumstances. Customer shall notify PTC of obvious +Errors in writing +within one week of delivery and of latent Errors within one week of discovery of such Error. The periods specified are +preclusion periods. + +4.4 Remedies. In the event of an Error, PTC in its sole discretion may: (a) replace the Licensed Product +(s) or (b) repair +the Error, provided that notice of the Error is received by PTC within the periods set forth in Section +4.2 and Customer +provides such additional information regarding the Error as PTC may reasonably request. If the repair +(either by providing +a bug fix, a workaround or otherwise) or replacement is not successful (after at least two repair attempts for the same Error +by PTC within a reasonable period of time), Customer shall be entitled, at Customer's choice, to either: +(i) rescission of the +affected order so that PTC provides a refund of the license fees paid by Customer for the applicable +Licensed Product(s) +upon return of such Licensed Product(s) and any copies made thereof or (ii) a reasonable reduction in the purchase price. +Replacements or repairs shall be made without acknowledgement of a legal obligation and shall not suspend the limitation +period for warranty claims related to the Licensed Products. + +4.5 No Additional Warranties. No employee, partner, distributor (including any Reseller) or agent of +PTC or any of its +resellers or sales agents is authorized to give representations, warranties or covenants greater or different than those +contained in this Agreement, except as specifically set forth in a written agreement signed on behalf of +Customer by an +authorized officer and on behalf of PTC by its legal counsel or Corporate Controller. Apart from claims for damages based +on Errors that are subject to the limitation of liability as set forth in Section 6, the obligations provided for in this Section 4 +shall be PTC's exclusive liability in case of warranty claims. + +4.6 Customer Responsibility. The Licensed Products are intended to be used by trained professionals and are not a +substitute for the exercise by Customer of professional judgement, testing, safety and utility in their use. Customer is +solely responsible for any results which were obtained by using the Licensed Products, including the adequacy of +independent testing of reliability and accuracy of any item designed using Licensed Products. + +4.7 Qualities (Beschaffenheit), Guarantees. Qualities of the Licensed Products stated in publications of +PTC or its sales +representatives, in particular in advertising, in drawings, brochures or other documents, including presentations in the +Internet, or on packaging and labeling of the Licensed Products, or which fall under trade usages, shall only be deemed to +be covered by the contractual quality of the Licensed Products if such qualities are expressly contained in an offer or an +order confirmation in writing. Guarantees, in particular guarantees as to quality, shall be binding on +PTC only to the extent +to which they (i) are contained in an offer or an order confirmation in writing, (ii) are expressly designated as "guarantee" +or "guarantee as to condition" (Beschaffenheitsgarantie), and (iii) expressly stipulate the obligations for +PTC resulting from such guarantee. + +Section 6 is hereby replaced by the following provisions: +6. Limitation of Liability + + 6.1 Liability Categories. PTC shall be liable for damages, regardless of the legal grounds, only if: (i) PTC breaches a +material contractual obligation (cardinal obligation) culpably (i.e., at least negligently), or (ii) the damage has been caused +by gross negligence or wilfull intent on the part of PTC or (iii) PTC has assumed a guarantee. + + 6.2 Predictability. PTC's liability shall be limited to the typical, foreseeable damage: (i) if PTC +breaches material +contractual obligations (cardinal obligations) with slight negligence, or (ii) if employees or agents of +PTC who are not +officers or executive staff have breached other obligations by gross negligence, or (iii) if PTC has assumed a guarantee, +unless such guarantee is expressly designated as guarantee as to condition (Beschaffenheitsgarantie). + + 6.3 Maximum Amount. In the cases of Section 6.2 (i) and (ii), PTC's liability shall be limited to a maximum amount of +EURO 1,000,000 or, in case of purely financial losses, to a maximum amount of EURO 100,000. + + 6.4 Indirect Damages. In the cases of Section 6.2, PTC shall not be liable for indirect damages, consequential damages or +loss of profit. + + 6.5 Liability Period. Customer's claims for damages against PTC and/or PTC's affiliates, regardless of the legal grounds, +shall expire at the latest one year from the time the Customer gains knowledge of the damage or, irrespective of this +knowledge, at the latest two years after the damaging event. For claims based on Errors of the Licensed +Product(s), the +warranty limitation period pursuant to Section 4.2 shall apply. + + 6.6 Mandatory Liability. PTC's liability pursuant to the German Product Liability Act +(Produkthaftungsgesetz), for injury +of life, body and health, for fraudulent concealment of a defect or for the assumption of a guarantee as to condition +(Beschaffenheitsgarantie) remains unaffected. + + 6.7 Employees. Sections 6.1 to 6.6 shall also apply in the case of any claims for damages of Customer against employees +or agents of PTC and/or PTC's affiliates. + + 6.8 Contributory Negligence. In the event of a guarantee or liability claim against PTC any contributory fault of +Customer must be taken into account accordingly, particularly in the event of inadequate fault notification or +inadequate data securing. It constitutes inadequate data securing if the client, among others, does not, by way of +appropriate state of the art security measures, take precautions against external influences, e.g. computer viruses and other +phenomena which could put individual data or an entire data stock at risk. Schedule B - Definitions + +"Concurrent User Products" means the Licensed Products licensed on a concurrent user basis, as +specified either in the Quote or at the Licensing Basis Webpage. + +"Designated Computer" means the central processing unit(s) designated in writing by Customer to PTC +at the time of installation of +the Licensed Products (as may be modified in accordance with Section 1.2 of this Agreement). + +"Designated Computer Product" means the Licensed Products licensed on a "Designated Computer" basis or otherwise designated as +"fixed," "locked" or "node-locked", as specified either in the Quote or at the Licensing Basis Webpage. Designated Computer +Products may not be remotely accessed or installed in a virtual environment. + +"Designated Country" means the country of installation specified in writing by Customer to PTC at the time Customer places its +order of the Licensed Products. The Designated Country may be changed only in accordance with +Section 1.2 of this Agreement. + +"Designated Network" means the network designated in writing by Customer to PTC at the time of installation of the Licensed +Products (as may be modified in accordance with Section 1.2 of this Agreement). + +"Designated Server" means a computer server designated in writing by Customer to PTC at the time of installation of the Licensed +Products (as may be modified in accordance with Section 1.2 of this Agreement) that has one unique instance of the applicable +installed Licensed Product application. + +"Designated Server Products" means the Licensed Products licensed on a Designated Server basis, as specified either in the Quote or +at the Licensing Basis Webpage. + +"Documentation" means the applicable Licensed Software user manuals provided or made available by electronic means by PTC at +the time of shipment of the Licensed Software. + +"Educational Software" means Licensed Products identified as "Priced for Education," "Student +Edition," "Schools Edition," + +"Schools Advanced Edition," "University Edition," "Professor's Edition/Version" or "Academic +Edition/Version," or otherwise +designated as educational or academic licenses. + +"Error" means a failure of the Licensed Software to conform substantially to the applicable +Documentation, provided that Customer +informs PTC of such failure in writing and PTC is able to replicate such failure after making reasonable efforts. + +"External User" means a Registered User who is a vendor or other third party external to the Customer and its affiliates. + +"License" shall have the meaning set out in Section 1.1 of the body of the Agreement. + +"License Term" means the time period during which the License for the applicable Licensed Products shall be in effect, as specified +in the name of the Licensed Product or in the applicable Quote (subject to earlier termination pursuant +to the terms hereof) or, if no +Quote was provided to Customer, as otherwise communicated by PTC to Customer. In the absence of a stated license term, the +License Term shall be perpetual, except that the License Term for evaluation Licenses shall be no longer than thirty days from the +date of Customer's request for an evaluation license, unless otherwise specifically designated by PTC, and the evaluation License +will cease to be operational after such term expires. The License Term of a "subscription" License is as specified in the Quote and/or +the invoice, and such License includes Support Services during such License Term at no additional fee. "License Locked Product" means a Licensed Product licensed for use with another PTC product to which the License Locked +Product is an extension. The License Locked Product will assume the licensing basis of such other product.. License Locked +Products are specified either in the Quote or at the Licensing Basis Webpage. + +"Licensed Products" means collectively the Licensed Software and the Documentation. + +"Licensed Software" means, collectively, the computer software product identified in the applicable +Quote, as well as (i) any +software product that is provided to operate with such computer software product (e.g., modules, software bundled with this software +product, etc.), but excluding any software that is a consulting services deliverable, (ii) any Error corrections pursuant to Section 4.4 +hereof, (iii) any updates, Error corrections and/or New Releases provided to Customer by PTC pursuant to Support Services +purchased by Customer and (iv) any computer software provided to Customer in the course of PTC's delivery of Training Services. + +"Licensing Basis Webpage" means the "Licensing Basis" document at http://www.ptc. com/support/customer_agreements/ +index.htm, which specifies the licensing basis of PTC's different products and states certain additional product-specific terms and +conditions. + +"Support Services" means the provision of New Releases and, depending on the level of Support +Services ordered, may also include +telephone support, web-based support tools, and correction of Errors, all in accordance with Schedule C +attached to this Agreement. + +"New Release" means a modified or enhanced version of a Licensed Product that is designated by PTC +as a new release of that +product and that PTC makes generally available to its Support Services customers. + +"Permitted User" means an individual who is authorized by Customer to use the Licensed Products, such use to be solely in +accordance with the terms and conditions of the Agreement. Permitted Users are limited to Customer's employees, consultants, +subcontractors, suppliers, business partners and customers who (i) are not competitors of PTC or employed by competitors of PTC +and (ii) are directly involved in the utilization of the Licensed Products solely in support of Customer's internal business purposes. +Customer shall at all times be responsible for its Permitted Users' compliance with this Agreement. + +"Per Instance Product" means a Licensed Product for which one License is required for each instance of a system to which the +applicable Licensed Product connects. For example, if an adapter that is licensed on a Per Instance basis enables Windchill to +connect to an ERP system and a CRM system, two licenses of such adapter will be required. The +Licensed Products that are Per +Instance Products are identified either in the Quote or at the Licensing Basis Webpage. + +"Quote" means the PTC product schedule, quote or order confirmation provided to Customer in connection with the purchase of the +applicable Licensed Product or, if no such document is provided, Customer's purchase order for such +Licensed Product, if any. + +"Registered User" means a Permitted User for whom Customer has purchased a License to use a +Registered User Product and for +whom Customer has issued a password or other unique identifier to enable such individual to use the +Registered User Product. + +"Registered User Products" means the Licensed Products licensed on a Registered User basis, as specified either in the Quote or at +the Licensing Basis Webpage. + +"Reseller" means a third-party appointed and authorized by PTC to resell or distribute any Licensed +Product. . + +"Services" means collectively Support Services and Training Services. + +"Site License" means a Licensed Product for which one License is required for each Customer location, as specified either in the +Quote or at the Licensing Basis Webpage. Multiple customer facilities located in the same city or town +(based on postal address) +shall be considered one "location," whereas locations located in different cities or towns will require multiple Site Licenses. + +"Training Services" means instruction or other training provided by PTC in the use of the Licensed +Products. "Training Services" +does not include PTC's e-Learning training products (e.g., "PTCU"), which are considered Licensed +Products for purposes of this +Agreement. + +"Uplift Fee" means a fee based upon the difference between the License fee applicable to installation of the applicable Licensed +Product in the original Designated Country and the License fee applicable to the installation of such +Licensed Product in the +Designated Country to which Customer wishes to move the Licensed Product. + +"Usage License Fee" means an ongoing fee that commences upon installation of the applicable +Licensed Product and that, during the +period for which the Usage License Fee is paid, entitles Customer to (i) continued use of the Licensed +Product in accordance with the +terms of the License and (ii) telephone support, Error corrections or workarounds, and New Releases for such software. + +Schedule C - PTC Support Services Terms and Conditions +The following additional terms and conditions apply to the provision of Support Services by PTC: Support Services Plan; Levels of Support Services. Upon PTC's acceptance of Customer's order for Support Services in respect of +the Licensed Products, PTC and/or its authorized subcontractors shall provide Support Services in accordance with these terms for a +time period of twelve (12) months or for such other period specified in Customer's order accepted by +PTC (a "Support Services +Plan"). All Support Services are provided subject to Customer's payment for such services at PTC's then-current rates, provided that +for Licensed Product licensed on a subscription basis, such License includes Support Services during such License Term at no +additional fee. If Customer does not order Support Services to commence on shipment of the Licensed +Product(s), or if Customer at +any time discontinues Support Services, and in either case subsequently wishes to obtain Support +Services, Customer must pay (i) the +then current fees for Support Services and (ii) the fees for Support Services for any period for which + +Customer has not purchased +Support Services. The then current levels of Support Services offered and the corresponding services provided thereunder are +described on http://www.ptc.com at http://www.ptc.com/support/maintenance/maintenance_support_policies.htm + +A Support Services Plan may not be cancelled by Customer following PTC's acceptance of an order for such Support Services Plan. +With respect to Registered User Products, e-Learning products and Integrity Concurrent User and +Server Licensed Products, Support +Services ordered by Customer must cover all Licenses granted to Customer for such Licensed Products. PTC is obligated to provide +Support Services only during periods for which Customer has paid the applicable Support Services fees and only in accordance with +the level of Support Services Customer has purchased. The services offered under any Support Services +Plan may change from time +to time, and PTC may cease to offer Support Services Plans at any time without notice, subject only to the obligation to refund to +Customer the unused portion of any previously paid applicable Support Services fee (on a prorated basis). + +(a) Telephone Support. If Customer purchases Support Services at a level that includes telephone support, Customer may utilize +PTC's telephone support service to report problems and seek assistance in use of the Licensed Products. The hours during which +PTC will provide telephone support will vary depending upon the level of Support Services ordered by +Customer. For all levels of +Support Services that include telephone support, PTC will provide telephone support in the languages, and during normal business +hours for the countries, listed on PTC's website at the website URL listed above. For levels of Support + +Services that include +telephone support during non-business hours, PTC will provide such support in the English language only. Regardless of the total +number of the Licensed Products licensed by Customer, Customer is entitled to telephone support only in direct connection with +Licenses that are covered by a Support Services Plan at a level that includes telephone support. + +(b) Repair of Errors. If Customer's Support Services Plan includes repair or workaround of Errors, PTC +shall use diligent efforts +to repair Errors or provide workarounds as required in such Support Services Plan, provided notice of the Error is received by PTC +during the term of a Support Services Plan and Customer supplies such additional information regarding the Error as PTC may +reasonably request. + +© New Releases. PTC will provide Customer with one copy of each New Release for each Licensed +Product for which +Customer is entitled to Support Services at the time the applicable language version of the New Release is made generally available. +Subject to different terms for particular products set forth at http://www.ptc.com/support/maintenance/maintenance_support_policies.htm, following shipment of the New Release, the previous +release shall remain "current" for purposes of this Agreement for a period of ninety (90) days; +thereafter only such New Release will be current. + +(d) Exclusions. + +(1) PTC is not obligated to perform investigation and/or repair of Errors (i) found by PTC to be in other than a current (as +described above), unaltered release of the Licensed Products; (ii) caused by changes to the Customer's operating systems, +environment, databases or other system components which adversely affect the Licensed Products; (iii) +caused by Customer's +modification of the Licensed Product or use thereof in combination or interconnection with software not provided by PTC; (iv) use of +the Licensed Product on a computer, operating system, software or peripherals other than a computer, operating system, software or +peripherals for which such Licensed Product was designed for and licensed for use on; (v) caused by improper or unauthorized use of +the Licensed Products; (vi) due to external causes such as, but not limited to, power failures or electric power surges; or (vii) due to a +failure by the Customer to implement recommendations in respect of solutions to Errors previously +provided by PTC to Customer. + +(2) PTC shall only be responsible for responding to problems reported by one of the two (2) technical contacts for +Customer's main location (which technical contacts and main location have previously been identified in writing to PTC by +Customer), and for sending New Releases to the "Central Support Location" designated by Customer in writing. Customer is +responsible for the distribution of New Releases to any of Customer's additional locations where +Licensed Products are authorized to +be used. Customer is responsible for providing to PTC in writing the name, address, phone number, fax number, and e-mail address +for each of Customer's designated contacts and Customer's Central Support Location. + +(3) PTC is not obligated to perform any Support Services with respect to modifications or customizations of the Licensed +Products, nor with respect to any developments resulting from Customer's use, development or customization of functionality +contained within the Licensed Products, all of which are Customer's sole responsibility + + + + +## MIT JsonCpp +============================ + + +The JsonCpp library's source code, including accompanying documentation, tests and demonstration applications, are licensed under the following conditions... + + +The author (Baptiste Lepilleur) explicitly disclaims copyright in all jurisdictions which recognize such a disclaimer. In such jurisdictions, this software is released into the Public Domain. + + +In jurisdictions which do not recognize Public Domain property (e.g. Germany as of +2010), this software is Copyright © 2007-2010 by Baptiste Lepilleur, and is released under the terms of the MIT License (see below). + + +In jurisdictions which recognize Public Domain property, the user of this software may choose to accept it either as 1) Public Domain, 2) under the conditions of the MIT License (see below), or 3) under the terms of dual Public Domain/MIT License conditions described here, as they choose. + + +The MIT License is about as close to Public Domain as a license can get, and is described in clear, concise terms at: + + +http://en.wikipedia.org/wiki/MIT_License + + +### The full text of the MIT License follows: +Copyright © 2007-2010 Baptiste Lepilleur + + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, +modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + + +The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. + + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. + +(END LICENSE TEXT) + + +The MIT license is compatible with both the GPL and commercial software, affording one all of the rights of Public Domain with the minor nuisance of being required to keep the above copyright notice and license text in the source code. Note also that by accepting the Public Domain "license" you can re-license your copy using whatever license you like. + + + +## Open source HPND License + +PIL +The Python Imaging Library (PIL) is + + +Copyright © 1997-2011 by Secret Labs AB Copyright © 1995-2011 by Fredrik Lundh + + +Pillow is the friendly PIL fork. It is + + +Copyright © 2010-2022 by Alex Clark and contributors +Like PIL, Pillow is licensed under the open source HPND License: + + +By obtaining, using, and/or copying this software and/or its associated documentation, you agree that you have read, understood, and will comply with the following terms and conditions: + + +Permission to use, copy, modify, and distribute this software and its associated documentation for any purpose and without fee is hereby granted, provided that the above copyright notice appears in all copies, and that +both that copyright notice and this permission notice appear in supporting documentation, and that the name of Secret Labs AB or the author not be used in advertising or publicity pertaining to distribution of the software without specific, written prior permission. + + +SECRET LABS AB AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS +SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. +IN NO EVENT SHALL SECRET LABS AB OR THE AUTHOR BE LIABLE FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM +LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE +OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. + + + + +END OF (3) ) Ion Chef™ Instrument Software Version 5.18 END USER LICENSE AGREEMENT +**************************************************** +**************************************************** +**************************************************** +**************************************************** +**************************************************** +(4) BEGINS: + +LIFE TECHNOLOGIES CORPORATION +END USER LICENSE AGREEMENT and LIMITED PRODUCT WARRANTY +FOR ION GENESTUDIOTM S5 INSTRUMENT SOFTWAREVERSION 5.18 INSTRUMENT OPERATING SOFTWARE +NOTICE TO USER: PLEASE READ THIS DOCUMENT CAREFULLY. THIS IS THE CONTRACT BETWEEN YOU AND LIFE TECHNOLOGIES CORPORATION ("LIFE TECHNOLOGIES") REGARDING THE OPERATING SOFTWARE FOR YOUR LIFE TECHNOLOGIES WORKSTATION OR OTHER INSTRUMENT AND BUNDLED SOFTWARE INSTALLED WITH YOUR OPERATING SOFTWARE. THIS AGREEMENT CONTAINS WARRANTY AND LIABILITY DISCLAIMERS AND LIMITATIONS. YOUR INSTALLATION AND USE OF THIS LIFE TECHNOLOGIES SOFTWARE IS SUBJECT TO THE TERMS AND CONDITIONS CONTAINED IN THIS END USER SOFTWARE LICENSE AGREEMENT, AND YOU WILL BE BOUND BY THESE TERMS AND CONDITIONS IF YOU INSTALL AND USE THE SOFTWARE. + +IF YOU DO NOT AGREE TO THESE TERMS AND CONDITIONS, YOU SHOULD PROMPTLY RETURN THIS SOFTWARE, TOGETHER WITH ALL PACKAGING, TO LIFE TECHNOLOGIES AND YOUR PURCHASE PRICE WILL BE REFUNDED. +This Life Technologies End User License Agreement accompanies a Life Technologies software product ("Software") and related explanatory materials ("Documentation"). The term "Software" also includes any upgrades, modified versions, updates, additions and copies of the Software licensed to you by Life Technologies. The term "License" or "Agreement" means this End User Software License Agreement. The term "you" or "Licensee" means the purchaser or user of this license to the Software. This Agreement includes herein by reference any additional use restrictions or Limited Use Label Licenses listed in or on user manuals, labeling, product inserts, technical notes, literature (including but not limited to Documentation) and/or splash screens related to this Software ("Supplemental Terms"). To the extent such Supplemental Terms are more restrictive than those contained herein, the more restrictive usage terms shall control. +This Software may use third-party software components from several sources. Portions of these software components are copyrighted and licensed by their respective owners. Various components require distribution of source code or if a URL is used to point the end-user to a source-code repository, and the source code is not available at such site, the distributor must, for a time determined by the license, offer to provide the source code. In such cases, please contact your Life Technologies representative. As well, various licenses require that the end-user receive a copy of the license. Such licenses, if any, may be found in Appendix 1 below. In order to use this Software, the end-user must abide by the terms and conditions of these third-party licenses. + +TITLE + +Title, ownership rights and intellectual property rights in and to the Software and Documentation shall at all times remain with Life Technologies and its subsidiaries, and their suppliers. All rights not specifically granted by this License, including Federal and international copyrights, are reserved by Life Technologies or their respective owners. + +COPYRIGHT + +The Software, including its structure, organization, code, user interface and associated Documentation, is a proprietary product of Life Technologies or its suppliers, and is protected by international laws of copyright. The law provides for civil and criminal penalties for anyone in violation of the laws of copyright. + +LICENSE + +USE OF THE SOFTWARE + +Subject to the terms and conditions of this Agreement, Life Technologies grants the purchaser of this product a non-exclusive, non-transferable (except in connection with the sale of the instrument on which it is hereby pre-installed) license, with no rights to sublicense, only to use the Software in object code (machine readable) format only on the single instrument on which it has been pre-installed by Life Technologies. + +RESTRICTIONS + +Unless permitted by applicable law, and in such cases only to the extent permitted by such law: + +7. You shall not copy, transfer (except temporarily in the event of a computer malfunction), rent, modify, distribute, electronically transmit, lend, lease, use, create derivative works based on the Software or merge the Software, or the associated Documentation, in whole or in part, whether alone or combined with any other products, except as expressly permitted in this Agreement. +8. You shall not reverse assemble, decompile, discover the source code or otherwise reverse engineer the Software. +9. You shall not remove any proprietary, copyright, trade secret or warning legend from the Software or any Documentation. +10. You agree to comply fully with all export laws and restrictions and regulations of the United States or applicable foreign agencies or authorities. You agree that you will not export or reexport, directly or indirectly, the Software and the Documentation into any country prohibited by the United States Export Administration Act and the regulations thereunder or other applicable United States law. +11. You may not use the Software or Documentation for the benefit of any third party by means of an outsourcing or service bureau relationship or for any similar commercial time-sharing or third-party training use. +12. You shall not sell, rent, transfer, resell for profit, or distribute this license or the Software, or any part thereof or any interest therein, unless the next user agrees to comply with the terms of this End User License Agreement. + +VERIFICATION + +At the written request of Life Technologies, not more frequently than annually, you shall furnish Life Technologies with a signed certification verifying that the Software is being used pursuant to the provisions of this License. + +TRIAL + +If this license is granted on a trial basis, you are hereby notified that license management software may be included to automatically cause the Software to cease functioning at the end of the trial period (and in any case you agree to discontinue usage at the end of the trial period or at the express written request of Life Technologies). + +TERMINATION + +You may terminate this Agreement by discontinuing use of the Software, removing all copies from your computers and storage media, and returning the Software and Documentation, and all copies thereof, to Life Technologies. Life Technologies may terminate this Agreement if you fail to comply with all of its terms, in which case you agree to discontinue using the Software, remove all copies from your computers and storage media, and return the Software and Documentation, and all copies thereof, to Life Technologies. + +U.S. GOVERNMENT END USERS + +The Software is a "commercial item," as that term is defined in 48 C.F.R. 2.101 (Oct. 1995), consisting of "commercial computer software" and "commercial computer software documentation," as such terms are used in 48 C.F.R. 12.212 (Sept. 1995). Consistent with 48 C.F.R. 12.212 and 48 C.F.R. 227.7202-1 through 227.7202-4 (June 1995), all U.S. Government End Users acquire the Software with only those rights set forth herein. + +EUROPEAN UNION END USERS + +If this Software is used within a country of the European Union, nothing in this Agreement shall be construed as restricting any rights available under Directive 2009/24/EC of the European Parliament and of the Council of 23 April 2009 on the legal protection of computer programs. + +LIMITED WARRANTY AND LIMITATION OF REMEDIES + +Limited Warranty. Life Technologies warrants that, except for Software provided on a trial basis, for a period of ninety days from the beginning of the applicable warranty period (as described below) the Software will, under normal use and as unmodified, function substantially in accordance with the functions and features described in the Documentation delivered with the Software when properly installed, and that for a period of ninety days from the beginning of the applicable warranty period (as described below) the tapes, CDs, diskettes or other media bearing the Software will be free of defects in materials and workmanship under normal use. +The above warranties do not apply to defects resulting from misuse, neglect, or accident, including without limitation: operation outside of the environmental or use specifications, or not in conformance with the instructions for any instrument system, software, or accessories; improper or inadequate maintenance by the user; installation of software or interfacing, or use in combination with software or products not supplied or authorized by Life Technologies; and modification or repair of the products not authorized by Life Technologies. +Warranty Period Commencement Date. The applicable warranty period for software begins on the earlier of the date of installation or three (3) months from the date of shipment for software installed by Life Technologies personnel. For software installed by the purchaser or anyone other than Life Technologies, the warranty period begins on the date the software is delivered to you. The applicable warranty period for media begins on the date the media is delivered to the purchaser. + +LIFE TECHNOLOGIES MAKES NO OTHER WARRANTIES OF ANY KIND WHATSOEVER, EXPRESS OR IMPLIED, WITH RESPECT TO THE SOFTWARE, DATA GENERATED FROM THE USE OF THE SOFTWARE ("GENERATED DATA") OR DOCUMENTATION, INCLUDING BUT NOT LIMITED TO WARRANTIES OF FITNESS FOR A PARTICULAR PURPOSE OR MERCHANTABILITY, NON-INFRINGEMENT OR NON-MISSAPROPRIATION OF INTELLECTUAL PROPERTY RIGHTS OF A THIRD PARTY, CUSTOM, TRADE, QUIET ENJOYMENT, ACCURACY OF INFORMATIONAL CONTENT, OR SYSTEM INTEGRATION. ALL OTHER WARRANTIES ARE EXPRESSLY DISCLAIMED. WITHOUT LIMITING THE GENERALITY OF THE FOREGOING, LIFE TECHNOLOGIES MAKES NO WARRANTIES THAT THE SOFTWARE WILL MEET YOUR REQUIREMENTS, THAT OPERATION OF THE SOFTWARE WILL BE UNINTERRUPTED OR ERROR FREE OR COMPLETELY SECURE, WILL OPERATE IN COMBINATION WITH THIRD PARTY HARDWARE OR SOFTWARE PRODUCTS, OR WILL CONFORM EXACTLY TO THE DOCUMENTATION, OR THAT LIFE TECHNOLOGIES WILL CORRECT ALL PROGRAM ERRORS. LIFE TECHNOLOGIES SOLE LIABILITY AND RESPONSIBILITY FOR BREACH OF WARRANTY RELATING TO THE SOFTWARE OR DOCUMENTATION SHALL BE LIMITED, AT LIFE TECHNOLOGIES SOLE OPTION, TO (1) CORRECTION OF ANY ERROR IDENTIFIED TO LIFE TECHNOLOGIES IN A WRITING FROM YOU IN A SUBSEQUENT RELEASE OF THE SOFTWARE, WHICH SHALL BE SUPPLIED TO YOU FREE OF CHARGE, (2) ACCEPTING A RETURN OF THE PRODUCT, AND REFUNDING THE PURCHASE PRICE UPON RETURN OF THE PRODUCT AND REMOVAL OF ALL COPIES OF THE SOFTWARE FROM YOUR COMPUTERS AND STORAGE DEVICES, (3) REPLACEMENT OF THE DEFECTIVE SOFTWARE WITH A FUNCTIONALLY EQUIVALENT PROGRAM AT NO CHARGE TO YOU, OR (4) PROVIDING A REASONABLE WORK AROUND WITHIN A REASONABLE TIME. LIFE TECHNOLOGIES SOLE LIABILITY AND RESPONSIBILITY UNDER THIS AGREEMENT FOR BREACH OF WARRANTY RELATING TO MEDIA IS THE REPLACEMENT OF DEFECTIVE MEDIA RETURNED WITHIN 90 DAYS OF THE DELIVERY DATE. THESE ARE YOUR SOLE AND EXCLUSIVE REMEDIES FOR ANY BREACH OF WARRANTY. WARRANTY CLAIMS MUST BE MADE WITHIN THE APPLICABLE WARRANTY PERIOD. +YOU ACKNOWLEDGE THAT LIFE TECHNOLOGIES HAS NO CONTROL OVER THE SPECIFIC CONDITIONS UNDER WHICH YOU USE THE SOFTWARE. ACCORDINGLY, EXCEPT FOR THE FOREGOING EXPRESS WARRANTY, LICENSOR CANNOT AND DOES NOT WARRANT THE PERFORMANCE OF THE SOFTWARE OR ANY PARTICULAR RESULTS THAT MAY BE OBTAINED BY THE USE OF THE SOFTWARE. THE SOFTWARE DOES NOT REPLACE YOUR OBLIGATION TO EXERCISE YOUR INDEPENDENT JUDGMENT IN USING THE SOFTWARE. The warranties made by Life Technologies may be voided by abuse or misuse of the Software. + +LIMITATION OF LIABILITY + +IN NO EVENT SHALL LIFE TECHNOLOGIES OR ITS SUPPLIERS BE RESPONSIBLE OR LIABLE, WHETHER IN CONTRACT, TORT, WARRANTY OR UNDER ANY STATUTE (INCLUDING WITHOUT LIMITATION ANY TRADE PRACTICE, UNFAIR COMPETITION OR OTHER STATUTE OF SIMILAR IMPORT) OR ON ANY OTHER BASIS FOR DAMAGES ARISING FROM PERSONAL INJURY OR DEATH OR SPECIAL, INDIRECT, INCIDENTAL, MULTIPLE, PUNITIVE, OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE POSSESSION OR USE OF, OR THE INABILITY TO USE, THE SOFTWARE, THE GENERATED DATA OR DOCUMENTATION, EVEN IF LIFE TECHNOLOGIES IS ADVISED IN ADVANCE OF THE POSSIBILITY OF SUCH DAMAGES, INCLUDING WITHOUT LIMITATION DAMAGES OR EXPENSES ARISING FROM OR RELATED TO, OR ALLEGED TO HAVE ARISEN FROM OR BE RELATED TO, LOSS OF USE, LOSS OF DATA, DOWNTIME, OR FOR LOSS OF REVENUE, PROFITS, GOODWILL OR BUSINESS OR OTHER FINANCIAL LOSS. IN ANY CASE, THE ENTIRE LIABILITY OF LIFE TECHNOLOGIES AND ITS SUPPLIERS UNDER THIS LICENSE, OR ARISING OUT OF THE USE OF THE SOFTWARE OR DOCUMENTATION OR GENERATED DATA, SHALL NOT EXCEED, IN THE AGGREGATE, THE PURCHASE PRICE OF THE PRODUCT. +SOME STATES, COUNTRIES OR JURISDICTIONS LIMIT THE SCOPE OF OR PRECLUDE LIMITATIONS OR EXCLUSION OF REMEDIES OR DAMAGES, OR OF LIABILITY, SUCH AS LIABILITY FOR GROSS NEGLIGENCE OR WILLFUL MISCONDUCT, AS OR TO THE EXTENT SET FORTH ABOVE, OR DO NOT ALLOW IMPLIED WARRANTIES TO BE EXCLUDED. IN SUCH STATES, COUNTRIES OR JURISDICTIONS, THE LIMITATION OR EXCLUSION OF WARRANTIES, REMEDIES, DAMAGES OR LIABILITY SET FORTH ABOVE MAY NOT APPLY TO YOU. HOWEVER, ALTHOUGH THEY SHALL NOT APPLY TO THE EXTENT PROHIBITED BY LAW, THEY SHALL APPLY TO THE FULLEST EXTENT PERMITTED BY LAW. YOU MAY ALSO HAVE OTHER RIGHTS THAT VARY BY STATE, COUNTRY OR OTHER JURISDICTION. +CONFIDENTIALITY + +You agree to protect Life Technologies Confidential Information with the same degree of care used to protect your own confidential information (but in no event less than a reasonable standard of care), and not to use or disclose any portion of such Confidential Information to third parties, except as expressly authorized in this Agreement. You acknowledge that the Software, including its content, structure, organization and design constitute proprietary and valuable trade secrets (and other intellectual property rights) of Life Technology and/or its licensors. The term "Confidential Information" means, collectively, non-public information that Life Technologies (and its licensors) provide and reasonably consider to be of a confidential, proprietary or trade secret nature, including but not limited to (i) the Software, and (ii) confidential elements of the Software and Life Technologies (and its licensors') technology and know-how, whether in tangible or intangible form, whether designated as confidential or not, and whether or not stored, compiled or memorialized physically, electronically, graphically, photographically, or in writing. Confidential Information does not include any information which you can demonstrate by credible evidence: (a) is, as of the time of its disclosure, or thereafter becomes part of the public domain through no fault of yours; (b) was rightfully known to you prior to the time of its disclosure, or to have been independently developed by you without use of Confidential Information; and/or © is subsequently learned from a third party not under a confidentiality obligation with respect to such Confidential Information. Confidential Information that is required to be disclosed by you pursuant to a duly authorized subpoena, court order, or government authority shall continue to be Confidential Information for all other purposes and you agree, prior to disclosing pursuant to a subpoena, court order, or government authority, to provide prompt written notice and assistance to Life Technologies prior to such disclosure, so that Life Technologies may seek a protective order or other appropriate remedy to protect against disclosure. + +SOFTWARE IMPROVEMENTS + +You acknowledge and agree that any ideas, enhancements, modifications, and the like disclosed by you to Life Technologies with respect to the Software ("Software Improvements and Feedback") will be the property of Life Technologies. You agree to assign, and hereby assign, all right, title, and interest worldwide in the Software Improvements and Feedback to Life Technologies and agree to assist Life Technologies, at Life Technologies' expense, in perfecting and enforcing Life Technologies rights thereto and ownership thereof. You acknowledge and agree that Life Technologies may use such Software Improvements and Feedback for its business purposes without restriction. + +GENERAL + +This Agreement shall be governed by laws of the State of California, exclusive of its conflict of laws provisions. This Agreement shall not be governed by the United Nations Convention on Contracts for the International Sale of Goods. This Agreement contains the complete agreement between the parties with respect to the subject matter hereof, and supersedes all prior or contemporaneous agreements or understandings, whether oral or written. If any provision of this Agreement is held by a court of competent jurisdiction to be contrary to law, that provision will be enforced to the maximum extent permissible and the remaining provisions of this Agreement will remain in full force and effect. The controlling language of this Agreement, and any proceedings relating to this Agreement, shall be English. You agree to bear any and all costs of translation, if necessary. The headings to the sections of this Agreement are used for convenience only and shall have no substantive meaning. All questions concerning this Agreement shall be directed to: Life Technologies Corporation, 5781 Van Allen Way, Carlsbad, CA 92008, Attention: Legal Department. +Unpublished rights reserved under the copyright laws of the United States. Life Technologies Corporation, 5781 Van Allen Way, Carlsbad, CA 92008. +Life Technologies is a trademark of Life Technologies Corporation or its subsidiaries in the U.S. and certain other countries. +All other trademarks are the sole property of their respective owners. + +May 26, 2022 + +Appendix 1 + +Life Technologies Corporation +Third Party Copyright Notices and Licenses + +Ion GeneStudioTM S5 Instrument Software VERSION 5.18 INSTRUMENT OPERATING SOFTWARE +This software uses third party software components from several sources. Portions of these software components are copyrighted and licensed by their respective owners as indicated below. Various licenses require distribution of source code or if a link is used to point the end-user to a source-code repository, and the source code is not available at such site, the distributor must, for a time determined by license, offer to provide source code. In such cases, please contact your Life Technologies representative. As well, various licenses require that the end-user receive a copy of the license or certain notices. Such licenses and notices may be found in this appendix. + +MIT/X derivate license libcurl +The curl license +COPYRIGHT AND PERMISSION NOTICE + + +Copyright © 1996 - 2022, Daniel Stenberg, daniel@haxx.se, and many contributors, see the THANKS +file. + + +All rights reserved. + + +Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. + + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT OF THIRD PARTY RIGHTS. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. + + +Except as contained in this notice, the name of a copyright holder shall not be used in advertising or otherwise to promote the sale, use or other dealings in this Software without prior written authorization of the copyright holder. + + + +## MIT +json library + +Copyright © 2007-2010 Baptiste Lepilleur and The JsonCpp Authors + + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, +modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + + +The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. + + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. + +======================================================================== +(END LICENSE TEXT) + + +The MIT license is compatible with both the GPL and commercial software, affording one all of the rights of Public Domain with the minor nuisance of being required to keep the above copyright notice and license text in the source code. Note also that by accepting the Public Domain "license" you can re-license your copy using whatever license you like. + + + +## LGPL-2.1 + +libjpeg + +Format-Specification: http://svn.debian.org/wsvn/dep/web/deps/dep5.mdwn?op=file&rev=135 + +Name: libjpeg8-empty + + +Files: * + +Copyright: 2011 Linaro Limited + +License: LGPL-2.1 + +This library is free software; you can redistribute it and/or modify it under the terms of the GNU Library General Public License (LGPL) as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. + +* This library is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Library General Public License for more details. +* You should have received a copy of the GNU Library General Public License along with this library; see the file COPYING.LIB. If not, write to +the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. +* On Debian systems, the complete text of the GNU Library General Public +License, version 2, can be found in /usr/share/common-licenses/LGPL-2.1. + + + +## LGPL-2.1 libpthread +This is the Debian prepackaged version of the Embedded GNU C Library version 2.19. + + +It was put together by the GNU Libc Maintainers +from + + +* Most of the GNU C library is under the following copyright: + + +Copyright © 1991,92,93,94,95,96,97,98,99,2000,2001,2002,2003,2004,2005, +2006,2007,2008,2009,2010,2011 Free Software Foundation, Inc. + + +The GNU C Library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. + + +The GNU C Library is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. + + +You should have received a copy of the GNU Lesser General Public License along with the GNU C Library; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA +02110-1301 USA + +On Debian systems, the complete text of the GNU Library +General Public License can be found in `/usr/share/common-licenses/LGPL-2.1'. + + +* The utilities associated with GNU C library is under the following copyright: + + +Copyright © 1991,92,93,94,95,96,97,98,99,2000,2001,2002,2003,2004,2005, +2006,2007,2008,2009,2010,2011 Free Software Foundation, Inc. + + +This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; version 2 of the License, or +(at your option) any later version. + + +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. + + +You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + + +On Debian systems, the complete text of the GNU Library +General Public License can be found in `/usr/share/common-licenses/GPL-2'. + + +* All code incorporated from 4.4 BSD is distributed under the following license: + + +Copyright © 1991 Regents of the University of California. All rights reserved. + + +Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: + + +1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. +2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. +3. [This condition was removed.] +4. Neither the name of the University nor the names of its contributors may be used to endorse or promote products derived from this software +without specific prior written permission. + + +THIS SOFTWARE IS PROVIDED BY THE REGENTS AND CONTRIBUTORS ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +PURPOSE +ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR +CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS +OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, +STRICT +LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +* The DNS resolver code, taken from BIND 4.9.5, is copyrighted both by UC Berkeley and by Digital Equipment Corporation. The DEC portions are under the following license: +Portions Copyright © 1993 by Digital Equipment Corporation. Permission to use, copy, modify, and distribute this software for any +purpose with or without fee is hereby granted, provided that the above +copyright notice and this permission notice appear in all copies, and that the name of Digital Equipment Corporation not be used in advertising or publicity pertaining to distribution of the document or software without specific, written prior permission. + + +THE SOFTWARE IS PROVIDED ``AS IS'' AND DIGITAL EQUIPMENT CORP. +DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL DIGITAL EQUIPMENT CORPORATION BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER +RESULTING +FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. + + +* The Sun RPC support (from rpcsrc-4.0) is covered by the following license: +Copyright © 2010, Oracle America, Inc. + + +Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: + + +* Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. +* Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. +* Neither the name of the "Oracle America, Inc." nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. + + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS +FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +* The following CMU license covers some of the support code for Mach, derived from Mach 3.0: + + +Mach Operating System +Copyright © 1991,1990,1989 Carnegie Mellon University +All Rights Reserved. + + +Permission to use, copy, modify and distribute this software and its documentation is hereby granted, provided that both the copyright notice and this permission notice appear in all copies of the software, derivative works or modified versions, and any portions thereof, and that both notices appear in supporting documentation. + + +CARNEGIE MELLON ALLOWS FREE USE OF THIS SOFTWARE IN ITS ``AS IS'' CONDITION. CARNEGIE MELLON DISCLAIMS ANY LIABILITY OF ANY KIND FOR ANY DAMAGES WHATSOEVER RESULTING FROM THE USE OF THIS SOFTWARE. + + +Carnegie Mellon requests users of this software to return to + + +Software Distribution Coordinator School of Computer Science Carnegie Mellon University Pittsburgh PA 15213-3890 + + +or Software.Distribution@CS.CMU.EDU any improvements or extensions that they make and grant Carnegie Mellon the rights to redistribute these changes. +* The file if_ppp.h is under the following CMU license: Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions +are met: +1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. +2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. +3. Neither the name of the University nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. + + +THIS SOFTWARE IS PROVIDED BY CARNEGIE MELLON UNIVERSITY AND CONTRIBUTORS ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE UNIVERSITY OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN +IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +* The following license covers the files from Intel's "Highly Optimized +Mathematical Functions for Itanium" collection: + +Intel License Agreement + + +Copyright © 2000, Intel Corporation + + +All rights reserved. + + +Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: + + +* Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. + + +* Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. + + +* The name of Intel Corporation may not be used to endorse or promote products derived from this software without specific prior written permission. + + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL INTEL OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +* The files inet/getnameinfo.c and sysdeps/posix/getaddrinfo.c are copyright +© by Craig Metz and are distributed under the following license: + + +* The Inner Net License, Version 2.00 + + +The author(s) grant permission for redistribution and use in source and +binary forms, with or without modification, of the software and documentation provided that the following conditions are met: + + +0. If you receive a version of the software that is specifically labelled +as not being for redistribution (check the version message and/or README), +you are not permitted to redistribute that version of the software in any way or form. +1. All terms of the all other applicable copyrights and licenses must be followed. +2. Redistributions of source code must retain the authors' copyright notice(s), this list of conditions, and the following disclaimer. +3. Redistributions in binary form must reproduce the authors' copyright notice(s), this list of conditions, and the following disclaimer in the documentation and/or other materials provided with the distribution. +4. [The copyright holder has authorized the removal of this clause.] +5. Neither the name(s) of the author(s) nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. + + +THIS SOFTWARE IS PROVIDED BY ITS AUTHORS AND CONTRIBUTORS ``AS IS'' AND ANY +EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +ARE +DISCLAIMED. IN NO EVENT SHALL THE AUTHORS OR CONTRIBUTORS BE LIABLE FOR ANY +DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES +(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; +LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON +ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS +SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. If these license terms cause you a real problem, contact the author. */ + +## MIT +libxml + +https://gitlab.gnome.org/GNOME/libxml2/-/wikis/home + + +The MIT License +OSI Approved License LogoLicense Copyright: Unknown. License License: Unknown. +License Contact: Unknown. + +SPDX short identifier: MIT Further resources... + +Begin license text. +Copyright + + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + + +The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. + + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. + + +End license text. + + + + +## LGPL-2.1+ +libudev + +Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: systemd +Upstream-Contact: systemd-devel@lists.freedesktop.org +Source: https://www.freedesktop.org/wiki/Software/systemd/ + + +Files: debian/* +Copyright: 2010-2013 Tollef Fog Heen +2013-2015 Michael Biebl +2013 Michael Stapelberg License: LGPL-2.1+ + + +Files: * + +Copyright: 2008-2015 Kay Sievers + +2010-2015 Lennart Poettering +2012-2015 Zbigniew Ja ™ drzejewski-Szmek +2013-2015 Tom Gundersen +2013-2015 Daniel Mack +2010-2015 Harald Hoyer +2013-2015 David Herrmann +2013, 2014 Thomas H.P. Andersen +2013, 2014 Daniel Buch +2014 Susant Sahani +2009-2015 Intel Corporation +2000, 2005 Red Hat, Inc. +2009 Alan Jenkins +2010 ProFUSION embedded systems +2010 Maarten Lankhorst +1995-2004 Miquel van Smoorenburg +1999 Tom Tromey +2011 Michal Schmidt +2012 B. Poettering +2012 Holger Hans Peter Freyther +2012 Dan Walsh +2012 Roberto Sassu +2013 David Strauss +2013 Marius Vollmer +2013 Jan Janssen +2013 Simon Peeters +License: LGPL-2.1+ + + +Files: src/basic/siphash24.h src/basic/siphash24.c +Copyright: 2012 Jean-Philippe Aumasson +2012 Daniel J. Bernstein License: CC0-1.0 + + +Files: src/basic/securebits.h +Copyright: Linus Torvalds License: GPL-2 + + +Files: src/basic/ioprio.h +Copyright: Jens Axboe License: GPL-2 + + +Files: src/shared/linux/auto_dev-ioctl.h +Copyright: 2008 Red Hat, Inc. +2008 Ian Kent License: GPL-2+ + + +Files: src/basic/sparse-endian.h +Copyright: 2012 Josh Triplett License: Expat + + +Files: src/journal/lookup3.c src/journal/lookup3.h +Copyright: none +License: public-domain +You can use this free for any purpose. It's in the public domain. It has no warranty. + + +Files: src/udev/* +Copyright: 2003-2012 Kay Sievers +2003-2004 Greg Kroah-Hartman +2004 Chris Friesen +2004, 2009, 2010 David Zeuthen +2005, 2006 SUSE Linux Products GmbH +2003 IBM Corp. +2007 Hannes Reinecke +2009 Canonical Ltd. +2009 Scott James Remnant +2009 Martin Pitt +2009 Piter Punk +2009, 2010 Lennart Poettering +2009 Filippo Argiolas +2010 Maxim Levitsky +2011 ProFUSION embedded systems +2011 Karel Zak +2014 Zbigniew Ja ™ drzejewski-Szmek +2014 David Herrmann +2014 Carlos Garnacho License: GPL-2+ + + +Files: src/udev/udev-ctrl.c src/udev/udevadm-hwdb.c src/udev/udev-builtin.c src/udev/udev-builtin-net_id.c +src/udev/udev-builtin-net_setup_link.c src/udev/udev-builtin-hwdb.c src/udev/udev-builtin-btrfs.c src/udev/udev-builtin-keyboard.c +src/udev/net/link-config.h src/udev/net/link-config.c src/udev/net/ethtool-util.c src/udev/net/ethtool-util.h +Copyright: 2007-2013 Kay Sievers +2013 Tom Gundersen License: LGPL-2.1+ + + +Files: src/udev/scsi_id/scsi.h Copyright: 2003 IBM Corp. License: GPL-2 + + +License: Expat + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to +deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + +* The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. +* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS +IN THE SOFTWARE. + + +## License: GPL-2 +This program is free software; you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by the Free Software Foundation; version 2 of the License. +* This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. +You should have received a copy of the GNU General Public License +along with this program; if not, write to the Free Software Foundation, Inc., +51 Franklin St, Fifth Floor, Boston, MA 02110-1301, USA. +*On Debian and systems the full text of the GNU General Public +License version 2 can be found in the file +`/usr/share/common-licenses/GPL-2` + + +## License: GPL-2+ +This program is free software; you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2, or (at your option) +any later version. + +* This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. +* You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, +Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. +* On Debian systems, the complete text of the GNU General Public License version 2 can be found in `/usr/share/common-licenses/GPL-2` ™ . + + +## License: LGPL-2.1+ +This program is free software; you can redistribute it and/or modify +it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1, or (at your option) +any later version. + +* This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. +* You should have received a copy of the GNU Lesser General Public License along with this program; if not, write to the Free Software Foundation, +Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. +* On Debian systems, the complete text of the GNU Lesser General Public +License version 2.1 can be found in `/usr/share/common-licenses/LGPL-2.1`™ . + +## License: CC0-1.0 +To the extent possible under law, the author(s) have dedicated all copyright and related and neighboring rights to this software to the public domain worldwide. This software is distributed without any warranty. + +* You should have received a copy of the CC0 Public Domain Dedication along with this software. If not, see . +* On Debian systems, the complete text of the CC0 1.0 Universal license can be found in `/usr/share/common-licenses/CC0-1.0` ™ . + + +## Libpng license libpng12 + +COPYRIGHT NOTICE, DISCLAIMER, and LICENSE + + +### PNG Reference Library License version 2 + + +* Copyright © 1995-2019 The PNG Reference Library Authors. +* Copyright © 2018-2019 Cosmin Truta. +* Copyright © 2000-2002, 2004, 2006-2018 Glenn Randers-Pehrson. +* Copyright © 1996-1997 Andreas Dilger. +* Copyright © 1995-1996 Guy Eric Schalnat, Group 42, Inc. + + +The software is supplied "as is", without warranty of any kind, express or implied, including, without limitation, the warranties of merchantability, fitness for a particular purpose, title, and +non-infringement. In no event shall the Copyright owners, or anyone distributing the software, be liable for any damages or other liability, whether in contract, tort or otherwise, arising from, out of, or in connection with the software, or the use or other dealings in the software, even if advised of the possibility of such damage. + + +Permission is hereby granted to use, copy, modify, and distribute this software, or portions hereof, for any purpose, without fee, subject to the following restrictions: + + +1. The origin of this software must not be misrepresented; you must not claim that you wrote the original software. If you +use this software in a product, an acknowledgment in the product documentation would be appreciated, but is not required. +2. Altered source versions must be plainly marked as such, and must not be misrepresented as being the original software. + + +3. This Copyright notice may not be removed or altered from any source or altered source distribution. + + + +## PNG Reference Library License version 1 (for libpng 0.5 through 1.6.35) + + +libpng versions 1.0.7, July 1, 2000, through 1.6.35, July 15, 2018 are Copyright © 2000-2002, 2004, 2006-2018 Glenn Randers-Pehrson, are derived from libpng-1.0.6, and are distributed according to the same disclaimer and license as libpng-1.0.6 with the following individuals added to the list of Contributing Authors: + + +Simon-Pierre Cadieux +Eric S. Raymond Mans Rullgard Cosmin Truta Gilles Vollant James Yu +Mandar Sahastrabuddhe +Google Inc. Vadim Barkov + + +and with the following additions to the disclaimer: + + +There is no warranty against interference with your enjoyment of the library or against infringement. There is no warranty that our efforts or the library will fulfill any of your particular purposes +or needs. This library is provided with all faults, and the entire risk of satisfactory quality, performance, accuracy, and effort is with the user. + + +Some files in the "contrib" directory and some configure-generated files that are distributed with libpng have other copyright owners, and are released under other open source licenses. + + +libpng versions 0.97, January 1998, through 1.0.6, March 20, 2000, are Copyright © 1998-2000 Glenn Randers-Pehrson, are derived from libpng-0.96, and are distributed according to the same disclaimer and license as libpng-0.96, with the following individuals added to the list of Contributing Authors: + +Tom Lane +Glenn Randers-Pehrson +Willem van Schaik + + +libpng versions 0.89, June 1996, through 0.96, May 1997, are +Copyright © 1996-1997 Andreas Dilger, are derived from libpng-0.88, and are distributed according to the same disclaimer and license as libpng-0.88, with the following individuals added to the list of Contributing Authors: + + +John Bowler Kevin Bracey Sam Bushell +Magnus Holmgren +Greg Roelofs +Tom Tanner + + +Some files in the "scripts" directory have other copyright owners, but are released under this license. + + +libpng versions 0.5, May 1995, through 0.88, January 1996, are +Copyright © 1995-1996 Guy Eric Schalnat, Group 42, Inc. + + +For the purposes of this copyright and license, "Contributing Authors" is defined as the following set of individuals: + + +Andreas Dilger Dave Martindale Guy Eric Schalnat Paul Schmidt +Tim Wegner + +The PNG Reference Library is supplied "AS IS". The Contributing Authors and Group 42, Inc. disclaim all warranties, expressed or implied, including, without limitation, the warranties of merchantability and of fitness for any purpose. The Contributing Authors and Group 42, Inc. assume no liability for direct, indirect, incidental, special, exemplary, or consequential damages, which may result from the use of the PNG Reference Library, even if advised of the possibility of such damage. + + +Permission is hereby granted to use, copy, modify, and distribute this source code, or portions hereof, for any purpose, without fee, subject to the following restrictions: + + +1. The origin of this source code must not be misrepresented. + + +2. Altered versions must be plainly marked as such and must not be misrepresented as being the original source. + + +3. This Copyright notice may not be removed or altered from any source or altered source distribution. + + +The Contributing Authors and Group 42, Inc. specifically permit, without fee, and encourage the use of this source code as a component to supporting the PNG file format in commercial products. If you use +this source code in a product, acknowledgment is not required but would be appreciated. + + +LGPL-2.1 libnuma +This package was debianized by Ian Wienand +on Wed, 15 Dec 2004. + + +libnuma sources are available from https://github.com/numactl/numactl + + +Upstream Authors: +Andi Kleen Copyright © 2004 Andi Kleen +numactl and the demo programs are under the GNU General Public License, v.2 libnuma is under the GNU Lesser General Public License, v2.1. +The manpages are under the same license as the Linux manpages (see the files) + + +This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, +or (at your option) any later version. The full text of the License may be found in /usr/share/common-licenses/GPL. + + +The redistribution of portions of this program are controlled by the GNU Lesser General Public License as published by the Free Software Foundation. The full text of the License may be found in + + +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. + + +Parts of the numademo program are derived from the STREAM benchmark, available from + +http://www.cs.virginia.edu/stream/ + + +Proprietary license from PTC Axeda Agent Embedded +PTC CUSTOMER AGREEMENT + +THIS PTC CUSTOMER AGREEMENT ("AGREEMENT") IS A LEGAL AGREEMENT BETWEEN THE INDIVIDUAL, OR THE COMPANY OR OTHER ORGANIZATION ON WHOSE BEHALF SUCH INDIVIDUAL ACCEPTS THIS AGREEMENT, THAT EITHER (A) CLICKS THE "I ACCEPT" BUTTON BELOW OR (B) INSTALLS, ACCESSES, OR USES ANY SOFTWARE OR DOCUMENTATION FROM PTC ("CUSTOMER"), AND PTC INC. OR, IF THE PURCHASE WAS MADE IN A COUNTRY SPECIFIED ON SCHEDULE A TO THIS AGREEMENT, THE PTC AFFILIATE SPECIFIED ON SCHEDULE A (AS APPLICABLE, "PTC"). + +PLEASE READ THE TERMS AND CONDITIONS OF THIS AGREEMENT CAREFULLY BEFORE ACCEPTING THIS AGREEMENT. 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Notwithstanding the foregoing: + + (a) If the Licensed Product is being provided by PTC on an "evaluation" or "trial" basis, such License will be instead to install and use the Licensed Product solely to evaluate such Licensed Products, and Customer agrees not to use the Licensed Product in any commercial applications or for productive purposes. + + (b) If the Licensed Software is Educational Software, Customer must be enrolled in, or employed by, an accredited, academic institution, and shall use the Licensed Software solely for educational purposes in a degree-granting program. If Customer does not meet one of these qualifications, Customer has no rights under this Agreement. Without limitation, non- educational research or funded educational research conducted using the facilities of an academic institution or under an academic name does not qualify as "educational purposes" and use of Educational Software for such purposes represents a violation of the terms of this Agreement. + + © If the Licensed Software is sold on a "demo and test" or "non-production" basis (or similar designation), such Licensed +Software may not be used in a production environment. + + 1.2 Designated Country/Computers/Networks. Subject to Section 1.3, Customer may only install and operate Licensed Products on the applicable Designated Computers or Designated Networks on computer systems and networks situated in the applicable Designated Country. Customer may, from time to time, change the Designated Computer, Designated Network, and/or the Designated Country in which Customer seeks to install or operate a Licensed Product, provided that in each case (i) Customer shall give prior written notice to PTC of any such change, and (ii) upon moving the Licensed Products to a different Designated Country, Customer shall pay all applicable Uplift Fees. Notwithstanding the foregoing, Registered Users need not be located in the Designated Country when accessing a Registered User Product. + + 1.3 Global/Restricted Global Licenses. If a Concurrent User Licensed Product is licensed by PTC on a "Global" or "Restricted +Global" basis, Section 1.2 shall not apply to such Licensed Products and the following provisions shall apply instead: + + (i) Global Licenses. Subject to the other requirements of this Agreement, a Global License allows the Customer to install, operate and use such Licensed Product at any Customer site(s) throughout the world. + + (ii) Restricted Global Licenses. Subject to the other requirements of this Agreement, a Restricted Global License allows the Customer to install, operate and use such Licensed Product at any Customer site(s) located in the Designated Country and/or in any Permitted Country. "Permitted Countries" means China, India, Russia, the Czech Republic, Poland, Hungary, Malaysia, South Africa, Israel, Mexico, Brazil, Argentina, and Romania. + + 1.4 Additional Restrictions on Use. Customer shall not permit any persons who are not Permitted Users to access or use the +Licensed Products. Customer shall not and shall not permit any third party(ies) to: + + (i) modify or create any derivative work of any part of the Licensed Products; (ii) rent, lease, or loan the Licensed Products; + + (iii) use the Licensed Products, or permit them to be used, for third-party training, to deliver software implementation or consulting services to any third parties, or for commercial time-sharing or service bureau use; + + (iv) disassemble, decompile or reverse engineer the Licensed Products or the file format of the Licensed Products, or otherwise attempt to gain access to the source code or file format of the Licensed Products, except as expressly permitted in Schedule A, if applicable; + + (v) sell, license, sublicense, loan, assign, or otherwise transfer (whether by sale, exchange, gift, operation of law, or otherwise) to any third party the Licensed Products, any copy thereof, or any License or other rights thereto, in whole or in part, without in each case obtaining PTC's prior written consent, except to the extent that any of the foregoing are explicitly authorized in the Quote and/or the Licensing Basis Webpage; + + (vi) alter, remove, or obscure any copyright, trade secret, patent, trademark, logo, proprietary and/or other legal notices on or in any copies of the Licensed Products; and + + (vii) copy or otherwise reproduce the Licensed Products in whole or in part, except (a) as may be required for their installation into computer memory for the purpose of executing the Licensed Products in accordance with this Section 1, and/or (b) to make a reasonable number of copies solely for back-up purposes (provided that any such permitted copies shall be the property of PTC, and Customer shall reproduce thereon all PTC copyright, trade secret, patent, trademark, logo, proprietary and/or other legal notices contained in the original copy of the Licensed Product obtained from PTC). + + If Customer uses any unlicensed or unauthorized copies of any PTC software, Customer agrees that, without limiting PTC's right to terminate this Agreement for breach in accordance with Section 7 and without limiting any other remedies to which PTC may be +entitled, Customer will pay to PTC the PTC then-current list price for all such unlicensed software, in addition to any fines or penalties that may be imposed by law. + + 1.5 Additional Restrictions on Use Applicable to Concurrent User Products. If the Licensed Product is a Concurrent User Product, the following provisions apply: + + (i) The number of Permitted Users accessing or operating a Concurrent User Product at any point in time may not exceed the number of Licenses in effect at such time for that particular Licensed Product. + + (ii) Except with respect to Integrity and Implementer Products, only Permitted Users physically located in the Designated Country may access, operate and/or use the Licensed Products. Permitted Users who are not employees of Customer may use the Licensed Products while physically located at Customer's site only. + + (iii) Where a Concurrent User Product is Licensed on a "fixed," "locked" or "node-locked" basis, or the Licensed Product is licensed as a "Designated Computer" product, such Licensed Product is licensed to operate solely on the Designated Computer on which it is installed. + + 1.6 Additional Restrictions on Use Applicable to Registered User Products. A License is required for each individual who accesses a Registered User product or the data contained therein, whether directly or through a web portal or other mechanism for "batching" or otherwise achieving indirect access to the Licensed Product or such data. Generic or shared log-ins are not permitted. Customer may add and/or substitute from time to time new Registered Users as long as the aggregate number of Registered Users does not exceed at any point in time the number of Licenses in effect at such time for that particular Licensed Product and, provided further, that if a person who was previously a Registered User returns to Registered User status, a new License fee must be paid to PTC at PTC's then current rates. + + 1.7 Additional Restrictions on Use Applicable to Designated Server Products. Each Designated Server product may only be used on the computer server that is designated by the Customer in connection with the initial installation of such product and that has one unique instance of the applicable installed product application. In the event a computer server is partitioned in any manner (physically, logically or otherwise), the reference in the preceding sentence to "computer server" shall mean each partition of such server, and such Designated Server product may only be used on one of such partitions. Customer may, from time to time, change the Designated Server(s) for a Designated Server Product, and/or the location thereof, provided that in each case +(a) Customer shall give prior written notice to PTC of any such change, and (b) upon transferring the Designated Server Products to a different Designated Country, Customer pays all applicable Uplift Fees. + + 1.8 Third Party Components and Bundled Third Party Products. Certain of the Licensed Products may contain third party software components for which additional terms apply ("Third Party Components"). The current additional terms are set forth on the Schedule of Third Party Terms available in the legal policies and guidelines section of http://www.ptc.com. Separately, third party software products that PTC resells and/or bundles for distribution with the Licensed Products are licensed to Customer directly by the manufacturer of such third party software products ("Bundled Third Party Products"). Such Bundled Third Party Products are also described on the Schedule of Third Party Terms. Customer agrees that its use of Third Party Components and/or Bundled Third Party Products is subject to the terms of the Schedule of Third Party Terms. New Releases containing Third Party Components or Bundled Third Party Products may be subject to additional or different third party terms, of which PTC shall notify the Customer at the time such New Releases are delivered to the Customer. + + 1.9 Upgrades: If the Licensed Software was licensed as an upgrade from a previous version, Customer must first be licensed for the Licensed Software identified by PTC as eligible for the upgrade and Customer must be active on Support Services for such software. After installing the upgrade, Licensed Software licensed as an upgrade replaces and/or supplements the product that formed the basis of Customer's eligibility for the upgrade and Customer may no longer use the original Licensed Software that formed the basis for Customer's upgrade eligibility. + +2. Compliance. + + 2.1 License Usage Assessments. To confirm Customer's compliance with the terms and conditions hereof, Customer agrees that PTC may perform a usage assessment with respect to Customer's use of the Licensed Products. Customer agrees to provide PTC access to Customer's facilities and computer systems, and cooperation from Customer's employees and consultants, as reasonably requested by PTC in order to perform such assessment, all during normal business hours, and after reasonable prior notice from PTC. + + 2.2 Reports. Upon written request from PTC, Customer agrees to provide to PTC an installation and/or usage report with respect to the Licensed Products (and in the case of Registered User Products, such report shall include a list of all users for whom Customer has issued a password or other unique identifier to enable such individual to use the Registered User Product). Such report shall be certified by an authorized representative of Customer as to its accuracy within ten (10) business days after receipt of any written request from PTC. For any period in which Customer's use of the Licensed Products exceeds the number and/or the scope of the Licenses in effect during such period for such Licensed Products, Customer agrees to pay for any such excess usage, including applicable license and Support Services fees, and without limiting any other rights or remedies to which it is entitled, failure to pay shall be grounds for termination in accordance with Section 7 hereof. + +3. Intellectual Property. PTC and its licensors are the sole owners of the Licensed Products and of any copies of the Licensed Products, and of all copyright, trade secret, patent, trademark and other intellectual or industrial property rights in and to the Licensed Products. All copies of the Licensed Products, in whatever form provided by PTC or made by Customer, shall remain the property of PTC, and such copies shall be deemed to be on loan to Customer during the License Term. Customer acknowledges that the License granted hereunder does not provide Customer with title to or ownership of the Licensed Products or any copies thereof, but only a right of limited use consistent with the express terms and conditions of this Agreement. Customer shall have no rights to the source code for the Licensed Products, and Customer agrees that only PTC shall have the right to maintain, enhance, or otherwise modify the Licensed Products. + +4. Support Services; Warranty; Disclaimer of Warranties. + + See Schedule A for a modified version of this Section 4 for Licensed Products licensed and used in Germany, Austria or Switzerland. + + 4.1 Support Services. Upon PTC's acceptance of an order for Support Services or for Licensed Products for which Usage License Fees apply, PTC agrees that it or its designated service provider shall provide the applicable Support Services in accordance with Schedule C. + + 4.2 Warranty. PTC warrants to Customer that PTC is authorized to grant the License(s) and that, subject to Section 4.3, the Licensed Products will be free from Errors for a period of ninety (90) days following PTC's initial shipment to Customer or Customer's designee of such Licensed Products (the "Warranty Period"). + + 4.3 Warranty Exceptions. PTC shall have no warranty obligations hereunder with respect to any (i) evaluation, "trial" or "express" Licenses, (ii) New Releases, (iii) computer software provided to Customer in the course of PTC's delivery of Training Services, (iv) Errors attributable to the use of the Licensed Product in an application or environment for which it was not designed or contemplated, (v) Errors attributable to any modifications or customizations of the Licensed Products, (vi) Licensed Products that are provided by PTC free of charge to Customer, and/or (vii) Sun Software, Oracle Software and/or Bundled Third Party Products. + + 4.4 Sole Remedy. PTC's and its licensors' entire liability and Customer's exclusive remedy for any breach by PTC of the warranty given in Section 4.2 above shall be, at PTC's sole discretion, either to (a) replace the Licensed Product(s) or (b) use diligent efforts to repair the Error. PTC's obligations set forth in the preceding sentence shall apply only if notice of the Error is received by PTC within the Warranty Period and Customer supplies such additional information regarding the Error as PTC may reasonably request. If PTC does not replace the applicable Licensed Product(s) and/or does not repair the Error (either by providing a bug fix, a workaround or otherwise) within a reasonable time after notice of the Error and associated information from Customer is received by PTC, PTC will provide a refund of the license fees paid by Customer for the applicable Licensed Product(s) upon return of such Licensed Product(s) and any copies thereof. + + 4.5 No Additional Warranties. No third party, including any employee, partner, distributor (including any Reseller) or agent of PTC or any of its resellers or sales agents, is authorized to give any representations, warranties or covenants greater or different than those contained in this Agreement with respect to any Licensed Products or Services, except as specifically set forth in a written agreement signed on behalf of Customer by an authorized officer and on behalf of PTC by its legal counsel or Corporate Controller. + + 4.6 Disclaimer of Warranties. EXCEPT AS EXPRESSLY STATED IN SECTION 4, PTC DISCLAIMS (AND CUSTOMER WAIVES) ALL WARRANTIES, WHETHER EXPRESS, IMPLIED, OR STATUTORY, WRITTEN OR ORAL, INCLUDING ANY WARRANTY OF MERCHANTABILITY, SATISFACTORY QUALITY, FITNESS FOR A PARTICULAR PURPOSE, NON-INFRINGEMENT, AND/OR ANY WARRANTY THAT CUSTOMER WILL ACHIEVE ANY PARTICULAR RETURN ON INVESTMENT. THE LICENSED PRODUCTS ARE INTENDED TO BE USED BY TRAINED PROFESSIONALS AND ARE NOT A SUBSTITUTE FOR PROFESSIONAL JUDGMENT, TESTING, SAFETY AND UTILITY. CUSTOMER IS SOLELY RESPONSIBLE FOR ANY RESULTS OBTAINED FROM USING THE LICENSED PRODUCTS, INCLUDING THE ADEQUACY OF INDEPENDENT TESTING OF RELIABILITY AND ACCURACY OF ANY ITEM DESIGNED USING LICENSED PRODUCTS. PTC does not warrant that the operation or other use of the Licensed Products will be uninterrupted or error free or will not cause damage or disruption to Customer's data, computers or networks. + +5. Indemnification; Infringement. + + 5.1 P TC's Ob li gati on to Ind emn ify C u sto mer . PTC, at its own expense, will defend any action brought against Customer based on a claim that any Licensed Product infringes a United States, European Union or Japanese patent, copyright or trademark and, at its option, will settle any such action or will pay any final judgment awarded against Customer, provided that: (a) PTC shall be notified promptly in writing by Customer of any notice of any such claim; (b) PTC shall have the sole control of the defense of any action on such claim and all negotiations for its settlement or compromise and shall bear the costs of the same (save where one or more of the exclusions in Section 5.3 applies); and © Customer shall cooperate fully at PTC's expense with PTC in the defense, settlement or compromise of such claim. This Section 5 states PTC's sole and exclusive liability, and Customer's sole remedy, for any and all claims relating to infringement of any intellectual property right. + + 5.2 P TC's Righ t to Act to P reven t a Clai m + + + If a claim described in Section 5.1 hereof occurs or, in PTC's opinion, may occur, +Customer shall permit PTC, at PTC's option and expense to: (a) procure for Customer the right to continue using the Licensed Product; (b) modify the Licensed Product so that it becomes non-infringing without materially impairing its functionality; or © terminate the applicable Licenses, accept return of the Licensed Products and grant Customer a credit thereon. For Licenses purchased with a perpetual License Term, such credit shall be equal to the License fees paid by Customer for such Licensed Product depreciated on a straight-line, five year basis. For Licenses purchased on a term license or subscription basis, such credit shall be equal to the prepaid license or subscription fees for the remainder of the License Term. + + 5.3 Exclu sio n s fro m P TC's Ob li gati o n to In d emn ify Cu sto mer . PTC shall have no liability to Customer under Section 5.1 hereof or otherwise to the extent that any infringement or claim thereof is based upon: (a) use of the Licensed Product in combination with equipment or software not supplied hereunder where the Licensed Product itself would not be infringing; (b) use of the Licensed Product in an application or environment for which it was not designed or not contemplated under this Agreement; © use of other than a current release of the Licensed Product(s) provided to Customer; (d) modification of the Licensed Product by anyone other than PTC or its employees or agents; or (e) any claims of infringement of any patent, copyright, trade secret, trademark or other proprietary right in which Customer has an interest. + + +6. Limitation of Liability. + + See Schedule A for a modified version of this Section 6 for Licensed Products licensed and used in Germany, Austria or Switzerland. + + 6.1 The warranty and indemnification provisions of Sections 4 and 5 hereof state the entire liability of PTC, its subsidiaries and affiliates, and each of their respective directors, officers, employees or agents, with respect to the Licensed Products and Services, including (without limitation) any liability for breach of warranty, or for infringement or alleged infringement of patent, copyrights, trademarks, trade secrets and other intellectual or proprietary rights by the Licensed Products, or their use. + + 6.2 EXCEPT FOR PTC'S INDEMNIFICATION OBLIGATIONS IDENTIFIED IN SECTION 5.1 ABOVE, THE MAXIMUM LIABILITY OF PTC AND ITS LICENSORS ARISING OUT OF, OR RELATING TO, THE CREATION, LICENSE, FUNCTIONING, USE OR SUPPLY OF THE LICENSED PRODUCTS OR THE PROVISION OF SERVICES OR OTHERWISE RELATING TO THIS AGREEMENT, WHETHER BASED UPON WARRANTY, CONTRACT, TORT, OR OTHERWISE, SHALL NOT, (I) FOR LICENSES PURCHASED ON A PERPETUAL BASIS, EXCEED THE FEES PAID BY CUSTOMER FOR THE LICENSED PRODUCTS OR SERVICES THAT GAVE RISE TO THE CLAIM AND (II) FOR LICENSES PURCHASED ON A TERM OR SUBSCRIPTION BASIS, EXCEED THE FEES PAID BY CUSTOMER IN THE TWELVE MONTH PERIOD IMMEDIATELY PRECEDING THE EVENT GIVING RISE TO DAMAGES FOR THE LICENSED PRODUCTS OR SERVICES THAT GAVE RISE TO THE CLAIM. + + 6.3 IN NO EVENT SHALL PTC, ITS LICENSORS, ITS AFFILIATES (INCLUDING ITS SUBSIDIARY COMPANIES), OR ANY OF THEIR RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES OR AGENTS BE LIABLE FOR: (A) ANY LOSS OF PROFIT, LOSS OF USE DAMAGES, LOSS OF GOODWILL, LOSS OF BUSINESS OPPORTUNITY, LOSS OF SALES, LOSS OF REPUTATION OR LOSS OF ANTICIPATED SAVINGS; (B) ANY LOSS OR INACCURACY OF DATA OR BUSINESS INFORMATION OR FAILURE OR INADEQUACY OF ANY SECURITY SYSTEM OR FEATURE; AND © SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE OR CONSEQUENTIAL LOSS OR DAMAGE HOWSOEVER CAUSED; IN EACH CASE EVEN IF PTC HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. + + 6.4 Customer agrees not to bring any suit or action against PTC, and/or its subsidiaries and affiliates, and/or any of their respective directors, officers, employees or agents for any reason whatsoever more than one year after the cause of action arises. Customer recognizes that fees paid by Customer for the Licensed Products and Services are based in part on the disclaimer of warranty and limitation of liability provisions set forth herein and that, in the absence of Customer's agreement to such terms, the charges for the Licensed Products would be significantly higher. The limitations and exclusions set forth in this Section 6 shall not apply to any claim in respect of death or personal injury. + +7. Term and Termination. + + 7.1 Events Causing Termination. This Agreement and all Licenses will terminate: + + (a) Automatically and without notice on the following events: (I) Customer's breach of any of clauses (i) through (vii) of Section 1.4 or Sections 3 or 8.4 hereof; (II) a receiver, trustee, liquidator, or such similar officer is appointed for Customer or for any of Customer's properties or assets; (III) Customer makes a general assignment for the benefit of Customer's creditors; (IV) Customer files a petition for its reorganization, dissolution or liquidation, or such a petition is filed against Customer and is not dismissed within sixty (60) days thereafter; or (V) Customer ceases doing business or commence dissolution or liquidation proceedings; or + + (b) Thirty (30) days after written notice from PTC specifying a breach (other than as listed in Section 7.1(a) above) of this Agreement, including failure to make any payment due to either PTC or a Reseller in connection with the Licensed Products in a timely manner, if that breach is not, within that thirty (30) day period, remedied to PTC's reasonable satisfaction. + + 7.2 Effects of Expiration or Termination. Upon expiration of a given License Term and/or any expiration or termination of this Agreement, Customer shall promptly pay all sums owed by Customer, return to PTC the original copies of all Licensed Products for which the License Term has expired or has been terminated, destroy and/or delete all copies and backup copies thereof from Customer's computer libraries, storage facilities and/or hosting facilities, and certify in writing by an officer that Customer is in +compliance with the foregoing requirements and that such Licensed Products are no longer in Customer's possession or in use. + + 7.3 Survival. Sections 2, 3, 4.6, 5, 6, 7.2, 7.3 and 8 shall survive expiration or termination of this Agreement. + +8. General. + + 8.1 Governing Law and Jurisdiction. Unless otherwise stated in Schedule A, all disputes arising under, out of, or in any way connected with this Agreement shall be governed by and construed in accordance with the laws of the Commonwealth of Massachusetts without reference to conflict of laws principles (and specifically excluding the Uniform Computer Information Transactions Act). The parties hereby expressly disclaim the application of the U.N. Convention for the International Sale of Goods. All disputes arising under, out of, or in any way connected with this Agreement shall be litigated exclusively in the state or federal courts situated in the Commonwealth of Massachusetts, and in no other court or jurisdiction. Notwithstanding the foregoing or anything to the contrary, PTC shall have the right to bring a claim in any court of competent jurisdiction to enforce any intellectual property rights and/or protect any confidential information. Customer agrees that the state and federal courts situated in the Commonwealth of Massachusetts shall have personal jurisdiction over its person, and Customer hereby irrevocably (i) submits to the personal jurisdiction of said courts and (ii) consents to the service of process, pleadings, and notices in connection with any and all actions initiated in said courts. The parties agree that a final judgment in any such action or proceeding shall be conclusive and binding and may be enforced in any other jurisdiction. Each party waives its right to trial by jury in connection with any dispute arising out of this Agreement. + + 8.2 Notices. Any notice or communication required or permitted under this Agreement shall be in writing. In the case of notice to Customer, the notice shall be directed to the address set forth on the Customer's purchase order or to such other address as may be provided to PTC in writing. In the case of notice to PTC, such notice shall be directed to PTC, 140 Kendrick Street, Needham, MA +02494; Attn: Corporate Controller, with a copy to General Counsel. Any notice provided under this section shall be deemed to have been received: (a) if given by hand, immediately; (b) if given by mail, five (5) business days after posting; © if given by express courier service, the second business day following dispatch in the jurisdiction of the sender; or (d) if given by fax, upon receipt +thereof by the recipient's fax machine or as stated in the sender's transmission confirmation report as produced electronically by sender's fax machine. + + 8.3 Assignment, Waiver, Modification. Customer may not assign, transfer, delegate or sublicense any of Customer's rights or obligations hereunder (including without limitation by operation of law or by sale of Customer assets, whether directly or by merger, and a change in control of Customer shall be deemed to be an "assignment" for purposes of the foregoing) without PTC's prior written consent, and any such attempted delegation, assignment, transfer or sublicense shall be void and a breach of this Agreement. No waiver, consent, modification, amendment or change of the terms of this Agreement shall be binding unless in writing and signed by PTC and Customer. PTC reserves the right to charge a transfer fee for any proposed assignment, transfer or sublicense of this Agreement. + + 8.4 Compliance with Laws. Each party shall be responsible for its own compliance with applicable laws, regulations and other legal requirements relating to the conduct of its business and this Agreement. Further Customer represents and warrants that it will use the Licensed Products, as well as related technology and services, in full compliance with applicable laws and regulations. Customer acknowledges and agrees that the Licensed Products and related technical data and services are subject to the export control laws and regulations of the United States and any country in which the Licensed Products or related technical data or services are developed, received, downloaded, used, or performed. Further, Customer understands and acknowledges that the release of software or technology to a non-U.S. person within the United States or elsewhere abroad is deemed to be an export to the non-U.S. person's home country or countries, and that the transfer of the Licensed Products or related technology to Customer's employees, affiliates, or any third party, may require a license from the United States Government and possibly other applicable authorities. Customer shall be solely responsible for determining whether Customer's use or transfer of the Licensed Products or related technology or services requires an export license or approval from U.S. or other authorities, and for securing all required authorizations. Customer hereby warrants and represents that: (x) neither Customer nor any of Customer's directors, officers or affiliates is identified on the U.S. Commerce Department's Denied Persons List, Entity List, or Unverified List, the U.S. State Department's Nonproliferation Sanctions List, the U.S. Treasury Department's List of Specially Designated Nationals and Blocked Persons or any similar Export Controls Division-Foreign Affairs and International Trade Canada listing that designates individuals or entities to which export restrictions apply (collectively, the "Restricted Parties Lists"), (y) except as specifically authorized or licensed by the United States Government and other applicable authorities, Customer will not sell, offer, transfer, deliver, release, either directly or indirectly, the Licensed Products or related technology or services to any end-user: (A) that is either located in, a national of, or acting on behalf of a country subject to U.S. economic embargoes, or (B) that have been designated as prohibited or restricted parties by the U.S. Government, including but not limited to persons listed on the Restricted Parties Lists, or © engaged in activities related to the design, development, stockpiling, or proliferation of nuclear, chemical, or biological weapons, or missiles or missile systems, or (D) engaged in maritime nuclear propulsion activities. Customer represents and warrants that it will ensure that any person or entity to which Customer has granted access to the Licensed Products or related technology or services has been made aware of, and will comply with, this provision and U.S. and other applicable export control laws and regulations. Unless prohibited by applicable law and without waiving sovereign immunity, Customer shall indemnify and hold harmless PTC and its employees against any damage, loss, liability or expense (including attorneys' fees) that PTC may incur as a result of Customer's failure to comply with this Section + + 8.4. Such indemnification shall survive the expiration or termination of this Agreement. + + 8.5 Severability. It is intended that this Agreement shall not violate any applicable law and the unenforceability or invalidity of any provision (other than the provisions obligating Customer to make payments to PTC) shall not affect the force and validity of the remaining provisions and such provisions determined to be invalid shall be deemed severed from this Agreement and, to the extent possible, be replaced with terms which as closely as possible approximate the interest and economic intent of such invalid provisions. + + 8.6 Entire Agreement. This Agreement is the complete and exclusive statement of the contract between PTC and Customer with respect to the subject matter hereof. No waiver, consent, modification, amendment or change of this Agreement shall be binding unless in writing and signed or otherwise expressly acknowledged by PTC and Customer. + + 8.7 Third Party Beneficiaries. It is agreed by the parties to this Agreement that PTC's third party licensors are intended beneficiaries of this Agreement and have the right to rely upon and directly enforce its terms with respect to the products of such licensors. + + 8.8 Marketing. Customer agrees that while this Agreement is in effect, PTC shall be authorized to identify Customer as a customer/end-user of PTC software and services (as applicable) in public relations and marketing materials. + + 8.9 Government Licensees. If Customer is a United States Governmental entity, Customer agrees that the Licensed Products are "commercial computer software" under the applicable federal acquisition regulations and are provided with the commercial license rights and restrictions described elsewhere herein. If Customer is acquiring the Licensed Product(s) under a United States government contract, Customer agrees that Customer will include all necessary and applicable restricted rights legends on the Licensed Products to protect PTC's proprietary rights under the FAR or other similar regulations of other federal agencies. Customer agrees to always include such legends whenever the Licensed Products are, or are deemed to be, a deliverable under a government contract. + + +Schedule A - Purchases from PTC Affiliates + +If the Customer has obtained a License to any Licensed Products in one of the following countries, the entity granting the License is specified below and, notwithstanding Section 8.1 of this Agreement, the governing law and jurisdiction shall be as set forth below. + +Country PTC Affiliate Licensing Entity Governing Law/Jurisdiction for + Disputes +Belgium, Netherlands, Parametric Technology Nederland B.V. Netherlands +Luxembourg +Austria, Germany Parametric Technology GmbH German Law*, Landgericht Munchen I, +Germany +France Parametric Technology S.A. France +Ireland PTC Software and Services (Ireland) +Limited Republic of Ireland +Italy Parametric Technology Italia S.r.L. Italy +Spain, Portugal Parametric Technology Espana, S.A. Spain +Switzerland Parametric Technology (Schweiz) AG German Law*, Landgericht Munchen I, +Germany +United Kingdom Parametric Technology (UK) Limited United Kingdom +Remaining countries of the PTC Software and Services (Ireland) +Limited Republic of Ireland +European Union +Turkey, Kosovo, Serbia, PTC Software and Services (Ireland) +Limited Republic of Ireland +Macedonia, Montenegro, Croatia, Bosnia and Herzegovina, and +Albania +The Russian Federation PTC International LLC Russian Law / International +Commercial Arbitration Court at the +Chamber of Commerce and Industry of the Russian Federation in Moscow + +Belarus Moldova, Ukraine, PTC Software and Services (Ireland) +Limited Republic of Ireland +Armenia, Georgia, Azerbaijan, +Kazakhstan, Kyrgyz stan, +Tajikistan, Turkmenistan, and +Uzbekistan +Norway, Sweden, and Denmark, PTC Sweden AB Sweden +Finland, Iceland, and the Faeroe +Islands +Japan PTC Japan K.K. Japan / Tokyo District Court + + +Country PTC Affiliate Licensing Entity Governing Law/Jurisdiction for + Disputes +China Parametric Technology (Shanghai) The People's Republic of China/China +International Economic and Trade +Arbitration Commission in Shanghai + Software Co., Ltd. +Taiwan Parametric Technology Taiwan Limited Taiwan / Courts of Taipei, Taiwan +India Parametric Technology (India) Private +Limited India +Korea Parametric Technology Korea Ltd. Republic of Korea +Other Asia Pacific Countries PTC Inc. Special Administrative Region of Hong +Kong / Hong Kong International +Arbitration Centre +including Australia and New +Zealand, but excluding China, +Japan and Taiwan) +Canada PTC (Canada) Inc. Ontario +Any other country PTC Inc., or such other affiliate of PTC as +PTC directs at the time of the order Commonwealth of Massachu setts, + United States + +* Specific Provisions for Austria, Germany and Switzerland: + +For Licensed Products licensed and used in Austria, Germany or Switzerland, the following provisions shall apply. The following provisions shall have no applicability to any Licensed Products or Services purchased outside of Austria, Germany or Switzerland. References to sections below are references to the applicable sections in the body of the Agreement. + +* Section 1.4 (iv) above shall not apply to the extent that (i) the processes Customer undertakes are required to achieve information necessary to achieve interoperability of an independently created computer program with other software programs, (ii) the further requirements of Section 69e of the German Copyright Act are fulfilled and (iii) PTC, upon Customer's written request, has not made available the information required for this within a reasonable period. + +* Sections 4.2 (Warranty), 4.4 (Sole Remedy), 4.5 (No Additional Warranties) and 4.6 (Disclaimer of Warranties) are hereby replaced by the following provisions: + +4.2 Warranty Period, Restarts and Investigation Duty. The limitation period for warranty claims shall be twelve (12) months from delivery. Any replacement of the Licensed Product(s) and/or repair of Errors will not restart the warranty period. The pre-requisite for the Customer's warranty claims (Mangelanspruche) is that: (i) the Customer inspects the Licensed Products according to Section 377 German Commercial Code, (ii) the defect is an Error as defined in this Agreement, (iii) the Error already existed at the time of delivery and (iv) the Customer effects a proper notification of the Error. Customer shall provide notifications of Errors to PTC in writing and Customer shall provide specific details of the Error as deemed reasonable under the specific circumstances. Customer shall notify PTC of obvious Errors in writing within one week of delivery and of latent Errors within one week of discovery of such Error. The periods specified are preclusion periods. + +4.4 Remedies. In the event of an Error, PTC in its sole discretion may: (a) replace the Licensed Product(s) or (b) repair the Error, provided that notice of the Error is received by PTC within the periods set forth in Section 4.2 and Customer provides such additional information regarding the Error as PTC may reasonably request. If the repair (either by providing a bug fix, a workaround or otherwise) or replacement is not successful (after at least two repair attempts for the same Error by PTC within a reasonable period of time), Customer shall be entitled, at Customer's choice, to either: (i) rescission of the affected order so that PTC provides a refund of the license fees paid by Customer for the applicable Licensed Product(s) upon return of such Licensed Product(s) and any copies made thereof or (ii) a reasonable reduction in the purchase price. Replacements or repairs shall be made without acknowledgement of a legal obligation and shall not suspend the limitation period for warranty claims related to the Licensed Products. + +4.5 No Additional Warranties. No employee, partner, distributor (including any Reseller) or agent of PTC or any of its resellers or sales agents is authorized to give representations, warranties or covenants greater or different than those contained in this Agreement, except as specifically set forth in a written agreement signed on behalf of Customer by an authorized officer and on behalf of PTC by its legal counsel or Corporate Controller. Apart from claims for damages based on Errors that are subject to the limitation of liability as set forth in Section 6, the obligations provided for in this Section 4 shall be PTC's exclusive liability in case of warranty claims. + +4.6 Customer Responsibility. The Licensed Products are intended to be used by trained professionals and are not a substitute for the exercise by Customer of professional judgement, testing, safety and utility in their use. Customer is solely responsible for any results which were obtained by using the Licensed Products, including the adequacy of independent testing of reliability and accuracy of any item designed using Licensed Products. + +4.7 Qualities (Beschaffenheit), Guarantees. Qualities of the Licensed Products stated in publications of PTC or its sales representatives, in particular in advertising, in drawings, brochures or other documents, including presentations in the Internet, or on packaging and labeling of the Licensed Products, or which fall under trade usages, shall only be deemed to be covered by the contractual quality of the Licensed Products if such qualities are expressly contained in an offer or an order confirmation in writing. Guarantees, in particular guarantees as to quality, shall be binding on PTC only to the extent to which they (i) are contained in an offer or an order confirmation in writing, (ii) are expressly designated as "guarantee" or "guarantee as to condition" (Beschaffenheitsgarantie), and (iii) expressly stipulate the obligations for PTC resulting from such guarantee. + +* Section 6 is hereby replaced by the following provisions: + +6.Limitation of Liability + +6.1 Liability Categories. PTC shall be liable for damages, regardless of the legal grounds, only if: (i) PTC breaches a material contractual obligation (cardinal obligation) culpably (i.e., at least negligently), or (ii) the damage has been caused by gross negligence or wilfull intent on the part of PTC or (iii) PTC has assumed a guarantee. + +6.2 Predictability. PTC's liability shall be limited to the typical, foreseeable damage: (i) if PTC breaches material contractual obligations (cardinal obligations) with slight negligence, or (ii) if employees or agents of PTC who are not officers or executive staff have breached other obligations by gross negligence, or (iii) if PTC has assumed a guarantee, unless such guarantee is expressly designated as guarantee as to condition (Beschaffenheitsgarantie). + +6.3 Maximum Amount. In the cases of Section 6.2 (i) and (ii), PTC's liability shall be limited to a maximum amount of +EURO 1,000,000 or, in case of purely financial losses, to a maximum amount of EURO 100,000. + +6.4 Indirect Damages. In the cases of Section 6.2, PTC shall not be liable for indirect damages, consequential damages or loss of profit. + +6.5 Liability Period. Customer's claims for damages against PTC and/or PTC's affiliates, regardless of the legal grounds, shall expire at the latest one year from the time the Customer gains knowledge of the damage or, irrespective of this knowledge, at the latest two years after the damaging event. For claims based on Errors of the Licensed Product(s), the warranty limitation period pursuant to Section 4.2 shall apply. + +6.6 Mandatory Liability. PTC's liability pursuant to the German Product Liability Act (Produkthaftungsgesetz), for injury of life, body and health, for fraudulent concealment of a defect or for the assumption of a guarantee as to condition (Beschaffenheitsgarantie) remains unaffected. + +6.7 Employees. Sections 6.1 to 6.6 shall also apply in the case of any claims for damages of Customer against employees +or agents of PTC and/or PTC's affiliates. + +6.8 Contributory Negligence. In the event of a guarantee or liability claim against PTC any contributory fault of Customer must be taken into account accordingly, particularly in the event of inadequate fault notification or inadequate data securing. It constitutes inadequate data securing if the client, among others, does not, by way of appropriate state of the art security measures, take precautions against external influences, e.g. computer viruses and other phenomena which could put individual data or an entire data stock at risk. + +Schedule B - Definitions + +"Concurrent User Products" means the Licensed Products licensed on a concurrent user basis, as specified either in the Quote or at +the Licensing Basis Webpage. + +"Designated Computer" means the central processing unit(s) designated in writing by Customer to PTC at the time of installation of the Licensed Products (as may be modified in accordance with Section 1.2 of this Agreement). + +"Designated Computer Product" means the Licensed Products licensed on a "Designated Computer" basis or otherwise designated as "fixed," "locked" or "node-locked", as specified either in the Quote or at the Licensing Basis Webpage. Designated Computer Products may not be remotely accessed or installed in a virtual environment. + +"Designated Country" means the country of installation specified in writing by Customer to PTC at the time Customer places its +order of the Licensed Products. The Designated Country may be changed only in accordance with Section 1.2 of this Agreement. + +"Designated Network" means the network designated in writing by Customer to PTC at the time of installation of the Licensed +Products (as may be modified in accordance with Section 1.2 of this Agreement). + +"Designated Server" means a computer server designated in writing by Customer to PTC at the time of installation of the Licensed Products (as may be modified in accordance with Section 1.2 of this Agreement) that has one unique instance of the applicable installed Licensed Product application. + +"Designated Server Products" means the Licensed Products licensed on a Designated Server basis, as specified either in the Quote or +at the Licensing Basis Webpage. + +"Documentation" means the applicable Licensed Software user manuals provided or made available by electronic means by PTC at the time of shipment of the Licensed Software. + +"Educational Software" means Licensed Products identified as "Priced for Education," "Student Edition," "Schools Edition," "Schools Advanced Edition," "University Edition," "Professor's Edition/Version" or "Academic Edition/Version," or otherwise designated as educational or academic licenses. + +"Error" means a failure of the Licensed Software to conform substantially to the applicable Documentation, provided that Customer informs PTC of such failure in writing and PTC is able to replicate such failure after making reasonable efforts. + +"External User" means a Registered User who is a vendor or other third party external to the Customer and its affiliates. "License" shall have the meaning set out in Section 1.1 of the body of the Agreement. +"License Term" means the time period during which the License for the applicable Licensed Products shall be in effect, as specified in the name of the Licensed Product or in the applicable Quote (subject to earlier termination pursuant to the terms hereof) or, if no Quote was provided to Customer, as otherwise communicated by PTC to Customer. In the absence of a stated license term, the License Term shall be perpetual, except that the License Term for evaluation Licenses shall be no longer than thirty days from the date of Customer's request for an evaluation license, unless otherwise specifically designated by PTC, and the evaluation License will cease to be operational after such term expires. The License Term of a "subscription" License is as specified in the Quote and/or the invoice, and such License includes Support Services during such License Term at no additional fee. + +"License Locked Product" means a Licensed Product licensed for use with another PTC product to which the License Locked Product is an extension. The License Locked Product will assume the licensing basis of such other product.. License Locked Products are specified either in the Quote or at the Licensing Basis Webpage. + +"Licensed Products" means collectively the Licensed Software and the Documentation. + +"Licensed Software" means, collectively, the computer software product identified in the applicable Quote, as well as (i) any software product that is provided to operate with such computer software product (e.g., modules, software bundled with this software product, etc.), but excluding any software that is a consulting services deliverable, (ii) any Error corrections pursuant to Section 4.4 hereof, (iii) any updates, Error corrections and/or New Releases provided to Customer by PTC pursuant to Support Services purchased by Customer and (iv) any computer software provided to Customer in the course of PTC's delivery of Training Services. + +"Licensing Basis Webpage" means the "Licensing Basis" document at http://www.ptc.com/support/customer_agreements/ +index.htm, which specifies the licensing basis of PTC's different products and states certain additional product-specific terms and conditions. + +"Support Services" means the provision of New Releases and, depending on the level of Support Services ordered, may also include telephone support, web-based support tools, and correction of Errors, all in accordance with Schedule C attached to this Agreement. + +"New Release" means a modified or enhanced version of a Licensed Product that is designated by PTC as a new release of that +product and that PTC makes generally available to its Support Services customers. + +"Permitted User" means an individual who is authorized by Customer to use the Licensed Products, such use to be solely in accordance with the terms and conditions of the Agreement. Permitted Users are limited to Customer's employees, consultants, subcontractors, suppliers, business partners and customers who (i) are not competitors of PTC or employed by competitors of PTC and (ii) are directly involved in the utilization of the Licensed Products solely in support of Customer's internal business purposes. Customer shall at all times be responsible for its Permitted Users' compliance with this Agreement. + +"Per Instance Product" means a Licensed Product for which one License is required for each instance of a system to which the applicable Licensed Product connects. For example, if an adapter that is licensed on a Per Instance basis enables Windchill to connect to an ERP system and a CRM system, two licenses of such adapter will be required. The Licensed Products that are Per Instance Products are identified either in the Quote or at the Licensing Basis Webpage. + +"Quote" means the PTC product schedule, quote or order confirmation provided to Customer in connection with the purchase of the applicable Licensed Product or, if no such document is provided, Customer's purchase order for such Licensed Product, if any. + +"Registered User" means a Permitted User for whom Customer has purchased a License to use a Registered User Product and for +whom Customer has issued a password or other unique identifier to enable such individual to use the Registered User Product. + +"Registered User Products" means the Licensed Products licensed on a Registered User basis, as specified either in the Quote or at +the Licensing Basis Webpage. + +"Reseller" means a third-party appointed and authorized by PTC to resell or distribute any Licensed Product. . + +"Services" means collectively Support Services and Training Services. + +"Site License" means a Licensed Product for which one License is required for each Customer location, as specified either in the Quote or at the Licensing Basis Webpage. Multiple customer facilities located in the same city or town (based on postal address) shall be considered one "location," whereas locations located in different cities or towns will require multiple Site Licenses. + +"Training Services" means instruction or other training provided by PTC in the use of the Licensed Products. "Training Services" does not include PTC's e-Learning training products (e.g., "PTCU"), which are considered Licensed Products for purposes of this Agreement. + +"Uplift Fee" means a fee based upon the difference between the License fee applicable to installation of the applicable Licensed Product in the original Designated Country and the License fee applicable to the installation of such Licensed Product in the Designated Country to which Customer wishes to move the Licensed Product. + +"Usage License Fee" means an ongoing fee that commences upon installation of the applicable Licensed Product and that, during the period for which the Usage License Fee is paid, entitles Customer to (i) continued use of the Licensed Product in accordance with the terms of the License and (ii) telephone support, Error corrections or workarounds, and New Releases for such software. + + +Schedule C - PTC Support Services Terms and Conditions +The following additional terms and conditions apply to the provision of Support Services by PTC: + +Support Services Plan; Levels of Support Services. Upon PTC's acceptance of Customer's order for Support Services in respect of the Licensed Products, PTC and/or its authorized subcontractors shall provide Support Services in accordance with these terms for a time period of twelve (12) months or for such other period specified in Customer's order accepted by PTC (a "Support Services Plan"). All Support Services are provided subject to Customer's payment for such services at PTC's then-current rates, provided that for Licensed Product licensed on a subscription basis, such License includes Support Services during such License Term at no additional fee. If Customer does not order Support Services to commence on shipment of the Licensed Product(s), or if Customer at any time discontinues Support Services, and in either case subsequently wishes to obtain Support Services, Customer must pay (i) the then current fees for Support Services and (ii) the fees for Support Services for any period for which Customer has not purchased Support Services. The then current levels of Support Services offered and the corresponding services provided thereunder are described on http://www.ptc.com at + +http://www.ptc.com/support/maintenance/maintenance_support_policies.htm + +A Support Services Plan may not be cancelled by Customer following PTC's acceptance of an order for such Support Services Plan. With respect to Registered User Products, e-Learning products and Integrity Concurrent User and Server Licensed Products, Support Services ordered by Customer must cover all Licenses granted to Customer for such Licensed Products. PTC is obligated to provide Support Services only during periods for which Customer has paid the applicable Support Services fees and only in accordance with the level of Support Services Customer has purchased. The services offered under any Support Services Plan may change from time to time, and PTC may cease to offer Support Services Plans at any time without notice, subject only to the obligation to refund to Customer the unused portion of any previously paid applicable Support Services fee (on a prorated basis). + +(a) Telephone Support. If Customer purchases Support Services at a level that includes telephone support, Customer may utilize PTC's telephone support service to report problems and seek assistance in use of the Licensed Products. The hours during which PTC will provide telephone support will vary depending upon the level of Support Services ordered by Customer. For all levels of Support Services that include telephone support, PTC will provide telephone support in the languages, and during normal business hours for the countries, listed on PTC's website at the website URL listed above. For levels of Support Services that include telephone support during non-business hours, PTC will provide such support in the English language only. Regardless of the total number of the Licensed Products licensed by Customer, Customer is entitled to telephone support only in direct connection with Licenses that are covered by a Support Services Plan at a level that includes telephone support. + +(b) Repair of Errors. If Customer's Support Services Plan includes repair or workaround of Errors, PTC shall use diligent efforts to repair Errors or provide workarounds as required in such Support Services Plan, provided notice of the Error is received by PTC during the term of a Support Services Plan and Customer supplies such additional information regarding the Error as PTC may reasonably request. + +© New Releases. PTC will provide Customer with one copy of each New Release for each Licensed Product for which Customer is entitled to Support Services at the time the applicable language version of the New Release is made generally available. Subject to different terms for particular products set forth at http://www.ptc.com/support/maintenance/maintenance_support_policies.htm, following shipment of the New Release, the previous release shall remain "current" for purposes of this Agreement for a period of ninety (90) days; thereafter only such New Release will be current. + +(d) Exclusions. + +(1) PTC is not obligated to perform investigation and/or repair of Errors (i) found by PTC to be in other than a current (as described above), unaltered release of the Licensed Products; (ii) caused by changes to the Customer's operating systems, environment, databases or other system components which adversely affect the Licensed Products; (iii) caused by Customer's modification of the Licensed Product or use thereof in combination or interconnection with software not provided by PTC; (iv) use of the Licensed Product on a computer, operating system, software or peripherals other than a computer, operating system, software or peripherals for which such Licensed Product was designed for and licensed for use on; (v) caused by improper or unauthorized use of the Licensed Products; (vi) due to external causes such as, but not limited to, power failures or electric power surges; or (vii) due to a failure by the Customer to implement recommendations in respect of solutions to Errors previously provided by PTC to Customer. + +(2) PTC shall only be responsible for responding to problems reported by one of the two (2) technical contacts for Customer's main location (which technical contacts and main location have previously been identified in writing to PTC by Customer), and for sending New Releases to the "Central Support Location" designated by Customer in writing. Customer is responsible for the distribution of New Releases to any of Customer's additional locations where Licensed Products are authorized to be used. Customer is responsible for providing to PTC in writing the name, address, phone number, fax number, and e-mail address for each of Customer's designated contacts and Customer's Central Support Location. + +(3) PTC is not obligated to perform any Support Services with respect to modifications or customizations of the Licensed Products, nor with respect to any developments resulting from Customer's use, development or customization of functionality contained within the Licensed Products, all of which are Customer's sole responsibility. + + +END OF (4) Ion GeneStudio™ S5 V5.18 END USER LICENSE AGREEMENT +**************************************************** -2. Redistributions in binary form must reproduce the above copyright -notice, -this list of conditions and the following disclaimer in the -documentation -and/or other materials provided with the distribution. - -THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS -IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE -LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL -DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR -SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED -AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR -TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF -THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - -**END OF (2) SERVICE & SUPPORT TELEMETRY MODULE Software VERSION 2.0.1 -END USER LICENSE AGREEMENT** diff --git a/buildTools/build.sh b/buildTools/build.sh index e6364a94..d4846696 100755 --- a/buildTools/build.sh +++ b/buildTools/build.sh @@ -16,7 +16,6 @@ MODULES=${MODULES-" pipeline publishers tsconfig - RSM "} PROJECT_ROOT=`pwd` diff --git a/buildTools/cmake/CMakeLists.compiler.txt b/buildTools/cmake/CMakeLists.compiler.txt index 742ddf28..c71b6dd2 100644 --- a/buildTools/cmake/CMakeLists.compiler.txt +++ b/buildTools/cmake/CMakeLists.compiler.txt @@ -92,6 +92,7 @@ if (${LSB_RELEASE_CODENAME} STREQUAL "bionic") "-maxrregcount=48" ) else() SET( CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS} + "-Wno-deprecated-gpu-targets" "-D_MWAITXINTRIN_H_INCLUDED" "-D_FORCE_INLINES" "-std=c++11" "-O2" "--compiler-options=-fno-strict-aliasing" "-g" "--use_fast_math" "-gencode=arch=compute_20,code=sm_20" "-gencode=arch=compute_30,code=sm_30" diff --git a/buildTools/cmake/CMakeLists.dependencies.TMAP.txt b/buildTools/cmake/CMakeLists.dependencies.TMAP.txt new file mode 100644 index 00000000..dd38fc10 --- /dev/null +++ b/buildTools/cmake/CMakeLists.dependencies.TMAP.txt @@ -0,0 +1,187 @@ +# Copyright (C) 2013 Ion Torrent Systems, Inc. All Rights Reserved + +set (ION_TS_EXTERNAL "${PROJECT_SOURCE_DIR}/../external/") +#set (ION_TS_EXTERNAL "${CMAKE_BINARY_DIR}/external/") + +set(ION_UPDATE_SERVER "updates.iontorrent.com") # internal developer can use just "updates" + +# Use the closest ION_UPDATE_SERVER we can find. +#message(STATUS "Searching for an ION_UPDATE_SERVER...") +#foreach ( SERVER updates updates.itw updates.iontorrent.com ) +# # See if we can look up the server in question. +# execute_process( COMMAND host -W 2 -t A ${SERVER} +# RESULT_VARIABLE NOT_FOUND OUTPUT_QUIET ERROR_QUIET ) +# +# # If we can find it, great! We're done! +# if ( NOT ${NOT_FOUND} ) +# set( ION_UPDATE_SERVER ${SERVER} ) +# break() +# endif() +#endforeach() + +# If we find a server, let everyone know. +if (ION_UPDATE_SERVER) + message(STATUS "Using ION_UPDATE_SERVER: ${ION_UPDATE_SERVER}") +else() + message(WARNING "Could not find a valid ION_UPDATE_SERVER.") +endif() + +include(ExternalProject) + +find_program(LSB_RELEASE_COMMAND lsb_release) +if(LSB_RELEASE_COMMAND) + execute_process(COMMAND ${LSB_RELEASE_COMMAND} -s -c + OUTPUT_VARIABLE TMP_LSB_RELEASE_CODENAME + OUTPUT_STRIP_TRAILING_WHITESPACE) + string(TOLOWER ${TMP_LSB_RELEASE_CODENAME} LSB_RELEASE_CODENAME) + message(STATUS "LSB release codename: ${LSB_RELEASE_CODENAME}") +endif(LSB_RELEASE_COMMAND) + +# If defined while running cmake look for mkl +# e.g. -DMKL_INSTALL_PATH=/home/ionadmin/intel/composer_xe_2013_sp1.0.080/mkl +if (DEFINED MKL_INSTALL_PATH) + message("Setting mkl root to ${MKL_INSTALL_PATH}") + include_directories(${MKL_INSTALL_PATH}/include) + set(MKL_LINK_LIBS "-Wl,--start-group ${MKL_INSTALL_PATH}/lib/intel64/libmkl_intel_lp64.a ${MKL_INSTALL_PATH}/lib/intel64/libmkl_core.a ${MKL_INSTALL_PATH}/lib/intel64/libmkl_sequential.a -Wl,--end-group") +else() + message("Not setting mkl root ${MKL_INSTALL_PATH}") +endif() + + +#option(ION_USE_MKL "Using Intel MKL" OFF) +#mark_as_advanced(ION_USE_MKL) + +#option(ION_USE_SYSTEM_CUDA "Use CUDA system libraries" OFF) +#mark_as_advanced(ION_USE_SYSTEM_CUDA) + +#option(ION_USE_CUDA "Compile CUDA code" ON) +#mark_as_advanced(ION_USE_CUDA) + +#option(ION_USE_SYSTEM_SAMTOOLS "Use samtools system libraries" OFF) +#mark_as_advanced(ION_USE_SYSTEM_SAMTOOLS) + +#option(ION_USE_SYSTEM_BAMTOOLS "Use bamtools system libraries" OFF) +#mark_as_advanced(ION_USE_SYSTEM_BAMTOOLS) + +option (ION_USE_SYSTEM_LIBSTATGEN "Use libstatgen system libraries" OFF) +mark_as_advanced(ION_USE_SYSTEM_LIBSTATGEN) + + + +# uncomment for profiling if gprofile installed +# add_library(PROFILE STATIC IMPORTED) +# set_property(TARGET PROFILE PROPERTY IMPORTED_LOCATION "/usr/local/lib/libprofiler.a") + +include_directories("${PROJECT_BINARY_DIR}") +include_directories("${PROJECT_SOURCE_DIR}") +include_directories("${PROJECT_SOURCE_DIR}/../external/jsoncpp-src-amalgated0.6.0-rc1") + +# wget https://github.com/samtools/htslib/archive/1.2.1.tar.gz +# md5sum : 81f5f1aa17a188a6b6250ca67d83384d +# tar xvzf 1.2.1.tar.gz +# tar cvzf htslib-1.2.1.tar.gz htslib-1.2.1 +# md5sum : 028c9110bd80d40e13dbd8270ee7eb2b +if(NOT ION_USE_SYSTEM_HTSLIB) + set(proj_name "htslib") + set(proj_version "1.2.1+ion2") + set(proj_name_version "${proj_name}-${proj_version}") + ExternalProject_add(${proj_name}_proj + URL "http://${ION_UPDATE_SERVER}/updates/software/external/htslib-1.2.1.tar.gz" + #URL_MD5 028c9110bd80d40e13dbd8270ee7eb2b + PREFIX ${PROJECT_BINARY_DIR}/../${proj_name_version}-prefix + SOURCE_DIR ${PROJECT_BINARY_DIR}/../${proj_name_version} + #BINARY_DIR ${PROJECT_BINARY_DIR}/../${proj_name_version}-build + BUILD_IN_SOURCE 1 + CONFIGURE_COMMAND "" + BUILD_COMMAND make + INSTALL_COMMAND "" + PATCH_COMMAND patch -p1 -t -N < "${ION_TS_EXTERNAL}/htslib-1.2+ion2.patch" + ) + set(ION_HTSLIB_LIBS "${PROJECT_BINARY_DIR}/../${proj_name_version}/libhts.a") + include_directories("${PROJECT_BINARY_DIR}/../${proj_name_version}") +else() + set(ION_HTSLIB_LIBS "hts") +endif() + + +# wget https://github.com/samtools/samtools/archive/1.2.tar.gz +# md5sum 2748356ef392c0694ca1142de37cf2aa +# tar xvzf 1.2.tar.gz +# tar cvzf samtools-1.2.tar.gz samtools-1.2 +# md5sum f94f6ea20f5d581459f90daa39020a60 +if (NOT ION_USE_SYSTEM_SAMTOOLS) + set(proj_name "samtools") + set(proj_version "1.2+ion4") + set(proj_name_version "${proj_name}-${proj_version}") + ExternalProject_add(${proj_name} + DEPENDS htslib_proj + URL "http://${ION_UPDATE_SERVER}/updates/software/external/samtools-1.2.tar.gz" + #URL_MD5 f94f6ea20f5d581459f90daa39020a60 + PREFIX ${PROJECT_BINARY_DIR}/../${proj_name_version}-prefix + SOURCE_DIR ${PROJECT_BINARY_DIR}/../${proj_name_version} + BUILD_IN_SOURCE 1 + CONFIGURE_COMMAND "" + BUILD_COMMAND make + INSTALL_COMMAND "" + PATCH_COMMAND patch -p1 -t -N < "${ION_TS_EXTERNAL}/samtools-1.2+ion4.patch" + ) + include_directories("${PROJECT_BINARY_DIR}/../${proj_name_version}") + set(ION_SAMTOOLS_LIBS "${PROJECT_BINARY_DIR}/../${proj_name_version}/libbam.a") + message(STATUS "SAMTOOLS_INCLUDE_DIRS: ${PROJECT_BINARY_DIR}/../${proj_name_version}") +else() + set(ION_SAMTOOLS_LIBS libbam.a) + include_directories("/usr/include/samtools") + message(STATUS "SAMTOOLS_INCLUDE_DIRS: /usr/include/samtools") +endif() + + +if (NOT ION_USE_SYSTEM_BAMTOOLS) + set(proj_name "bamtools") + if (${LSB_RELEASE_CODENAME} STREQUAL "bionic") + set(revision_tag 740562a67a3)#set date below accordingly + set(proj_version "2.4.2.20190207+git${revision_tag}") + else() + set(revision_tag 15eadb925f)#set date below accordingly + set(proj_version "2.4.0.20150702+git${revision_tag}") + endif() + + set(proj_name_version "${proj_name}-${proj_version}") + set(bamtools_patch_file "${proj_name_version}.patch") + ExternalProject_add(${proj_name} + URL "http://${ION_UPDATE_SERVER}/updates/software/external/${proj_name_version}.tar.gz" + PREFIX ${PROJECT_BINARY_DIR}/../${proj_name_version}-prefix + SOURCE_DIR ${PROJECT_BINARY_DIR}/../${proj_name_version} + BINARY_DIR ${PROJECT_BINARY_DIR}/../${proj_name_version}-build + CMAKE_ARGS + -DCMAKE_INSTALL_PREFIX:PATH=${PROJECT_BINARY_DIR}/../${proj_name_version}-install + PATCH_COMMAND patch -p0 -t -N < "${PROJECT_SOURCE_DIR}/../external/${bamtools_patch_file}" + ) + include_directories("${PROJECT_BINARY_DIR}/../${proj_name_version}-install/include/bamtools") + set(ION_BAMTOOLS_LIBS "${PROJECT_BINARY_DIR}/../${proj_name_version}-install/lib/bamtools/libbamtools.a") +else() + find_library(ION_BAMTOOLS_LIBS NAMES bamtools libbamtools) + include_directories("/usr/include/bamtools") + add_custom_target(bamtools) +endif() + +if (NOT ION_USE_SYSTEM_LIBSTATGEN) + set (proj_name "libStatGen") + set (proj_version "1.0.14") + set (proj_name_version "${proj_name}-${proj_version}") + ExternalProject_add(${proj_name} + URL "https://github.com/statgen/libStatGen/archive/v1.0.14.tar.gz" + PREFIX ${PROJECT_BINARY_DIR}/../${proj_name_version}-prefix + SOURCE_DIR ${PROJECT_BINARY_DIR}/../${proj_name_version} + BUILD_IN_SOURCE 1 + CONFIGURE_COMMAND "" + BUILD_COMMAND make USER_WARNINGS=-Wall + INSTALL_COMMAND "" + #PATCH_COMMAND patch -p1 -t -N < "${ION_TS_EXTERNAL}/libstatgen-1.0.14.patch" + ) + set(ION_STATGEN_LIBS "${PROJECT_BINARY_DIR}/../${proj_name_version}/libStatGen.a") + set(ION_STATGEN_INCLUDES "${PROJECT_BINARY_DIR}/../${proj_name_version}/include") +else() + find_library(ION_BAMTOOLS_LIBS NAMES libstatgen) + include_directories("/usr/include/libstatgen") + add_custom_target(libstatgen) +endif() diff --git a/buildTools/cmake/CMakeLists.dependencies.txt b/buildTools/cmake/CMakeLists.dependencies.txt index 471485d7..5e7d6841 100644 --- a/buildTools/cmake/CMakeLists.dependencies.txt +++ b/buildTools/cmake/CMakeLists.dependencies.txt @@ -3,7 +3,9 @@ set (ION_TS_EXTERNAL "${PROJECT_SOURCE_DIR}/../external/") #set (ION_TS_EXTERNAL "${CMAKE_BINARY_DIR}/external/") -set(ION_UPDATE_SERVER "updates.iontorrent.com") # internal developer can use just "updates" +if(NOT ION_UPDATE_SERVER) + set(ION_UPDATE_SERVER "updates.iontorrent.com") # internal developer can use just "updates" +endif() # Use the closest ION_UPDATE_SERVER we can find. #message(STATUS "Searching for an ION_UPDATE_SERVER...") @@ -206,9 +208,9 @@ endif() if(NOT ION_USE_SYSTEM_ARMADILLO) set(proj_name "armadillo") - set(proj_version "6.100.0+ion0") + set(proj_version "6.100.0+ion1") set(proj_name_version "${proj_name}-${proj_version}") - set(ARMADILLO_PATCH "${PROJECT_SOURCE_DIR}/../external/armadillo-6.100.0+ion0.patch") + set(ARMADILLO_PATCH "${PROJECT_SOURCE_DIR}/../external/armadillo-6.100.0+ion1.patch") ExternalProject_add(${proj_name}_proj URL "http://${ION_UPDATE_SERVER}/updates/software/external/armadillo-6.100.0.tar.gz" #URL_MD5 e8400bc7adb65fa0edc8c8ccb49b60eb @@ -285,7 +287,7 @@ include_directories("${PROJECT_SOURCE_DIR}/../external/jsoncpp-src-amalgated0.6. # md5sum : 028c9110bd80d40e13dbd8270ee7eb2b if(NOT ION_USE_SYSTEM_HTSLIB) set(proj_name "htslib") - set(proj_version "1.2.1+ion0") + set(proj_version "1.2.1+ion2") set(proj_name_version "${proj_name}-${proj_version}") ExternalProject_add(${proj_name}_proj URL "http://${ION_UPDATE_SERVER}/updates/software/external/htslib-1.2.1.tar.gz" @@ -297,7 +299,7 @@ if(NOT ION_USE_SYSTEM_HTSLIB) CONFIGURE_COMMAND "" BUILD_COMMAND make INSTALL_COMMAND "" - PATCH_COMMAND patch -p1 -t -N < "${ION_TS_EXTERNAL}/htslib-1.2+ion0.patch" + PATCH_COMMAND patch -p1 -t -N < "${ION_TS_EXTERNAL}/htslib-1.2+ion2.patch" ) set(ION_HTSLIB_LIBS "${PROJECT_BINARY_DIR}/../${proj_name_version}/libhts.a") include_directories("${PROJECT_BINARY_DIR}/../${proj_name_version}") @@ -313,7 +315,7 @@ endif() # md5sum f94f6ea20f5d581459f90daa39020a60 if (NOT ION_USE_SYSTEM_SAMTOOLS) set(proj_name "samtools") - set(proj_version "1.2+ion2") + set(proj_version "1.2+ion4") set(proj_name_version "${proj_name}-${proj_version}") ExternalProject_add(${proj_name} DEPENDS htslib_proj @@ -325,7 +327,7 @@ if (NOT ION_USE_SYSTEM_SAMTOOLS) CONFIGURE_COMMAND "" BUILD_COMMAND make INSTALL_COMMAND "" - PATCH_COMMAND patch -p1 -t -N < "${ION_TS_EXTERNAL}/samtools-1.2+ion2.patch" + PATCH_COMMAND patch -p1 -t -N < "${ION_TS_EXTERNAL}/samtools-1.2+ion4.patch" ) include_directories("${PROJECT_BINARY_DIR}/../${proj_name_version}") set(ION_SAMTOOLS_LIBS "${PROJECT_BINARY_DIR}/../${proj_name_version}/libbam.a") diff --git a/buildTools/terms-of-use.txt b/buildTools/terms-of-use.txt index 9edf73b6..8fb701c1 100644 --- a/buildTools/terms-of-use.txt +++ b/buildTools/terms-of-use.txt @@ -1,12 +1,13 @@ -Torrent Suite Software Version 5.8 +This end-user license agreement contains 4 separate and distinct licenses: (1) Torrent Suite(TM) Software Version 5.18 Open Source License (pgs. 1-32), (2) Service & Support Telemetry Module Software Version 2.0.1 End User License Agreement (pgs. 32 - 47), (3) Ion Chef(TM) Instrument Software Version 5.18 License Agreement (pgs. 47 - 182), and (4) Ion GeneStudio(TM) S5 V5.18 License Agreement (pgs. 182 - 236). + +(1) Torrent Suite(TM) Software Version 5.18 ===================================================================== -Torrent Suite(tm) Software v5.8: This software provides for the analysis and storage of data received from the Ion Personal Genome Machine(tm) Sequencer, -the Ion Proton(tm) Sequencer, the Ion GeneStudio S5 Sequencer or the Ion GeneStudio S5 XL Sequencer, -the Ion GeneStudio S5 Prime or the Ion GeneStudio S5 Pro. +Torrent Suite(TM) Software v5.18: This software provides for the analysis and storage of data received from the Ion Personal Genome Machine(TM) (PGM(TM)) Sequencer, the Ion Proton(TM) Sequencer, the Ion S5TM Sequencer, the Ion S5TM XL Sequencer, or the Ion GeneStudio(TM) S5 Prime. +The Ion Chef(TM) System provides automated, high-throughput template preparation and chip loading for use with an Ion Personal Genome Machine(TM) PGM(TM) Sequencer, Ion Proton(TM) Sequencer, Ion S5(TM) Sequencer, Ion S5(TM) XL Sequencer, or the Ion GeneStudio(TM) S5 Prime. -November 30, 2017 +May 26th, 2022 -Copyright (C) 2017 Life Technologies Corporation +Copyright (C) 2011 - 2022 Life Technologies Corporation All Rights Reserved. This program is free software; you can redistribute it and/or modify it @@ -23,12 +24,13 @@ with this program (see Section 2 below); if not, write to the Free Software Foun 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. You can also find the GPL version 2 on the GNU web site: https://www.gnu.org/licenses/gpl-2.0.html - -1. Third Party Software Notices and Licenses ===================================================================== - + 1. Third Party Software Notices and Licenses +===================================================================== + This software uses third party software components from several sources. Portions of these software components are copyrighted and licensed by their respective owners as indicated below. Various licenses require distribution of source code or if a link is used to point the end-user to a source-code repository, and the source code is not available at such site, the distributor must, for a time determined by license, offer to provide source code. In such cases, please contact your Life Technologies representative. As well, various licenses require that the end-user receive a copy of the license or certain notices. Such licenses and notices may be found below. In order to use this software, the end-user must abide by the terms and conditions of these third party licenses. + Armadillo ------------------------------------------------------------- @@ -37,622 +39,238 @@ Apache License Version 2.0, January 2004 http://www.apache.org/licenses/ -TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION - -1. Definitions. - - "License" shall mean the terms and conditions for use, reproduction, - and distribution as defined by Sections 1 through 9 of this document. - - "Licensor" shall mean the copyright owner or entity authorized by - the copyright owner that is granting the License. - - "Legal Entity" shall mean the union of the acting entity and all - other entities that control, are controlled by, or are under common - control with that entity. For the purposes of this definition, - "control" means (i) the power, direct or indirect, to cause the - direction or management of such entity, whether by contract or - otherwise, or (ii) ownership of fifty percent (50%) or more of the - outstanding shares, or (iii) beneficial ownership of such entity. - - "You" (or "Your") shall mean an individual or Legal Entity - exercising permissions granted by this License. - - "Source" form shall mean the preferred form for making modifications, - including but not limited to software source code, documentation - source, and configuration files. - - "Object" form shall mean any form resulting from mechanical - transformation or translation of a Source form, including but - not limited to compiled object code, generated documentation, - and conversions to other media types. - - "Work" shall mean the work of authorship, whether in Source or - Object form, made available under the License, as indicated by a - copyright notice that is included in or attached to the work - (an example is provided in the Appendix below). - - "Derivative Works" shall mean any work, whether in Source or Object - form, that is based on (or derived from) the Work and for which the - editorial revisions, annotations, elaborations, or other modifications - represent, as a whole, an original work of authorship. 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In no event and under no legal theory, - whether in tort (including negligence), contract, or otherwise, - unless required by applicable law (such as deliberate and grossly - negligent acts) or agreed to in writing, shall any Contributor be - liable to You for damages, including any direct, indirect, special, - incidental, or consequential damages of any character arising as a - result of this License or out of the use or inability to use the - Work (including but not limited to damages for loss of goodwill, - work stoppage, computer failure or malfunction, or any and all - other commercial damages or losses), even if such Contributor - has been advised of the possibility of such damages. - -9. Accepting Warranty or Additional Liability. While redistributing - the Work or Derivative Works thereof, You may choose to offer, - and charge a fee for, acceptance of support, warranty, indemnity, - or other liability obligations and/or rights consistent with this - License. However, in accepting such obligations, You may act only - on Your own behalf and on Your sole responsibility, not on behalf - of any other Contributor, and only if You agree to indemnify, - defend, and hold each Contributor harmless for any liability - incurred by, or claims asserted against, such Contributor by reason - of your accepting any such warranty or additional liability. - - -END OF TERMS AND CONDITIONS - -APPENDIX: How to apply the Apache License to your work. - -To apply the Apache License to your work, attach the following -boilerplate notice, with the fields enclosed by brackets "[]" -replaced with your own identifying information. (Don't include -the brackets!) The text should be enclosed in the appropriate -comment syntax for the file format. We also recommend that a -file or class name and description of purpose be included on the -same "printed page" as the copyright notice for easier -identification within third-party archives. - -Copyright [yyyy] [name of copyright owner] - -Licensed under the Apache License, Version 2.0 (the "License"); -you may not use this file except in compliance with the License. -You may obtain a copy of the License at - -http://www.apache.org/licenses/LICENSE-2.0 - -Unless required by applicable law or agreed to in writing, software -distributed under the License is distributed on an "AS IS" BASIS, -WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -See the License for the specific language governing permissions and -limitations under the License. - - -Mozilla Public License Version 2.0 -------------------------------------------------------------- - -1. Definitions -------------------------------------------------------------- - -1.1. "Contributor" - means each individual or legal entity that creates, contributes to - the creation of, or owns Covered Software. -1.2. "Contributor Version" - means the combination of the Contributions of others (if any) used - by a Contributor and that particular Contributor's Contribution. - -1.3. "Contribution" - means Covered Software of a particular Contributor. - -1.4. "Covered Software" - means Source Code Form to which the initial Contributor has attached - the notice in Exhibit A, the Executable Form of such Source Code - Form, and Modifications of such Source Code Form, in each case - including portions thereof. - -1.5. "Incompatible With Secondary Licenses" - means - - (a) that the initial Contributor has attached the notice described - in Exhibit B to the Covered Software; or - - (b) that the Covered Software was made available under the terms of - version 1.1 or earlier of the License, but not also under the - terms of a Secondary License. - -1.6. "Executable Form" - means any form of the work other than Source Code Form. - -1.7. "Larger Work" - means a work that combines Covered Software with other material, in - a separate file or files, that is not Covered Software. - -1.8. "License" - means this document. - -1.9. "Licensable" - means having the right to grant, to the maximum extent possible, - whether at the time of the initial grant or subsequently, any and - all of the rights conveyed by this License. - -1.10. "Modifications" - means any of the following: - - (a) any file in Source Code Form that results from an addition to, - deletion from, or modification of the contents of Covered - Software; or - - (b) any new file in Source Code Form that contains any Covered - Software. - -1.11. "Patent Claims" of a Contributor - means any patent claim(s), including without limitation, method, - process, and apparatus claims, in any patent Licensable by such - Contributor that would be infringed, but for the grant of the - License, by the making, using, selling, offering for sale, having - made, import, or transfer of either its Contributions or its - Contributor Version. - -1.12. "Secondary License" - means either the GNU General Public License, Version 2.0, the GNU - Lesser General Public License, Version 2.1, the GNU Affero General - Public License, Version 3.0, or any later versions of those - licenses. - -1.13. "Source Code Form" - means the form of the work preferred for making modifications. - -1.14. "You" (or "Your") - means an individual or a legal entity exercising rights under this - License. For legal entities, "You" includes any entity that - controls, is controlled by, or is under common control with You. For - purposes of this definition, "control" means (a) the power, direct - or indirect, to cause the direction or management of such entity, - whether by contract or otherwise, or (b) ownership of more than - fifty percent (50%) of the outstanding shares or beneficial - ownership of such entity. - -2. License Grants and Conditions -------------------------------------------------------------- - -2.1. Grants - -Each Contributor hereby grants You a world-wide, royalty-free, -non-exclusive license: - -(a) under intellectual property rights (other than patent or trademark) - Licensable by such Contributor to use, reproduce, make available, - modify, display, perform, distribute, and otherwise exploit its - Contributions, either on an unmodified basis, with Modifications, or - as part of a Larger Work; and - -(b) under Patent Claims of such Contributor to make, use, sell, offer - for sale, have made, import, and otherwise transfer either its - Contributions or its Contributor Version. - -2.2. Effective Date - -The licenses granted in Section 2.1 with respect to any Contribution -become effective for each Contribution on the date the Contributor first -distributes such Contribution. - -2.3. Limitations on Grant Scope - -The licenses granted in this Section 2 are the only rights granted under -this License. No additional rights or licenses will be implied from the -distribution or licensing of Covered Software under this License. -Notwithstanding Section 2.1(b) above, no patent license is granted by a -Contributor: - -(a) for any code that a Contributor has removed from Covered Software; - or - -(b) for infringements caused by: (i) Your and any other third party's - modifications of Covered Software, or (ii) the combination of its - Contributions with other software (except as part of its Contributor - Version); or - -(c) under Patent Claims infringed by Covered Software in the absence of - its Contributions. - -This License does not grant any rights in the trademarks, service marks, -or logos of any Contributor (except as may be necessary to comply with -the notice requirements in Section 3.4). - -2.4. Subsequent Licenses - -No Contributor makes additional grants as a result of Your choice to -distribute the Covered Software under a subsequent version of this -License (see Section 10.2) or under the terms of a Secondary License (if -permitted under the terms of Section 3.3). - -2.5. Representation - -Each Contributor represents that the Contributor believes its -Contributions are its original creation(s) or it has sufficient rights -to grant the rights to its Contributions conveyed by this License. - -2.6. Fair Use - -This License is not intended to limit any rights You have under -applicable copyright doctrines of fair use, fair dealing, or other -equivalents. - -2.7. Conditions - -Sections 3.1, 3.2, 3.3, and 3.4 are conditions of the licenses granted -in Section 2.1. - -3. Responsibilities -------------------------------------------------------------- - -3.1. Distribution of Source Form - -All distribution of Covered Software in Source Code Form, including any -Modifications that You create or to which You contribute, must be under -the terms of this License. You must inform recipients that the Source -Code Form of the Covered Software is governed by the terms of this -License, and how they can obtain a copy of this License. You may not -attempt to alter or restrict the recipients' rights in the Source Code -Form. - -3.2. Distribution of Executable Form - -If You distribute Covered Software in Executable Form then: - -(a) such Covered Software must also be made available in Source Code - Form, as described in Section 3.1, and You must inform recipients of - the Executable Form how they can obtain a copy of such Source Code - Form by reasonable means in a timely manner, at a charge no more - than the cost of distribution to the recipient; and - -(b) You may distribute such Executable Form under the terms of this - License, or sublicense it under different terms, provided that the - license for the Executable Form does not attempt to limit or alter - the recipients' rights in the Source Code Form under this License. - -3.3. Distribution of a Larger Work - -You may create and distribute a Larger Work under terms of Your choice, -provided that You also comply with the requirements of this License for -the Covered Software. If the Larger Work is a combination of Covered -Software with a work governed by one or more Secondary Licenses, and the -Covered Software is not Incompatible With Secondary Licenses, this -License permits You to additionally distribute such Covered Software -under the terms of such Secondary License(s), so that the recipient of -the Larger Work may, at their option, further distribute the Covered -Software under the terms of either this License or such Secondary -License(s). - -3.4. Notices - -You may not remove or alter the substance of any license notices -(including copyright notices, patent notices, disclaimers of warranty, -or limitations of liability) contained within the Source Code Form of -the Covered Software, except that You may alter any license notices to -the extent required to remedy known factual inaccuracies. - -3.5. Application of Additional Terms - -You may choose to offer, and to charge a fee for, warranty, support, -indemnity or liability obligations to one or more recipients of Covered -Software. However, You may do so only on Your own behalf, and not on -behalf of any Contributor. You must make it absolutely clear that any -such warranty, support, indemnity, or liability obligation is offered by -You alone, and You hereby agree to indemnify every Contributor for any -liability incurred by such Contributor as a result of warranty, support, -indemnity or liability terms You offer. You may include additional -disclaimers of warranty and limitations of liability specific to any -jurisdiction. - -4. Inability to Comply Due to Statute or Regulation ---------------------------------------------------- - -If it is impossible for You to comply with any of the terms of this -License with respect to some or all of the Covered Software due to -statute, judicial order, or regulation then You must: (a) comply with -the terms of this License to the maximum extent possible; and (b) -describe the limitations and the code they affect. Such description must -be placed in a text file included with all distributions of the Covered -Software under this License. Except to the extent prohibited by statute -or regulation, such description must be sufficiently detailed for a -recipient of ordinary skill to be able to understand it. - -5. Termination -------------------------------------------------------------- - -5.1. The rights granted under this License will terminate automatically -if You fail to comply with any of its terms. However, if You become -compliant, then the rights granted under this License from a particular -Contributor are reinstated (a) provisionally, unless and until such -Contributor explicitly and finally terminates Your grants, and (b) on an -ongoing basis, if such Contributor fails to notify You of the -non-compliance by some reasonable means prior to 60 days after You have -come back into compliance. Moreover, Your grants from a particular -Contributor are reinstated on an ongoing basis if such Contributor -notifies You of the non-compliance by some reasonable means, this is the -first time You have received notice of non-compliance with this License -from such Contributor, and You become compliant prior to 30 days after -Your receipt of the notice. - -5.2. If You initiate litigation against any entity by asserting a patent -infringement claim (excluding declaratory judgment actions, -counter-claims, and cross-claims) alleging that a Contributor Version -directly or indirectly infringes any patent, then the rights granted to -You by any and all Contributors for the Covered Software under Section -2.1 of this License shall terminate. - -5.3. In the event of termination under Sections 5.1 or 5.2 above, all -end user license agreements (excluding distributors and resellers) which -have been validly granted by You or Your distributors under this License -prior to termination shall survive termination. - - - -6. Disclaimer of Warranty -------------------------------------------------------------- - -Covered Software is provided under this License on an "as is" basis, without -warranty of any kind, either expressed, implied, or statutory, including, -without limitation, warranties that the Covered Software is free of defects, -merchantable, fit for a particular purpose or non-infringing. The entire risk -as to the quality and performance of the Covered Software is with You. Should -any Covered Software prove defective in any respect, You (not any Contributor) -assume the cost of any necessary servicing, repair, or correction. This -disclaimer of warranty constitutes an essential part of this License. No use of -any Covered Software is authorized under this License except under this -disclaimer. - - -7. Limitation of Liability -------------------------------------------------------------- - -Under no circumstances and under no legal theory, whether tort (including -negligence), contract, or otherwise, shall any Contributor, or anyone who -distributes Covered Software as permitted above, be liable to You for any -direct, indirect, special, incidental, or consequential damages of any -character including, without limitation, damages for lost profits, loss of -goodwill, work stoppage, computer failure or malfunction, or any and all other -commercial damages or losses, even if such party shall have been informed of -the possibility of such damages. This limitation of liability shall not apply -to liability for death or personal injury resulting from such party's -negligence to the extent applicable law prohibits such limitation. Some -jurisdictions do not allow the exclusion or limitation of incidental or -consequential damages, so this exclusion and limitation may not apply to You. - - -8. Litigation -------------------------------------------------------------- - -Any litigation relating to this License may be brought only in the -courts of a jurisdiction where the defendant maintains its principal -place of business and such litigation shall be governed by laws of that -jurisdiction, without reference to its conflict-of-law provisions. -Nothing in this Section shall prevent a party's ability to bring -cross-claims or counter-claims. - -9. Miscellaneous -------------------------------------------------------------- - -This License represents the complete agreement concerning the subject -matter hereof. If any provision of this License is held to be -unenforceable, such provision shall be reformed only to the extent -necessary to make it enforceable. Any law or regulation which provides -that the language of a contract shall be construed against the drafter -shall not be used to construe this License against a Contributor. - -10. Versions of the License -------------------------------------------------------------- - -10.1. New Versions - -Mozilla Foundation is the license steward. Except as provided in Section -10.3, no one other than the license steward has the right to modify or -publish new versions of this License. Each version will be given a -distinguishing version number. - -10.2. Effect of New Versions - -You may distribute the Covered Software under the terms of the version -of the License under which You originally received the Covered Software, -or under the terms of any subsequent version published by the license -steward. - -10.3. Modified Versions - -If you create software not governed by this License, and you want to -create a new license for such software, you may create and use a -modified version of this License if you rename the license and remove -any references to the name of the license steward (except to note that -such modified license differs from this License). - -10.4. Distributing Source Code Form that is Incompatible With Secondary -Licenses - -If You choose to distribute Source Code Form that is Incompatible With -Secondary Licenses under the terms of this version of the License, the -notice described in Exhibit B of this License must be attached. - -Exhibit A - Source Code Form License Notice -------------------------------------------------------------- - -This Source Code Form is subject to the terms of the Mozilla Public -License, v. 2.0. If a copy of the MPL was not distributed with this -file, You can obtain one at http://mozilla.org/MPL/2.0/. - -If it is not possible or desirable to put the notice in a particular -file, then You may include the notice in a location (such as a LICENSE -file in a relevant directory) where a recipient would be likely to look -for such a notice. - -You may add additional accurate notices of copyright ownership. - -Exhibit B - "Incompatible With Secondary Licenses" Notice -------------------------------------------------------------- - -This Source Code Form is "Incompatible With Secondary Licenses", as -defined by the Mozilla Public License, v. 2.0. - + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. Definitions. + + "License" shall mean the terms and conditions for use, reproduction, + and distribution as defined by Sections 1 through 9 of this document. + + "Licensor" shall mean the copyright owner or entity authorized by + the copyright owner that is granting the License. + + "Legal Entity" shall mean the union of the acting entity and all + other entities that control, are controlled by, or are under common + control with that entity. For the purposes of this definition, + "control" means (i) the power, direct or indirect, to cause the + direction or management of such entity, whether by contract or + otherwise, or (ii) ownership of fifty percent (50%) or more of the + outstanding shares, or (iii) beneficial ownership of such entity. + + "You" (or "Your") shall mean an individual or Legal Entity + exercising permissions granted by this License. + + "Source" form shall mean the preferred form for making modifications, + including but not limited to software source code, documentation + source, and configuration files. + + "Object" form shall mean any form resulting from mechanical + transformation or translation of a Source form, including but + not limited to compiled object code, generated documentation, + and conversions to other media types. + + "Work" shall mean the work of authorship, whether in Source or + Object form, made available under the License, as indicated by a + copyright notice that is included in or attached to the work + (an example is provided in the Appendix below). + + "Derivative Works" shall mean any work, whether in Source or Object + form, that is based on (or derived from) the Work and for which the + editorial revisions, annotations, elaborations, or other modifications + represent, as a whole, an original work of authorship. For the purposes + of this License, Derivative Works shall not include works that remain + separable from, or merely link (or bind by name) to the interfaces of, + the Work and Derivative Works thereof. + + "Contribution" shall mean any work of authorship, including + the original version of the Work and any modifications or additions + to that Work or Derivative Works thereof, that is intentionally + submitted to Licensor for inclusion in the Work by the copyright owner + or by an individual or Legal Entity authorized to submit on behalf of + the copyright owner. For the purposes of this definition, "submitted" + means any form of electronic, verbal, or written communication sent + to the Licensor or its representatives, including but not limited to + communication on electronic mailing lists, source code control systems, + and issue tracking systems that are managed by, or on behalf of, the + Licensor for the purpose of discussing and improving the Work, but + excluding communication that is conspicuously marked or otherwise + designated in writing by the copyright owner as "Not a Contribution." + + "Contributor" shall mean Licensor and any individual or Legal Entity + on behalf of whom a Contribution has been received by Licensor and + subsequently incorporated within the Work. + + 2. Grant of Copyright License. Subject to the terms and conditions of + this License, each Contributor hereby grants to You a perpetual, + worldwide, non-exclusive, no-charge, royalty-free, irrevocable + copyright license to reproduce, prepare Derivative Works of, + publicly display, publicly perform, sublicense, and distribute the + Work and such Derivative Works in Source or Object form. + + 3. Grant of Patent License. Subject to the terms and conditions of + this License, each Contributor hereby grants to You a perpetual, + worldwide, non-exclusive, no-charge, royalty-free, irrevocable + (except as stated in this section) patent license to make, have made, + use, offer to sell, sell, import, and otherwise transfer the Work, + where such license applies only to those patent claims licensable + by such Contributor that are necessarily infringed by their + Contribution(s) alone or by combination of their Contribution(s) + with the Work to which such Contribution(s) was submitted. 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You may reproduce and distribute copies of the + Work or Derivative Works thereof in any medium, with or without + modifications, and in Source or Object form, provided that You + meet the following conditions: + + (a) You must give any other recipients of the Work or + Derivative Works a copy of this License; and + + (b) You must cause any modified files to carry prominent notices + stating that You changed the files; and + + (C) You must retain, in the Source form of any Derivative Works + that You distribute, all copyright, patent, trademark, and + attribution notices from the Source form of the Work, + excluding those notices that do not pertain to any part of + the Derivative Works; and + + (d) If the Work includes a "NOTICE" text file as part of its + distribution, then any Derivative Works that You distribute must + include a readable copy of the attribution notices contained + within such NOTICE file, excluding those notices that do not + pertain to any part of the Derivative Works, in at least one + of the following places: within a NOTICE text file distributed + as part of the Derivative Works; within the Source form or + documentation, if provided along with the Derivative Works; or, + within a display generated by the Derivative Works, if and + wherever such third-party notices normally appear. The contents + of the NOTICE file are for informational purposes only and + do not modify the License. You may add Your own attribution + notices within Derivative Works that You distribute, alongside + or as an addendum to the NOTICE text from the Work, provided + that such additional attribution notices cannot be construed + as modifying the License. + + You may add Your own copyright statement to Your modifications and + may provide additional or different license terms and conditions + for use, reproduction, or distribution of Your modifications, or + for any such Derivative Works as a whole, provided Your use, + reproduction, and distribution of the Work otherwise complies with + the conditions stated in this License. + + 5. Submission of Contributions. Unless You explicitly state otherwise, + any Contribution intentionally submitted for inclusion in the Work + by You to the Licensor shall be under the terms and conditions of + this License, without any additional terms or conditions. + Notwithstanding the above, nothing herein shall supersede or modify + the terms of any separate license agreement you may have executed + with Licensor regarding such Contributions. + + 6. Trademarks. This License does not grant permission to use the trade + names, trademarks, service marks, or product names of the Licensor, + except as required for reasonable and customary use in describing the + origin of the Work and reproducing the content of the NOTICE file. + + 7. Disclaimer of Warranty. Unless required by applicable law or + agreed to in writing, Licensor provides the Work (and each + Contributor provides its Contributions) on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or + implied, including, without limitation, any warranties or conditions + of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A + PARTICULAR PURPOSE. You are solely responsible for determining the + appropriateness of using or redistributing the Work and assume any`` + risks associated with Your exercise of permissions under this License. + + 8. Limitation of Liability. In no event and under no legal theory, + whether in tort (including negligence), contract, or otherwise, + unless required by applicable law (such as deliberate and grossly + negligent acts) or agreed to in writing, shall any Contributor be + liable to You for damages, including any direct, indirect, special, + incidental, or consequential damages of any character arising as a + result of this License or out of the use or inability to use the + Work (including but not limited to damages for loss of goodwill, + work stoppage, computer failure or malfunction, or any and all + other commercial damages or losses), even if such Contributor + has been advised of the possibility of such damages. + + 9. Accepting Warranty or Additional Liability. While redistributing + the Work or Derivative Works thereof, You may choose to offer, + and charge a fee for, acceptance of support, warranty, indemnity, + or other liability obligations and/or rights consistent with this + License. However, in accepting such obligations, You may act only + on Your own behalf and on Your sole responsibility, not on behalf + of any other Contributor, and only if You agree to indemnify, + defend, and hold each Contributor harmless for any liability + incurred by, or claims asserted against, such Contributor by reason + of your accepting any such warranty or additional liability. + + +HTS Lib +Samtools + + + + The MIT/Expat License +Copyright (C) 2008-2014 Genome Research Ltd. -HTS Lib and Samtools -------------------------------------------------------------- + Permission is hereby granted, free of charge, to any person obtaining a copy + of this software and associated documentation files (the "Software"), to deal + in the Software without restriction, including without limitation the rights + to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + copies of the Software, and to permit persons to whom the Software is + furnished to do so, subject to the following conditions: -The MIT/Expat License -Copyright (C) 2008-2014 Genome Research Ltd. + The above copyright notice and this permission notice shall be included in + all copies or substantial portions of the Software. -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: -The above copyright notice and this permission notice shall be included in -all copies or substantial portions of the Software. -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL -THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING -FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER -DEALINGS IN THE SOFTWARE. + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL + THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER + DEALINGS IN THE SOFTWARE. -VCF Lib -------------------------------------------------------------- +## VCF Lib The MIT License (see text above) -Copyright (c) 2012 Erik Garrison -Blas and Lapack -------------------------------------------------------------- -Copyright (c) 1992-2013 The University of Tennessee and The University of Tennessee Research Foundation. All rights reserved. +Copyright (C) 2012 Erik Garrison -Copyright (c) 2000-2013 The University of California Berkeley. All rights reserved. +Blas -Copyright (c) 2006-2013 The University of Colorado Denver. All rights reserved. +Lapack + +Copyright (C) 1992-2013 The University of Tennessee and The University + of Tennessee Research Foundation. All rights + reserved. +Copyright (C) 2000-2013 The University of California Berkeley. All + rights reserved. +Copyright (C) 2006-2013 The University of Colorado Denver. All rights + reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: - - Redistributions of source code must retain the above copyright - notice, this list of conditions and the following disclaimer. - - Redistributions in binary form must reproduce the above copyright - notice, this list of conditions and the following disclaimer listed - in this license in the documentation and/or other materials - provided with the distribution. - - Neither the name of the copyright holders nor the names of its - contributors may be used to endorse or promote products derived from - this software without specific prior written permission. +* Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + +* Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer listed + in this license in the documentation and/or other materials + provided with the distribution. + +* Neither the name of the copyright holders nor the names of its + contributors may be used to endorse or promote products derived from + this software without specific prior written permission. The copyright holders provide no reassurances that the source code provided does not infringe any patent, copyright, or any other @@ -673,794 +291,608 @@ THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -Django -------------------------------------------------------------- -Copyright (c) Django Software Foundation and individual contributors. All rights reserved. - -Redistribution and use in source and binary forms, with or without modification, -are permitted provided that the following conditions are met: - -1. Redistributions of source code must retain the above copyright notice, - this list of conditions and the following disclaimer. -2. Redistributions in binary form must reproduce the above copyright - notice, this list of conditions and the following disclaimer in the - documentation and/or other materials provided with the distribution. -3. Neither the name of Django nor the names of its contributors may be used - to endorse or promote products derived from this software without - specific prior written permission. - -THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND -ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED -WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -DISCLAIMED. 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By downloading, installing, copying, or otherwise using the SOFTWARE, You (as defined below) agree to be bound by the terms of this Agreement. If You do not agree to the terms of this Agreement, do not download the SOFTWARE. Recitals Use of NVIDIA's SOFTWARE requires three elements: the SOFTWARE, an NVIDIA GPU or application processor ("NVIDIA Hardware"), and a computer system. The SOFTWARE is protected by copyright laws and international copyright treaties, as well as other intellectual property laws and treaties. The SOFTWARE is not sold, and instead is only licensed for Your use, strictly in accordance with this Agreement. The NVIDIA Hardware is protected by various patents, and is sold, but this Agreement does not cover the sale or use of such hardware, since it may not necessarily be sold as a package with the SOFTWARE. This Agreement sets forth the terms and conditions of the SOFTWARE only. - -1.1. Definitions - - 1.1.1. Licensee "You", or "Your" shall mean the entity or individual that downloads and uses the SOFTWARE. - - 1.1.2. Redistributable Software "Redistributable Software" shall mean the redistributable libraries referenced in Attachment A of this Agreement. - - 1.1.3. Software "SOFTWARE" shall mean the deliverables provided pursuant to this Agreement. SOFTWARE may be provided in either source or binary form, at NVIDIA's discretion. - -1.2. Grant of License - - 1.2.1. Rights and Limitations of Grant Provided that Licensee complies with the terms of this Agreement, NVIDIA hereby grants Licensee the following limited, non-exclusive, non-transferable, non-sublicensable (except as expressly permitted otherwise for Redistributable Software in Section 1.2.1.1 and Section 1.2.1.3 of this Agreement) right to use the SOFTWARE -- and, if the SOFTWARE is provided in source form, to compile the SOFTWARE -- with the following limitations: - - 1.2.1.1. Redistribution Rights Licensee may transfer, redistribute, and sublicense certain files of the Redistributable SOFTWARE, as defined in Attachment A of this Agreement, provided, however, that (a) the Redistributable SOFTWARE shall be distributed solely in binary form to Licensee's licensees ("Customers") only as a component of Licensee's own software products (each, a "Licensee Application"); (b) Licensee shall design the Licensee Application such that the Redistributable SOFTWARE files are installed only in a private (non-shared) directory location that is used only by the Licensee Application; (c) Licensee shall obtain each Customer's written or clickwrap agreement to the license terms under a written, legally enforceable agreement that has the effect of protecting the SOFTWARE and the rights of NVIDIA under terms no less restrictive than this Agreement. - - 1.2.1.2. Usage Rights Licensee may install and use multiple copies of the SOFTWARE on a shared computer or concurrently on different computers, and make multiple back-up copies of the SOFTWARE, solely for Licensee's use within Licensee's Enterprise. "Enterprise" shall mean individual use by Licensee or any legal entity (such as a corporation or university) and the subsidiaries it owns by more than 50 percent. - - 1.2.1.3. Further Redistribution Rights Subject to the terms and conditions of the Agreement, Licensee may authorize Customers to further redistribute the Redistributable SOFTWARE that such Customers receive as part of the Licensee Application, solely in binary form, provided, however, that Licensee shall require in their standard software license agreements with Customers that all such redistributions must be made pursuant to a license agreement that has the effect of protecting the SOFTWARE and the rights of NVIDIA whose terms and conditions are at least as restrictive as those in the applicable Licensee software license agreement covering the Licensee Application. For avoidance of doubt, termination of this Agreement shall not affect rights previously granted by Licensee to its Customers under this Agreement to the extent validly granted to Customers under Section 1.2.1.1. - - 1.2.1.4. Linux/FreeBSD Exception Notwithstanding the foregoing terms of Section 1.2.1.2, Section 1.2.1.1 and Section 1.2.1.3, SOFTWARE designed exclusively for use on the Linux or FreeBSD operating systems, or other operating systems derived from the source code to these operating systems, may be copied and redistributed, provided that the binary files thereof are not modified in any way (except for unzipping of compressed files). - - 1.2.1.5. Additional Licensing Obligations Licensee acknowledges and agrees that its use of certain third party components included with the SOFTWARE may be subject to additional licensing terms and conditions as set forth or referenced in Attachment B of this Agreement. - - 1.2.1.6. Limitations No Reverse Engineering If the SOFTWARE is provided in binary form, Licensee may not reverse engineer, decompile, or disassemble the SOFTWARE, nor attempt in any other manner to obtain the source code. 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This Agreement will automatically terminate if Licensee fails to comply with any of the terms and conditions hereof. In such event, Licensee must destroy all copies of the SOFTWARE and all of its component parts. Defensive Suspension If Licensee commences or participates in any legal proceeding against NVIDIA, then NVIDIA may, in its sole discretion, suspend or terminate all license grants and any other rights provided under this Agreement during the pendency of such legal proceedings. - -1.4. Copyright All rights, title, interest and copyrights in and to the SOFTWARE (including but not limited to all images, photographs, animations, video, audio, music, text, and other information incorporated into the SOFTWARE), the accompanying printed materials, and any copies of the SOFTWARE, are owned by NVIDIA, or its suppliers. The SOFTWARE is protected by copyright laws and international treaty provisions. 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The United Nations Convention on Contracts for the International Sale of Goods is specifically disclaimed. The courts of Santa Clara County, California shall have exclusive jurisdiction and venue over any dispute arising out of or relating to this Agreement. - -1.6. Disclaimer of Warranties and Limitations on Liability - - 1.6.1. No Warranties TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, THE SOFTWARE IS PROVIDED "AS IS" AND NVIDIA AND ITS SUPPLIERS DISCLAIM ALL WARRANTIES, EITHER EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR NONINFRINGEMENT. - - 1.6.2. 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Feedback Notwithstanding any Non-Disclosure Agreement executed by and between the parties, the parties agree that in the event Licensee or NVIDIA provides Feedback (as defined below) to the other party on how to design, implement, or improve the SOFTWARE or Licensee's product(s) for use with the SOFTWARE, the following terms and conditions apply the Feedback: - - 1.7.1.1. Exchange of Feedback Both parties agree that neither party has an obligation to give the other -party any suggestions, comments or other feedback, whether verbally or in written or source code form, relating to (i) the SOFTWARE; (ii) Licensee's products; (iii) Licensee's use of the SOFTWARE; or (iv) optimization/interoperability of Licensee's product with the SOFTWARE (collectively defined as "Feedback"). In the event either party provides Feedback to the other party, the party receiving the Feedback may use any Feedback that the other party voluntarily provides to improve the (i) SOFTWARE or other related NVIDIA technologies, respectively for the benefit of NVIDIA; or (ii) Licensee's product or other related Licensee technologies, respectively for the benefit of Licensee. Accordingly, if either party provides Feedback to the other party, both parties agree that the other party and its respective licensees may freely use, reproduce, license, distribute, and otherwise commercialize the Feedback in the (i) SOFTWARE or other related technologies; or (ii) Licensee's products or other related technologies, respectively, without the payment of any royalties or fees. - - 1.7.1.2. Residual Rights Licensee agrees that NVIDIA shall be free to use any general knowledge, skills and experience, (including, but not limited to, ideas, concepts, know-how, or techniques) ("Residuals"), contained in the (i) Feedback provided by Licensee to NVIDIA; (ii) Licensee's products shared or disclosed to NVIDIA in connection with the Feedback; or (c) Licensee's confidential information voluntarily provided to NVIDIA in connection with the Feedback, which are retained in the memories of NVIDIA's employees, agents, or contractors who have had access to such Residuals. Subject to the terms and conditions of this Agreement, NVIDIA's employees, agents, or contractors shall not be prevented from using Residuals as part of such employee's, agent's or contractor's general knowledge, skills, experience, talent, and/or expertise. 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No Implied Licenses Under no circumstances should anything in this Agreement be construed as NVIDIA granting by implication, estoppel or otherwise, (i) a license to any NVIDIA product or technology other than the SOFTWARE; or (ii) any additional license rights for the SOFTWARE other than the licenses expressly granted in this Agreement. If any provision of this Agreement is inconsistent with, or cannot be fully enforced under, the law, such provision will be construed as limited to the extent necessary to be consistent with and fully enforceable under the law. This Agreement is the final, complete and exclusive agreement between the parties relating to the subject matter hereof, and supersedes all prior or contemporaneous understandings and agreements relating to such subject matter, whether oral or written. This Agreement may only be modified in writing signed by an authorized officer of NVIDIA. Licensee agrees that it will not ship, transfer or export the SOFTWARE into any country, or use the SOFTWARE in any manner, prohibited by the United States Bureau of Industry and Security or any export laws, restrictions or regulations. The parties agree that the following sections of the Agreement will survive the termination of the License: Section 1.2.1.4, Section 1.4, Section 1.5, Section 1.6, and Section 1.7. -1.8. Attachment A Redistributable Software In connection with Section 1.2.1.1 of this Agreement, the following files may be redistributed with software applications developed by Licensee, including certain variations of these files that have version number or architecture specific information NVIDIA CUDA Toolkit License Agreement www.nvidia.com End User License Agreements (EULA) DR-06739-001_v01_v8.0 | 9 embedded in the file name - as an example only, for release version 6.0 of the 64-bit Windows software, the file cudart64_60.dll is redistributable. -Component : CUDA Runtime Windows : cudart.dll, cudart_static.lib, cudadevrt.lib Mac OSX : libcudart.dylib, libcudart_static.a, libcudadevrt.a Linux : libcudart.so, libcudart_static.a, libcudadevrt.a Android : libcudart.so, libcudart_static.a, libcudadevrt.a Component : CUDA FFT Library Windows : cufft.dll, cufftw.dll Mac OSX : libcufft.dylib, libcufft_static.a, libcufftw.dylib, libcufftw_static.a Linux : libcufft.so, libcufft_static.a, libcufftw.so, libcufftw_static.a Android : libcufft.so, libcufft_static.a, libcufftw.so, libcufftw_static.a Component : CUDA BLAS Library Windows : cublas.dll, cublas_device.lib Mac OSX : libcublas.dylib, libcublas_static.a, libcublas_device.a Linux : libcublas.so, libcublas_static.a, libcublas_device.a Android : libcublas.so, libcublas_static.a, libcublas_device.a Component : NVIDIA "Drop-in" BLAS Library Windows : nvblas.dll Mac OSX : libnvblas.dylib Linux : libnvblas.so Component : CUDA Sparse Matrix Library Windows : cusparse.dll Mac OSX : libcusparse.dylib, libcusparse_static.a Linux : libcusparse.so, libcusparse_static.a Android : libcusparse.so, libcusparse_static.a Component : CUDA Linear Solver Library Windows : cusolver.dll Mac OSX : libcusolver.dylib, libcusolver_static.a Linux : libcusolver.so, libcusolver_static.a Android : libcusolver.so, libcusolver_static.a Component : CUDA Random Number Generation Library Windows : curand.dll Mac OSX : libcurand.dylib, libcurand_static.a Linux : libcurand.so, libcurand_static.a Android : libcurand.so, libcurand_static.a Component : NVIDIA Performance Primitives Library Windows : nppc.dll, nppi.dll, npps.dll Mac OSX : libnppc.dylib, libnppi.dylib, libnpps.dylib, libnppc_static.a, libnpps_static.a, libnppi_static.a Linux : libnppc.so, libnppi.so, libnpps.so, libnppc_static.a, libnpps_static.a, libnppi_static.a Android : libnppc.so, libnppi.so, libnpps.so, libnppc_static.a, libnpps_static.a, libnppi_static.a Component : Internal common library required for statically linking to cuBLAS, cuSPARSE, cuFFT, cuRAND and NPP Mac OSX : libculibos.a Linux : libculibos.a Component : NVIDIA Runtime Compilation Library Windows : nvrtc.dll, nvrtc-builtins.dll Mac OSX : libnvrtc.dylib, libnvrtc-builtins.dylib Linux : libnvrtc.so, libnvrtc-builtins.so Component : NVIDIA Optimizing Compiler Library Windows : nvvm.dll Mac OSX : libnvvm.dylib Linux : libnvvm.so Component : NVIDIA Common Device Math Functions Library Windows : libdevice.compute_20.bc, libdevice.compute_30.bc, libdevice.compute_35.bc Mac OSX : libdevice.compute_20.bc, libdevice.compute_30.bc, libdevice.compute_35.bc Linux : libdevice.compute_20.bc, libdevice.compute_30.bc, libdevice.compute_35.bc Component : CUDA Occupancy Calculation Header Library All : cuda_occupancy.h Component : Profiling Tools Interface Library Windows : cupti.dll Mac OSX : libcupti.dylib Linux : libcupti.so - -1.9. Attachment B Additional Licensing Obligations The following third party components included in the SOFTWARE are licensed to Licensee pursuant to the following terms and conditions: - - -1. Licensee's use of the GDB third party component is subject to the terms and conditions of GNU GPL v3: This product includes copyrighted third-party software licensed under the terms of the GNU General Public License v3 ("GPL v3"). All third-party software packages are copyright by their respective authors. GPL v3 terms and conditions are hereby incorporated into the Agreement by this reference: http://www.gnu.org/licenses/gpl.txt Consistent with these licensing requirements, the software listed below is provided under the terms of the specified open source software licenses. To obtain source code for software provided under licenses that require redistribution of source code, including the GNU General Public License (GPL) and GNU Lesser General Public License (LGPL), contact oss-requests@nvidia.com. This offer is valid for a period of three (3) years from the date of the distribution of this product by NVIDIA CORPORATION. Component License CUDA-GDB GPL v3 - -2. Licensee represents and warrants that any and all third party licensing and/or royalty payment obligations in connection with Licensee's use of the H.264 video codecs are solely the responsibility of Licensee. - -3. Licensee's use of the Thrust library is subject to the terms and conditions of the Apache License Version 2.0. All third-party software packages are copyright by their respective authors. Apache License Version 2.0 terms and conditions are hereby incorporated into the Agreement by this reference. http://www.apache.org/licenses/ LICENSE-2.0.html. In addition, Licensee acknowledges the following notice: Thrust includes source code from the Boost Iterator, Tuple, System, and Random Number libraries. Boost Software License - Version 1.0 - August 17th, 2003 . . . . Permission is hereby granted, free of charge, to any person or organization obtaining a copy of the software and accompanying documentation covered by this license (the "Software") to use, reproduce, display, distribute, execute, and transmit the Software, and to prepare derivative works of the Software, and to permit third-parties to whom the Software is furnished to do so, all subject to the following: The copyright notices in the Software and this entire statement, including the above license grant, this restriction and the following disclaimer, must be included in all copies of the Software, in whole or in part, and all derivative works of the Software, unless such copies or derivative works are solely in the form of machine-executable object code generated by a source language processor. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. - -4. Licensee's use of the LLVM third party component is subject to the following terms and conditions: - - LLVM Release License - - University of Illinois/NCSA Open Source License Copyright (c) 2003-2010 University of Illinois at Urbana-Champaign. All rights reserved. Developed by: LLVM Team University of Illinois at Urbana-Champaign http://llvm.org Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal with the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimers. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimers in the documentation and/or other materials provided with the distribution. * Neither the names of the LLVM Team, University of Illinois at Urbana- Champaign, nor the names of its contributors may be used to endorse or promote products derived from this Software without specific prior written permission. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE. - -5. Licensee's use of the PCRE third party component is subject to the following terms and conditions: - - PCRE LICENCE - - PCRE is a library of functions to support regular expressions whose syntax and semantics are as close as possible to those of the Perl 5 language. Release 8 of PCRE is distributed under the terms of the "BSD" licence, as specified below. The documentation for PCRE, supplied in the "doc" directory, is distributed under the same terms as the software itself. The basic library functions are written in C and are freestanding. Also included in the distribution is a set of C++ wrapper functions, and a justin-time compiler that can be used to optimize pattern matching. These are both optional features that can be omitted when the library is built. - - - THE BASIC LIBRARY FUNCTIONS - - Written by: Philip Hazel - Email local part: ph10 - Email domain: cam.ac.uk University of Cambridge Computing Service, Cambridge, England. - Copyright (c) 1997-2012 University of Cambridge All rights reserved. - - PCRE JUST-IN-TIME COMPILATION SUPPORT - - Written by: Zoltan Herczeg - Email local part: hzmester - Emain domain: freemail.hu - Copyright(c) 2010-2012 Zoltan Herczeg All rights reserved. - - STACK-LESS JUST-IN-TIME COMPILER - - Written by: Zoltan Herczeg Email local part: hzmester Emain domain: freemail.hu Copyright(c) 2009-2012 Zoltan Herczeg All rights reserved. - - THE C++ WRAPPER FUNCTIONS - - Contributed by: Google Inc. 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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - - -6. Some of the cuBLAS library routines were written by or derived from code written by Vasily Volkov and are subject to the Modified Berkeley Software Distribution License as follows: Copyright (c) 2007-2009, Regents of the University of California All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the University of California, Berkeley nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - -7. Some of the cuBLAS library routines were written by or derived from code written by Davide Barbieri and are subject to the Modified Berkeley Software Distribution License as follows: Copyright (c) 2008-2009 Davide Barbieri @ University of Rome Tor Vergata. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * The name of the author may not be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - -8. Some of the cuBLAS library routines were derived from code developed by the University of Tennessee and are subject to the Modified Berkeley Software Distribution License as follows: Copyright (c) 2010 The University of Tennessee. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer listed in this license in the documentation and/or other materials provided with the distribution. * Neither the name of the copyright holders nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - -9. Some of the cuBLAS library routines were written by or derived from code written by Jonathan Hogg and are subject to the Modified Berkeley Software Distribution License as follows: Copyright (c) 2012, The Science and Technology Facilities Council (STFC). All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the STFC nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE STFC BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - -10. Some of the cuBLAS library routines were written by or derived from code written by Ahmad M. Abdelfattah, David Keyes, and Hatem Ltaief, and are subject to the Apache License, Version 2.0, as follows: -- (C) Copyright 2013 King Abdullah University of Science and Technology Authors: Ahmad Abdelfattah (ahmad.ahmad@kaust.edu.sa) David Keyes (david.keyes@kaust.edu.sa) Hatem Ltaief (hatem.ltaief@kaust.edu.sa) Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the King Abdullah University of Science and Technology nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - -11. Some of the cuSPARSE library routines were written by or derived from code written by Li-Wen Chang and are subject to the NCSA Open Source License as follows: Copyright (c) 2012, University of Illinois. All rights reserved. Developed by: IMPACT Group, University of Illinois, http:// impact.crhc.illinois.edu Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal with the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimers in the documentation and/or other materials provided with the distribution. * Neither the names of IMPACT Group, University of Illinois, nor the names of its contributors may be used to endorse or promote products derived from this Software without specific prior written permission. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE. - -12. Some of the cuRAND library routines were written by or derived from code written by Mutsuo Saito and Makoto Matsumoto and are subject to the following license: Copyright (c) 2009, 2010 Mutsuo Saito, Makoto Matsumoto and Hiroshima University. All rights reserved. Copyright (c) 2011 Mutsuo Saito, Makoto Matsumoto, Hiroshima University and University of Tokyo. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the Hiroshima University nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - -13. Some of the cuRAND library routines were derived from code developed by D. E. Shaw Research and are subject to the following license: Copyright 2010-2011, D. E. Shaw Research. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions, and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions, and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of D. E. Shaw Research nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - -14. Licensee's use of the lz4 third party component is subject to the following terms and conditions: Copyright (C) 2011-2013, Yann Collet. BSD 2-Clause License (http://www.opensource.org/licenses/bsd-license.php) Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - -15. The NPP library uses code from the Boost Math Toolkit, and is subject to the following license: Boost Software License - Version 1.0 - August 17th, 2003 . . . . 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SHOULD THE LIBRARY PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. -16. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE LIBRARY AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE LIBRARY (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE LIBRARY TO OPERATE WITH ANY OTHER SOFTWARE), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. OEM Plupload -------------------------------------------------------------------------- -GNU General Public License + GNU General Public License Version 2, June 1991 -Copyright (C) 1989, 1991 Free Software Foundation, Inc., - -51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA + Copyright (C) 1989, 1991 Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA See Section 2 below for text of GPL v2.0 license. 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GNU General Public License version 2 (GPL v2) ===================================================================== GNU GENERAL PUBLIC LICENSE -Version 2, June 1991 -Copyright (C) 1989, 1991 Free Software Foundation, Inc. +Version 2, June 1991 + +Copyright (C) 1989, 1991 Free Software Foundation, Inc. 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. -Preamble +###Preamble The licenses for most software are designed to take away your freedom to share and change it. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change free software--to make sure the software is free for all its users. This General Public License applies to most of the Free Software Foundation's software and to any other program whose authors commit to using it. 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To prevent this, we have made it clear that any patent must be licensed for everyone's free use or not licensed at all. - The precise terms and conditions for copying, distribution and modification follow. - TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION -------------------------------------------------------------- 0. This License applies to any program or other work which contains a notice placed by the copyright holder saying it may be distributed under the terms of this General Public License. The "Program", below, refers to any such program or work, and a "work based on the Program" means either the Program or any derivative work under copyright law: that is to say, a work containing the Program or a portion of it, either verbatim or with modifications and/or translated into another language. (Hereinafter, translation is included without limitation in the term "modification".) Each licensee is addressed as "you". Activities other than copying, distribution and modification are not covered by this License; they are outside its scope. The act of running the Program is not restricted, and the output from the Program is covered only if its contents constitute a work based on the Program (independent of having been made by running the Program). Whether that is true depends on what the Program does. - 1. You may copy and distribute verbatim copies of the Program's source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty; keep intact all the notices that refer to this License and to the absence of any warranty; and give any other recipients of the Program a copy of this License along with the Program. You may charge a fee for the physical act of transferring a copy, and you may at your option offer warranty protection in exchange for a fee. - 2. 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But when you distribute the same sections as part of a whole which is a work based on the Program, the distribution of the whole must be on the terms of this License, whose permissions for other licensees extend to the entire whole, and thus to each and every part regardless of who wrote it. - - Thus, it is not the intent of this section to claim rights or contest your rights to work written entirely by you; rather, the intent is to exercise the right to control the distribution of derivative or collective works based on the Program. - - In addition, mere aggregation of another work not based on the Program with the Program (or with a work based on the Program) on a volume of a storage or distribution medium does not bring the other work under the scope of this License. - +a) You must cause the modified files to carry prominent notices stating that you changed the files and the date of any change. +b) You must cause any work that you distribute or publish, that in whole or in part contains or is derived from the Program or any part thereof, to be licensed as a whole at no charge to all third parties under the terms of this License. +c) If the modified program normally reads commands interactively when run, you must cause it, when started running for such interactive use in the most ordinary way, to print or display an announcement including an appropriate copyright notice and a notice that there is no warranty (or else, saying that you provide a warranty) and that users may redistribute the program under these conditions, and telling the user how to view a copy of this License. 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You may copy and distribute the Program (or a work based on it, under Section 2) in object code or executable form under the terms of Sections 1 and 2 above provided that you also do one of the following: - - a) Accompany it with the complete corresponding machine-readable source code, which must be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, - b) Accompany it with a written offer, valid for at least three years, to give any third party, for a charge no more than your cost of physically performing source distribution, a complete machine-readable copy of the corresponding source code, to be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, - c) Accompany it with the information you received as to the offer to distribute corresponding source code. (This alternative is allowed only for noncommercial distribution and only if you received the program in object code or executable form with such an offer, in accord with Subsection b above.) +a) Accompany it with the complete corresponding machine-readable source code, which must be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, +b) Accompany it with a written offer, valid for at least three years, to give any third party, for a charge no more than your cost of physically performing source distribution, a complete machine-readable copy of the corresponding source code, to be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, +c) Accompany it with the information you received as to the offer to distribute corresponding source code. (This alternative is allowed only for noncommercial distribution and only if you received the program in object code or executable form with such an offer, in accord with Subsection b above.) The source code for a work means the preferred form of the work for making modifications to it. For an executable work, complete source code means all the source code for all modules it contains, plus any associated interface definition files, plus the scripts used to control compilation and installation of the executable. However, as a special exception, the source code distributed need not include anything that is normally distributed (in either source or binary form) with the major components (compiler, kernel, and so on) of the operating system on which the executable runs, unless that component itself accompanies the executable. If distribution of executable or object code is made by offering access to copy from a designated place, then offering equivalent access to copy the source code from the same place counts as distribution of the source code, even though third parties are not compelled to copy the source along with the object code. - 4. You may not copy, modify, sublicense, or distribute the Program except as expressly provided under this License. Any attempt otherwise to copy, modify, sublicense or distribute the Program is void, and will automatically terminate your rights under this License. However, parties who have received copies, or rights, from you under this License will not have their licenses terminated so long as such parties remain in full compliance. - 5. You are not required to accept this License, since you have not signed it. However, nothing else grants you permission to modify or distribute the Program or its derivative works. These actions are prohibited by law if you do not accept this License. Therefore, by modifying or distributing the Program (or any work based on the Program), you indicate your acceptance of this License to do so, and all its terms and conditions for copying, distributing or modifying the Program or works based on it. - 6. Each time you redistribute the Program (or any work based on the Program), the recipient automatically receives a license from the original licensor to copy, distribute or modify the Program subject to these terms and conditions. You may not impose any further restrictions on the recipients' exercise of the rights granted herein. You are not responsible for enforcing compliance by third parties to this License. - 7. If, as a consequence of a court judgment or allegation of patent infringement or for any other reason (not limited to patent issues), conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot distribute so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not distribute the Program at all. For example, if a patent license would not permit royalty-free redistribution of the Program by all those who receive copies directly or indirectly through you, then the only way you could satisfy both it and this License would be to refrain entirely from distribution of the Program. If any portion of this section is held invalid or unenforceable under any particular circumstance, the balance of the section is intended to apply and the section as a whole is intended to apply in other circumstances. - - It is not the purpose of this section to induce you to infringe any patents or other property right claims or to contest validity of any such claims; this section has the sole purpose of protecting the integrity of the free software distribution system, which is implemented by public license practices. Many people have made generous contributions to the wide range of software distributed through that system in reliance on consistent application of that system; it is up to the author/donor to decide if he or she is willing to distribute software through any other system and a licensee cannot impose that choice. +It is not the purpose of this section to induce you to infringe any patents or other property right claims or to contest validity of any such claims; this section has the sole purpose of protecting the integrity of the free software distribution system, which is implemented by public license practices. Many people have made generous contributions to the wide range of software distributed through that system in reliance on consistent application of that system; it is up to the author/donor to decide if he or she is willing to distribute software through any other system and a licensee cannot impose that choice. This section is intended to make thoroughly clear what is believed to be a consequence of the rest of this License. - 8. If the distribution and/or use of the Program is restricted in certain countries either by patents or by copyrighted interfaces, the original copyright holder who places the Program under this License may add an explicit geographical distribution limitation excluding those countries, so that distribution is permitted only in or among countries not thus excluded. In such case, this License incorporates the limitation as if written in the body of this License. - 9. The Free Software Foundation may publish revised and/or new versions of the General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. Each version is given a distinguishing version number. If the Program specifies a version number of this License which applies to it and "any later version", you have the option of following the terms and conditions either of that version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of this License, you may choose any version ever published by the Free Software Foundation. - 10. If you wish to incorporate parts of the Program into other free programs whose distribution conditions are different, write to the author to ask for permission. For software which is copyrighted by the Free Software Foundation, write to the Free Software Foundation; we sometimes make exceptions for this. Our decision will be guided by the two goals of preserving the free status of all derivatives of our free software and of promoting the sharing and reuse of software generally. NO WARRANTY - 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. - 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. + +###End of (1) Torrent Suite(TM) Software Version 5.18 Open Source License + +**************************************************** + (2) BEGINS: +================================================================================ + +LIFE TECHNOLOGIES CORPORATION + +END USER LICENSE AGREEMENT +## FOR SERVICE & SUPPORT TELEMETRY MODULE SOFTWARE VERSION 2.0.1 + +NOTICE TO USER: PLEASE READ THIS DOCUMENT CAREFULLY. THIS IS THE CONTRACT BETWEEN YOU AND LIFE TECHNOLOGIES CORPORATION ("LIFE TECHNOLOGIES") REGARDING THIS SOFTWARE PRODUCT. THIS AGREEMENT CONTAINS WARRANTY AND LIABILITY DISCLAIMERS AND LIMITATIONS. YOUR INSTALLATION AND/OR USE OF THIS LIFE TECHNOLOGIES SOFTWARE IS SUBJECT TO THE TERMS AND CONDITIONS CONTAINED IN THIS END USER SOFTWARE LICENSE AGREEMENT, AND YOU WILL BE BOUND BY THESE TERMS AND CONDITIONS IF YOU INSTALL AND/OR USE THE SOFTWARE. +IF YOU DO NOT AGREE TO THESE TERMS AND CONDITIONS, YOU SHOULD PROMPTLY RETURN THIS SOFTWARE, TOGETHER WITH ALL PACKAGING, TO LIFE TECHNOLOGIES AND YOUR PURCHASE PRICE WILL BE REFUNDED. +This Life Technologies End User License Agreement accompanies a Life Technologies software product ("Software") and related explanatory materials ("Documentation"). The term "Software" also includes any upgrades, modified versions, updates, additions and copies of the Software licensed to you by Life Technologies. The term "License" or "Agreement" means this End User Software License Agreement. The term "you" or "Licensee" means the purchaser or user of this license to the Software. This Agreement includes herein by reference any additional use restrictions or Limited Use Label Licenses listed in or on user manuals, labeling, product inserts, technical notes, literature (including but not limited to Documentation) and/or splash screens related to this Software ("Supplemental Terms"). To the extent such Supplemental Terms are more restrictive than those contained herein, the more restrictive usage terms shall control. +This Software may use third-party software components from several sources. Portions of these software components are copyrighted and licensed by their respective owners. Various components require distribution of source code or if a URL is used to point the end-user to a source-code repository, and the source code is not available at such site, the distributor must, for a time determined by the license, offer to provide the source code. In such cases, please contact your Life Technologies representative. As well, various licenses require that the end-user receive a copy of the license. Such licenses, if any, may be found in Appendix 1 below. In order to use this Software, the end-user must abide by the terms and conditions of these third-party licenses. + +TITLE + +Title, ownership rights and intellectual property rights in and to the Software and Documentation shall at all times remain with Life Technologies and its subsidiaries, and their suppliers. All rights not specifically granted by this License, including Federal and international copyrights, are reserved by Life Technologies or their respective owners. + +COPYRIGHT + +The Software, including its structure, organization, code, user interface and associated Documentation, is a proprietary product of Life Technologies or its suppliers, and is protected by international laws of copyright. The law provides for civil and criminal penalties for anyone in violation of the laws of copyright. + +LICENSE + +USE OF THE SOFTWARE + +Subject to the terms and conditions of this Agreement, Life Technologies grants the purchaser of this product a non-exclusive, non-transferable license, with no rights to sublicense, to install and/or use the Software only in object code (machine readable) format and only on single computers owned or controlled by you (or in a single network, if your Software is designated as a network version) for the sole purpose of managing, analyzing, viewing, editing, reporting and/or printing data provided by Life Technologies or generated by Life Technologies instruments for research use only. +If the software uses registration codes, access to the number of licenses copies of Software is controlled by a registration code. For example, if you have a registration code that enables you to use three copies of Software simultaneously, you cannot install Software on more than three separate computers. +You may make one copy of the Software in machine-readable form solely for backup or archival purposes. You must reproduce on any such copy all copyright notices and any other proprietary legends found on the original. You may not make any other copies of the Software. + +RESTRICTIONS + +Unless permitted by applicable law, and in such cases only to the extent permitted by such law: + +1. You shall not copy, transfer (except temporarily in the event of a computer malfunction), rent, modify, distribute, electronically transmit, lend, lease, use, create derivative works based on the Software or merge the Software, or the associated Documentation, in whole or in part, whether alone or combined with any other products, except as expressly permitted in this Agreement. +2. You shall not reverse assemble, decompile, discover the source code or otherwise reverse engineer the Software. +3. You shall not remove any proprietary, copyright, trade secret or warning legend from the Software or any Documentation. +4. You agree to comply fully with all export laws and restrictions and regulations of the United States or applicable foreign agencies or authorities. You agree that you will not export or reexport, directly or indirectly, the Software and the Documentation into any country prohibited by the United States Export Administration Act and the regulations thereunder or other applicable United States law. +5. You may not use the Software or Documentation for the benefit of any third party by means of an outsourcing or service bureau relationship or for any similar commercial time-sharing or third-party training use. +6. You agree to use Software, and data generated by Software, for the sole purpose of review and analysis of data generated by Life Technologies instruments. + +TRIAL + +If this license is granted on a trial basis, you are hereby notified that license management software may be included to automatically cause the Software to cease functioning at the end of the trial period (and in any case you agree to discontinue usage at the end of the trial period or at the express written request of Life Technologies). + +TERMINATION + +You may terminate this Agreement by discontinuing use of the Software, removing all copies from your computers and storage media, and returning the Software and Documentation, and all copies thereof, to Life Technologies. Life Technologies may terminate this Agreement if you fail to comply with all of its terms, in which case you agree to discontinue using the Software, remove all copies from your computers and storage media, and return the Software and Documentation, and all copies thereof, to Life Technologies. + +U.S. GOVERNMENT END USERS + +The Software is a "commercial item," as that term is defined in 48 C.F.R. 2.101 (Oct. 1995), consisting of "commercial computer software" and "commercial computer software documentation," as such terms are used in 48 C.F.R. 12.212 (Sept. 1995). Consistent with 48 C.F.R. 12.212 and 48 C.F.R. 227.7202-1 through 227.7202-4 (June 1995), all U.S. Government End Users acquire the Software with only those rights set forth herein. + +EUROPEAN UNION END USERS + +If this Software is used within a country of the European Union, nothing in this Agreement shall be construed as restricting any rights available under Directive 2009/24/EC of the European Parliament and of the Council of 23 April 2009 on the legal protection of computer programs. +YOU ACKNOWLEDGE THAT LIFE TECHNOLOGIES HAS NO CONTROL OVER THE SPECIFIC CONDITIONS UNDER WHICH YOU USE THE SOFTWARE. LICENSOR CANNOT AND DOES NOT WARRANT THE PERFORMANCE OF THE SOFTWARE OR ANY PARTICULAR RESULTS THAT MAY BE OBTAINED BY THE USE OF THE SOFTWARE. THE SOFTWARE DOES NOT REPLACE YOUR OBLIGATION TO EXERCISE YOUR INDEPENDENT JUDGMENT IN USING THE SOFTWARE. The warranties, if any, made by Life Technologies may be voided by abuse or misuse of the Software. +LIMITATION OF LIABILITY +IN NO EVENT SHALL LIFE TECHNOLOGIES OR ITS SUPPLIERS BE RESPONSIBLE OR LIABLE, WHETHER IN CONTRACT, TORT, WARRANTY OR UNDER ANY STATUTE (INCLUDING WITHOUT LIMITATION ANY TRADE PRACTICE, UNFAIR COMPETITION OR OTHER STATUTE OF SIMILAR IMPORT) OR ON ANY OTHER BASIS FOR DAMAGES ARISING FROM PERSONAL INJURY OR DEATH OR SPECIAL, INDIRECT, INCIDENTAL, MULTIPLE, PUNITIVE, OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE POSSESSION OR USE OF, OR THE INABILITY TO USE, THE SOFTWARE, THE GENERATED DATA OR DOCUMENTATION, EVEN IF LIFE TECHNOLOGIES IS ADVISED IN ADVANCE OF THE POSSIBILITY OF SUCH DAMAGES, INCLUDING WITHOUT LIMITATION DAMAGES OR EXPENSES ARISING FROM OR RELATED TO, OR ALLEGED TO HAVE ARISEN FROM OR BE RELATED TO, LOSS OF USE, LOSS OF DATA, DOWNTIME, OR FOR LOSS OF REVENUE, PROFITS, GOODWILL OR BUSINESS OR OTHER FINANCIAL LOSS. IN ANY CASE, THE ENTIRE LIABILITY OF LIFE TECHNOLOGIES AND ITS SUPPLIERS UNDER THIS LICENSE, OR ARISING OUT OF THE USE OF THE SOFTWARE OR DOCUMENTATION OR GENERATED DATA, SHALL NOT EXCEED, IN THE AGGREGATE, THE PURCHASE PRICE OF THE PRODUCT. +SOME STATES, COUNTRIES OR JURISDICTIONS LIMIT THE SCOPE OF OR PRECLUDE LIMITATIONS OR EXCLUSION OF REMEDIES OR DAMAGES, OR OF LIABILITY, SUCH AS LIABILITY FOR GROSS NEGLIGENCE OR WILLFUL MISCONDUCT, AS OR TO THE EXTENT SET FORTH ABOVE, OR DO NOT ALLOW IMPLIED WARRANTIES TO BE EXCLUDED. IN SUCH STATES, COUNTRIES OR JURISDICTIONS, THE LIMITATION OR EXCLUSION OF WARRANTIES, REMEDIES, DAMAGES OR LIABILITY SET FORTH ABOVE MAY NOT APPLY TO YOU. HOWEVER, ALTHOUGH THEY SHALL NOT APPLY TO THE EXTENT PROHIBITED BY LAW, THEY SHALL APPLY TO THE FULLEST EXTENT PERMITTED BY LAW. YOU MAY ALSO HAVE OTHER RIGHTS THAT VARY BY STATE, COUNTRY OR OTHER JURISDICTION. + +CONFIDENTIALITY + +You agree to protect Life Technologies Confidential Information with the same degree of care used to protect your own confidential information (but in no event less than a reasonable standard of care), and not to use or disclose any portion of such Confidential Information to third parties, except as expressly authorized in this Agreement. You acknowledge that the Software, including its content, structure, organization and design constitute proprietary and valuable trade secrets (and other intellectual property rights) of Life Technology and/or its licensors. The term "Confidential Information" means, collectively, non-public information that Life Technologies (and its licensors) provide and reasonably consider to be of a confidential, proprietary or trade secret nature, including but not limited to (i) the Software, and (ii) confidential elements of the Software and Life Technologies (and its licensors) technology and know-how, whether in tangible or intangible form, whether designated as confidential or not, and whether or not stored, compiled or memorialized physically, electronically, graphically, photographically, or in writing. Confidential Information does not include any information which you can demonstrate by credible evidence: (a) is, as of the time of its disclosure, or thereafter becomes part of the public domain through no fault of yours; (b) was rightfully known to you prior to the time of its disclosure, or to have been independently developed by you without use of Confidential Information; and/or (C) is subsequently learned from a third party not under a confidentiality obligation with respect to such Confidential Information. Confidential Information that is required to be disclosed by you pursuant to a duly authorized subpoena, court order, or government authority shall continue to be Confidential Information for all other purposes and you agree, prior to disclosing pursuant to a subpoena, court order, or government authority, to provide prompt written notice and assistance to Life Technologies prior to such disclosure, so that Life Technologies may seek a protective order or other appropriate remedy to protect against disclosure. + +SOFTWARE IMPROVEMENTS + +You acknowledge and agree that any ideas, enhancements, modifications, and the like disclosed by you to Life Technologies with respect to the Software ("Software Improvements and Feedback") will be the property of Life Technologies. You agree to assign, and hereby assign, all right, title, and interest worldwide in the Software Improvements and Feedback to Life Technologies and agree to assist Life Technologies, at Life Technologies' expense, in perfecting and enforcing Life Technologies rights thereto and ownership thereof. You acknowledge and agree that Life Technologies may use such Software Improvements and Feedback for its business purposes without restriction. + +GENERAL + +This Agreement shall be governed by laws of the State of California, exclusive of its conflict of laws provisions. This Agreement shall not be governed by the United Nations Convention on Contracts for the International Sale of Goods. This Agreement contains the complete agreement between the parties with respect to the subject matter hereof, and supersedes all prior or contemporaneous agreements or understandings, whether oral or written. If any provision of this Agreement is held by a court of competent jurisdiction to be contrary to law, that provision will be enforced to the maximum extent permissible and the remaining provisions of this Agreement will remain in full force and effect. The controlling language of this Agreement, and any proceedings relating to this Agreement, shall be English. You agree to bear any and all costs of translation, if necessary. The headings to the sections of this Agreement are used for convenience only and shall have no substantive meaning. All questions concerning this Agreement shall be directed to: Life Technologies Corporation, 5781 Van Allen Way, Carlsbad, CA 92008, Attention: Legal Department. +Unpublished rights reserved under the copyright laws of the United States. Life Technologies Corporation, 5781 Van Allen Way, Carlsbad, CA 92008. +Life Technologies is a trademark of Life Technologies Corporation or its subsidiaries in the U.S. and certain other countries. +All other trademarks are the sole property of their respective owners. + +July 15, 2020 + +Appendix 1 + +Life Technologies Corporation + +Third Party Copyright Notices and Licenses + SERVICE & SUPPORT TELEMETRY MODULE SOFTWARE VERSION 2.0.1 +This software uses third party software components from several sources. Portions of these software components are copyrighted and licensed by their respective owners as indicated below. Various licenses require distribution of source code or if a link is used to point the end-user to a source-code repository, and the source code is not available at such site, the distributor must, for a time determined by license, offer to provide source code. In such cases, please contact your Life Technologies representative. As well, various licenses require that the end-user receive a copy of the license or certain notices. Such licenses and notices may be found in this appendix. + +Asn1crypto Copyright (C) 2015-2018 Will Bond +Six Copyright (C) 2010-2018 Benjamin Peterson + + + +The MIT License + +Permission is hereby granted, free of charge, to any person obtaining a copy of + this software and associated documentation files (the "Software"), to deal in + the Software without restriction, including without limitation the rights to + use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies + of the Software, and to permit persons to whom the Software is furnished to do + so, subject to the following conditions: + + The above copyright notice and this permission notice shall be included in all + copies or substantial portions of the Software. + + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE + SOFTWARE. + +Boto3 + +Botocore + +Pelix + +S3transfer + +Apache License + +Version 2.0, January 2004 + +TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + +1. Definitions. +"License" shall mean the terms and conditions for use, reproduction, and distribution as defined by Sections 1 through 9 of this document. +"Licensor" shall mean the copyright owner or entity authorized by the copyright owner that is granting the License. +"Legal Entity" shall mean the union of the acting entity and all other entities that control, are controlled by, or are under common control with that entity. For the purposes of this definition, "control" means (i) the power, direct or indirect, to cause the direction or management of such entity, whether by contract or otherwise, or (ii) ownership of fifty percent (50%) or more of the outstanding shares, or (iii) beneficial ownership of such entity. +"You" (or "Your") shall mean an individual or Legal Entity exercising permissions granted by this License. +"Source" form shall mean the preferred form for making modifications, including but not limited to software source code, documentation source, and configuration files. +"Object" form shall mean any form resulting from mechanical transformation or translation of a Source form, including but not limited to compiled object code, generated documentation, and conversions to other media types. +"Work" shall mean the work of authorship, whether in Source or Object form, made available under the License, as indicated by a copyright notice that is included in or attached to the work (an example is provided in the Appendix below). +"Derivative Works" shall mean any work, whether in Source or Object form, that is based on (or derived from) the Work and for which the editorial revisions, annotations, elaborations, or other modifications represent, as a whole, an original work of authorship. For the purposes of this License, Derivative Works shall not include works that remain separable from, or merely link (or bind by name) to the interfaces of, the Work and Derivative Works thereof. +"Contribution" shall mean any work of authorship, including the original version of the Work and any modifications or additions to that Work or Derivative Works thereof, that is intentionally submitted to Licensor for inclusion in the Work by the copyright owner or by an individual or Legal Entity authorized to submit on behalf of the copyright owner. For the purposes of this definition, "submitted" means any form of electronic, verbal, or written communication sent to the Licensor or its representatives, including but not limited to communication on electronic mailing lists, source code control systems, and issue tracking systems that are managed by, or on behalf of, the Licensor for the purpose of discussing and improving the Work, but excluding communication that is conspicuously marked or otherwise designated in writing by the copyright owner as "Not a Contribution." +"Contributor" shall mean Licensor and any individual or Legal Entity on behalf of whom a Contribution has been received by Licensor and subsequently incorporated within the Work. +2. Grant of Copyright License. Subject to the terms and conditions of this License, each Contributor hereby grants to You a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable copyright license to reproduce, prepare Derivative Works of, publicly display, publicly perform, sublicense, and distribute the Work and such Derivative Works in Source or Object form. +3. Grant of Patent License. Subject to the terms and conditions of this License, each Contributor hereby grants to You a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable (except as stated in this section) patent license to make, have made, use, offer to sell, sell, import, and otherwise transfer the Work, where such license applies only to those patent claims licensable by such Contributor that are necessarily infringed by their Contribution(s) alone or by combination of their Contribution(s) with the Work to which such Contribution(s) was submitted. If You institute patent litigation against any entity (including a cross-claim or counterclaim in a lawsuit) alleging that the Work or a Contribution incorporated within the Work constitutes direct or contributory patent infringement, then any patent licenses granted to You under this License for that Work shall terminate as of the date such litigation is filed. +4. Redistribution. You may reproduce and distribute copies of the Work or Derivative Works thereof in any medium, with or without modifications, and in Source or Object form, provided that You meet the following conditions: +1. You must give any other recipients of the Work or Derivative Works a copy of this License; and +2. You must cause any modified files to carry prominent notices stating that You changed the files; and +3. You must retain, in the Source form of any Derivative Works that You distribute, all copyright, patent, trademark, and attribution notices from the Source form of the Work, excluding those notices that do not pertain to any part of the Derivative Works; and +4. If the Work includes a "NOTICE" text file as part of its distribution, then any Derivative Works that You distribute must include a readable copy of the attribution notices contained within such NOTICE file, excluding those notices that do not pertain to any part of the Derivative Works, in at least one of the following places: within a NOTICE text file distributed as part of the Derivative Works; within the Source form or documentation, if provided along with the Derivative Works; or, within a display generated by the Derivative Works, if and wherever such third-party notices normally appear. The contents of the NOTICE file are for informational purposes only and do not modify the License. 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Notwithstanding the above, nothing herein shall supersede or modify the terms of any separate license agreement you may have executed with Licensor regarding such Contributions. +6. Trademarks. This License does not grant permission to use the trade names, trademarks, service marks, or product names of the Licensor, except as required for reasonable and customary use in describing the origin of the Work and reproducing the content of the NOTICE file. +7. Disclaimer of Warranty. Unless required by applicable law or agreed to in writing, Licensor provides the Work (and each Contributor provides its Contributions) on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied, including, without limitation, any warranties or conditions of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A PARTICULAR PURPOSE. You are solely responsible for determining the appropriateness of using or redistributing the Work and assume any risks associated with Your exercise of permissions under this License. +8. Limitation of Liability. In no event and under no legal theory, whether in tort (including negligence), contract, or otherwise, unless required by applicable law (such as deliberate and grossly negligent acts) or agreed to in writing, shall any Contributor be liable to You for damages, including any direct, indirect, special, incidental, or consequential damages of any character arising as a result of this License or out of the use or inability to use the Work (including but not limited to damages for loss of goodwill, work stoppage, computer failure or malfunction, or any and all other commercial damages or losses), even if such Contributor has been advised of the possibility of such damages. +9. Accepting Warranty or Additional Liability. While redistributing the Work or Derivative Works thereof, You may choose to offer, and charge a fee for, acceptance of support, warranty, indemnity, or other liability obligations and/or rights consistent with this License. However, in accepting such obligations, You may act only on Your own behalf and on Your sole responsibility, not on behalf of any other Contributor, and only if You agree to indemnify, defend, and hold each Contributor harmless for any liability incurred by, or claims asserted against, such Contributor by reason of your accepting any such warranty or additional liability. + +Concurrent + +The Python Software Foundation License Version 2 + + 1. This LICENSE AGREEMENT is between the Python Software Foundation + ("PSF"), and the Individual or Organization ("Licensee") accessing and + otherwise using this software ("Python") in source or binary form and + its associated documentation. + + 2. 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This License Agreement does not grant permission to use PSF + trademarks or trade name in a trademark sense to endorse or promote + products or services of Licensee, or any third party. + + 8. By copying, installing or otherwise using Python, Licensee + agrees to be bound by the terms and conditions of this License + Agreement. + +Paho + +Eclipse Distribution License - v 1.0 + +Copyright (C) 2007, Eclipse Foundation, Inc. and its licensors. + +All rights reserved. + +Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: + +* Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. +* Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. +* Neither the name of the Eclipse Foundation, Inc. nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +AND + +Eclipse Public License - v 1.0 + +THE ACCOMPANYING PROGRAM IS PROVIDED UNDER THE TERMS OF THIS ECLIPSE PUBLIC LICENSE ("AGREEMENT"). ANY USE, REPRODUCTION OR DISTRIBUTION OF THE PROGRAM CONSTITUTES RECIPIENT'S ACCEPTANCE OF THIS AGREEMENT. + +1. DEFINITIONS + + + "Contribution" means: + + a) in the case of the initial Contributor, the initial code and documentation distributed under this Agreement, and + + b) in the case of each subsequent Contributor: + + i)changes to the Program, and + + ii)additions to the Program; + where such changes and/or additions to the Program originate from and are distributed by that particular Contributor. A Contribution 'originates' from a Contributor if it was added to the Program by such Contributor itself or anyone acting on such Contributor's behalf. Contributions do not include additions to the Program which: (i) are separate modules of software distributed in conjunction with the Program under their own license agreement, and (ii) are not derivative works of the Program. +"Contributor" means any person or entity that distributes the Program. +"Licensed Patents " mean patent claims licensable by a Contributor which are necessarily infringed by the use or sale of its Contribution alone or when combined with the Program. +"Program" means the Contributions distributed in accordance with this Agreement. +"Recipient" means anyone who receives the Program under this Agreement, including all Contributors. + +2. GRANT OF RIGHTS + + + a) Subject to the terms of this Agreement, each Contributor hereby grants Recipient a non-exclusive, worldwide, royalty-free copyright license to reproduce, prepare derivative works of, publicly display, publicly perform, distribute and sublicense the Contribution of such Contributor, if any, and such derivative works, in source code and object code form. + + b) Subject to the terms of this Agreement, each Contributor hereby grants Recipient a non-exclusive, worldwide, royalty-free patent license under Licensed Patents to make, use, sell, offer to sell, import and otherwise transfer the Contribution of such Contributor, if any, in source code and object code form. This patent license shall apply to the combination of the Contribution and the Program if, at the time the Contribution is added by the Contributor, such addition of the Contribution causes such combination to be covered by the Licensed Patents. The patent license shall not apply to any other combinations which include the Contribution. No hardware per se is licensed hereunder. + + c) Recipient understands that although each Contributor grants the licenses to its Contributions set forth herein, no assurances are provided by any Contributor that the Program does not infringe the patent or other intellectual property rights of any other entity. Each Contributor disclaims any liability to Recipient for claims brought by any other entity based on infringement of intellectual property rights or otherwise. As a condition to exercising the rights and licenses granted hereunder, each Recipient hereby assumes sole responsibility to secure any other intellectual property rights needed, if any. For example, if a third party patent license is required to allow Recipient to distribute the Program, it is Recipient's responsibility to acquire that license before distributing the Program. +d) Each Contributor represents that to its knowledge it has sufficient copyright rights in its Contribution, if any, to grant the copyright license set forth in this Agreement. + +3. REQUIREMENTS + + A Contributor may choose to distribute the Program in object code form under its own license agreement, provided that: + + a) it complies with the terms and conditions of this Agreement; and + + b) its license agreement: + + i) effectively disclaims on behalf of all Contributors all warranties and conditions, express and implied, including warranties or conditions of title and non-infringement, and implied warranties or conditions of merchantability and fitness for a particular purpose; + + ii) effectively excludes on behalf of all Contributors all liability for damages, including direct, indirect, special, incidental and consequential damages, such as lost profits; + + iii) states that any provisions which differ from this Agreement are offered by that Contributor alone and not by any other party; and + + iv) states that source code for the Program is available from such Contributor, and informs licensees how to obtain it in a reasonable manner on or through a medium customarily used for software exchange. +When the Program is made available in source code form: + + a) it must be made available under this Agreement; and + + b) a copy of this Agreement must be included with each copy of the Program. + Contributors may not remove or alter any copyright notices contained within the Program. + Each Contributor must identify itself as the originator of its Contribution, if any, in a manner that reasonably allows subsequent Recipients to identify the originator of the Contribution. + +4. COMMERCIAL DISTRIBUTION + + Commercial distributors of software may accept certain responsibilities with respect to end users, business partners and the like. While this license is intended to facilitate the commercial use of the Program, the Contributor who includes the Program in a commercial product offering should do so in a manner which does not create potential liability for other Contributors. Therefore, if a Contributor includes the Program in a commercial product offering, such Contributor ("Commercial Contributor") hereby agrees to defend and indemnify every other Contributor ("Indemnified Contributor") against any losses, damages and costs (collectively "Losses") arising from claims, lawsuits and other legal actions brought by a third party against the Indemnified Contributor to the extent caused by the acts or omissions of such Commercial Contributor in connection with its distribution of the Program in a commercial product offering. The obligations in this section do not apply to any claims or Losses relating to any actual or alleged intellectual property infringement. In order to qualify, an Indemnified Contributor must: a) promptly notify the Commercial Contributor in writing of such claim, and b) allow the Commercial Contributor to control, and cooperate with the Commercial Contributor in, the defense and any related settlement negotiations. The Indemnified Contributor may participate in any such claim at its own expense. + For example, a Contributor might include the Program in a commercial product offering, Product X. That Contributor is then a Commercial Contributor. If that Commercial Contributor then makes performance claims, or offers warranties related to Product X, those performance claims and warranties are such Commercial Contributor's responsibility alone. Under this section, the Commercial Contributor would have to defend claims against the other Contributors related to those performance claims and warranties, and if a court requires any other Contributor to pay any damages as a result, the Commercial Contributor must pay those damages. + +5. NO WARRANTY + + EXCEPT AS EXPRESSLY SET FORTH IN THIS AGREEMENT, THE PROGRAM IS PROVIDED ON AN "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, EITHER EXPRESS OR IMPLIED INCLUDING, WITHOUT LIMITATION, ANY WARRANTIES OR CONDITIONS OF TITLE, NON-INFRINGEMENT, MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. Each Recipient is solely responsible for determining the appropriateness of using and distributing the Program and assumes all risks associated with its exercise of rights under this Agreement , including but not limited to the risks and costs of program errors, compliance with applicable laws, damage to or loss of data, programs or equipment, and unavailability or interruption of operations. + +6. DISCLAIMER OF LIABILITY + + EXCEPT AS EXPRESSLY SET FORTH IN THIS AGREEMENT, NEITHER RECIPIENT NOR ANY CONTRIBUTORS SHALL HAVE ANY LIABILITY FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING WITHOUT LIMITATION LOST PROFITS), HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OR DISTRIBUTION OF THE PROGRAM OR THE EXERCISE OF ANY RIGHTS GRANTED HEREUNDER, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. + +7. GENERAL + + If any provision of this Agreement is invalid or unenforceable under applicable law, it shall not affect the validity or enforceability of the remainder of the terms of this Agreement, and without further action by the parties hereto, such provision shall be reformed to the minimum extent necessary to make such provision valid and enforceable. + + If Recipient institutes patent litigation against any entity (including a cross-claim or counterclaim in a lawsuit) alleging that the Program itself (excluding combinations of the Program with other software or hardware) infringes such Recipient's patent(s), then such Recipient's rights granted under Section 2(b) shall terminate as of the date such litigation is filed. + + All Recipient's rights under this Agreement shall terminate if it fails to comply with any of the material terms or conditions of this Agreement and does not cure such failure in a reasonable period of time after becoming aware of such noncompliance. If all Recipient's rights under this Agreement terminate, Recipient agrees to cease use and distribution of the Program as soon as reasonably practicable. However, Recipient's obligations under this Agreement and any licenses granted by Recipient relating to the Program shall continue and survive. +Everyone is permitted to copy and distribute copies of this Agreement, but in order to avoid inconsistency the Agreement is copyrighted and may only be modified in the following manner. The Agreement Steward reserves the right to publish new versions (including revisions) of this Agreement from time to time. No one other than the Agreement Steward has the right to modify this Agreement. The Eclipse Foundation is the initial Agreement Steward. The Eclipse Foundation may assign the responsibility to serve as the Agreement Steward to a suitable separate entity. Each new version of the Agreement will be given a distinguishing version number. The Program (including Contributions) may always be distributed subject to the version of the Agreement under which it was received. In addition, after a new version of the Agreement is published, Contributor may elect to distribute the Program (including its Contributions) under the new version. Except as expressly stated in Sections 2(a) and 2(b) above, Recipient receives no rights or licenses to the intellectual property of any Contributor under this Agreement, whether expressly, by implication, estoppel or otherwise. All rights in the Program not expressly granted under this Agreement are reserved. + + This Agreement is governed by the laws of the State of New York and the intellectual property laws of the United States of America. No party to this Agreement will bring a legal action under this Agreement more than one year after the cause of action arose. Each party waives its rights to a jury trial in any resulting litigation. + +## Docutils + + Public Domain Dedication + + The persons who have associated their work with this project (the "Dedicator": David Goodger and the many contributors to the Docutils project) hereby dedicate the entire copyright, less the exceptions listed below, in the work of authorship known as "Docutils" identified below (the "Work") to the public domain. + + The primary repository for the Work is the Internet World Wide Web site . The Work consists of the files within the "docutils" module of the Docutils project Subversion repository (Internet host docutils.svn.sourceforge.net, filesystem path /svnroot/docutils), whose Internet web interface is located at . Files dedicated to the public domain may be identified by the inclusion, near the beginning of each file, of a declaration of the form: + + Copyright: This document/module/DTD/stylesheet/file/etc. has been + placed in the public domain. + + Dedicator makes this dedication for the benefit of the public at large and to the detriment of Dedicator's heirs and successors. Dedicator intends this dedication to be an overt act of relinquishment in perpetuity of all present and future rights under copyright law, whether vested or contingent, in the Work. Dedicator understands that such relinquishment of all rights includes the relinquishment of all rights to enforce (by lawsuit or otherwise) those copyrights in the Work. + + Dedicator recognizes that, once placed in the public domain, the Work may be freely reproduced, distributed, transmitted, used, modified, built upon, or otherwise exploited by anyone for any purpose, commercial or non-commercial, and in any way, including by methods that have not yet been invented or conceived. + +## Dateutil + + Copyright (C) 2003-2011 - Gustavo Niemeyer + + Copyright (C) 2012-2014 - Tomi Pievilainen + + Copyright (C) 2014 - Yaron de Leeuw + + All rights reserved. + + Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + * Redistributions of source code must retain the above copyright notice, + this list of conditions and the following disclaimer. + * Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + * Neither the name of the copyright holder nor the names of its + contributors may be used to endorse or promote products derived from + this software without specific prior written permission. + + THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS +"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT +LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR +A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR +CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +## Enum + +Copyright (C) 2013, Ethan Furman. + +All rights reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions +are met: + + Redistributions of source code must retain the above + copyright notice, this list of conditions and the + following disclaimer. + + Redistributions in binary form must reproduce the above + copyright notice, this list of conditions and the following + disclaimer in the documentation and/or other materials + provided with the distribution. + + Neither the name Ethan Furman nor the names of any + contributors may be used to endorse or promote products + derived from this software without specific prior written + permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE +LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR +CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF +SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS +INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN +CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) +ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE +POSSIBILITY OF SUCH DAMAGE. + +## Jmespath + +Copyright (C) 2013 Amazon.com, Inc. or its affiliates. All Rights Reserved + +Permission is hereby granted, free of charge, to any person obtaining a +copy of this software and associated documentation files (the +"Software"), to deal in the Software without restriction, including +without limitation the rights to use, copy, modify, merge, publish, dis- +tribute, sublicense, and/or sell copies of the Software, and to permit +persons to whom the Software is furnished to do so, subject to the fol- +lowing conditions: + +The above copyright notice and this permission notice shall be included +in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS +OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABIL- +ITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT +SHALL THE AUTHOR BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, +WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS +IN THE SOFTWARE. + +## Oscrypto + +Copyright (C) 2015-2018 Will Bond + +Permission is hereby granted, free of charge, to any person obtaining a copy of +this software and associated documentation files (the "Software"), to deal in +the Software without restriction, including without limitation the rights to +use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies +of the Software, and to permit persons to whom the Software is furnished to do +so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. + +## Pubsub + +Copyright (C) since 2006, Oliver Schoenborn +All rights reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + +1. Redistributions of source code must retain the above copyright notice, this + list of conditions and the following disclaimer. +2. Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR +ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES +(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; +LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND +ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +###END OF (2) SERVICE & SUPPORT TELEMETRY MODULE SOFTWARE VERSION 2.0.1 END USER LICENSE AGREEMENT +**************************************************** +(3) BEGINS: +======================================== + + +LIFE TECHNOLOGIES CORPORATION + +END USER LICENSE AGREEMENT and LIMITED PRODUCT WARRANTY + +FOR ION CHEF(TM) INSTRUMENT SOFTWARE VERSION 5.18 INSTRUMENT OPERATING SOFTWARE + +NOTICE TO USER: PLEASE READ THIS DOCUMENT CAREFULLY. THIS IS THE CONTRACT BETWEEN YOU AND LIFE TECHNOLOGIES CORPORATION ("LIFE TECHNOLOGIES") REGARDING THE OPERATING SOFTWARE FOR YOUR LIFE TECHNOLOGIES WORKSTATION OR OTHER INSTRUMENT AND BUNDLED SOFTWARE INSTALLED WITH YOUR OPERATING SOFTWARE. THIS AGREEMENT CONTAINS WARRANTY AND LIABILITY DISCLAIMERS AND LIMITATIONS. YOUR INSTALLATION AND USE OF THIS LIFE TECHNOLOGIES SOFTWARE IS SUBJECT TO THE TERMS AND CONDITIONS CONTAINED IN THIS END USER SOFTWARE LICENSE AGREEMENT, AND YOU WILL BE BOUND BY THESE TERMS AND CONDITIONS IF YOU INSTALL AND USE THE SOFTWARE. + +IF YOU DO NOT AGREE TO THESE TERMS AND CONDITIONS, YOU SHOULD PROMPTLY RETURN THIS SOFTWARE, TOGETHER WITH ALL PACKAGING, TO LIFE TECHNOLOGIES AND YOUR PURCHASE PRICE WILL BE REFUNDED. +This Life Technologies End User License Agreement accompanies a Life Technologies software product ("Software") and related explanatory materials ("Documentation"). The term "Software" also includes any upgrades, modified versions, updates, additions and copies of the Software licensed to you by Life Technologies. The term "License" or "Agreement" means this End User Software License Agreement. The term "you" or "Licensee" means the purchaser or user of this license to the Software. This Agreement includes herein by reference any additional use restrictions or Limited Use Label Licenses listed in or on user manuals, labeling, product inserts, technical notes, literature (including but not limited to Documentation) and/or splash screens related to this Software ("Supplemental Terms"). To the extent such Supplemental Terms are more restrictive than those contained herein, the more restrictive usage terms shall control. +This Software may use third-party software components from several sources. Portions of these software components are copyrighted and licensed by their respective owners. Various components require distribution of source code or if a URL is used to point the end-user to a source-code repository, and the source code is not available at such site, the distributor must, for a time determined by the license, offer to provide the source code. In such cases, please contact your Life Technologies representative. As well, various licenses require that the end-user receive a copy of the license. Such licenses, if any, may be found in Appendix 1 below. In order to use this Software, the end-user must abide by the terms and conditions of these third-party licenses. + +TITLE + +Title, ownership rights and intellectual property rights in and to the Software and Documentation shall at all times remain with Life Technologies and its subsidiaries, and their suppliers. All rights not specifically granted by this License, including Federal and international copyrights, are reserved by Life Technologies or their respective owners. + +COPYRIGHT + +The Software, including its structure, organization, code, user interface and associated Documentation, is a proprietary product of Life Technologies or its suppliers, and is protected by international laws of copyright. The law provides for civil and criminal penalties for anyone in violation of the laws of copyright. + +LICENSE + +USE OF THE SOFTWARE + +Subject to the terms and conditions of this Agreement, Life Technologies grants the purchaser of this product a non-exclusive, non-transferable (except in connection with the sale of the instrument on which it is hereby pre-installed) license, with no rights to sublicense, only to use the Software in object code (machine readable) format only on the single instrument on which it has been pre-installed by Life Technologies. +RESTRICTIONS +Unless permitted by applicable law, and in such cases only to the extent permitted by such law: + +1. You shall not copy, transfer (except temporarily in the event of a computer malfunction), rent, modify, distribute, electronically transmit, lend, lease, use, create derivative works based on the Software or merge the Software, or the associated Documentation, in whole or in part, whether alone or combined with any other products, except as expressly permitted in this Agreement. +2. You shall not reverse assemble, decompile, discover the source code or otherwise reverse engineer the Software. +3. You shall not remove any proprietary, copyright, trade secret or warning legend from the Software or any Documentation. +4. You agree to comply fully with all export laws and restrictions and regulations of the United States or applicable foreign agencies or authorities. You agree that you will not export or reexport, directly or indirectly, the Software and the Documentation into any country prohibited by the United States Export Administration Act and the regulations thereunder or other applicable United States law. +5. You may not use the Software or Documentation for the benefit of any third party by means of an outsourcing or service bureau relationship or for any similar commercial time-sharing or third-party training use. +6. You shall not sell, rent, transfer, resell for profit, or distribute this license or the Software, or any part thereof or any interest therein, unless the next user agrees to comply with the terms of this End User License Agreement. + +VERIFICATION + +At the written request of Life Technologies, not more frequently than annually, you shall furnish Life Technologies with a signed certification verifying that the Software is being used pursuant to the provisions of this License. + +TRIAL + +If this license is granted on a trial basis, you are hereby notified that license management software may be included to automatically cause the Software to cease functioning at the end of the trial period (and in any case you agree to discontinue usage at the end of the trial period or at the express written request of Life Technologies). + +TERMINATION + +You may terminate this Agreement by discontinuing use of the Software, removing all copies from your computers and storage media, and returning the Software and Documentation, and all copies thereof, to Life Technologies. Life Technologies may terminate this Agreement if you fail to comply with all of its terms, in which case you agree to discontinue using the Software, remove all copies from your computers and storage media, and return the Software and Documentation, and all copies thereof, to Life Technologies. + +U.S. GOVERNMENT END USERS + +The Software is a "commercial item," as that term is defined in 48 C.F.R. 2.101 (Oct. 1995), consisting of "commercial computer software" and "commercial computer software documentation," as such terms are used in 48 C.F.R. 12.212 (Sept. 1995). Consistent with 48 C.F.R. 12.212 and 48 C.F.R. 227.7202-1 through 227.7202-4 (June 1995), all U.S. Government End Users acquire the Software with only those rights set forth herein. + +EUROPEAN UNION END USERS + +If this Software is used within a country of the European Union, nothing in this Agreement shall be construed as restricting any rights available under Directive 2009/24/EC of the European Parliament and of the Council of 23 April 2009 on the legal protection of computer programs. + +LIMITED WARRANTY AND LIMITATION OF REMEDIES + +Limited Warranty. Life Technologies warrants that, except for Software provided on a trial basis, for a period of ninety days from the beginning of the applicable warranty period (as described below) the Software will, under normal use and as unmodified, function substantially in accordance with the functions and features described in the Documentation delivered with the Software when properly installed, and that for a period of ninety days from the beginning of the applicable warranty period (as described below) the tapes, CDs, diskettes or other media bearing the Software will be free of defects in materials and workmanship under normal use. +The above warranties do not apply to defects resulting from misuse, neglect, or accident, including without limitation: operation outside of the environmental or use specifications, or not in conformance with the instructions for any instrument system, software, or accessories; improper or inadequate maintenance by the user; installation of software or interfacing, or use in combination with software or products not supplied or authorized by Life Technologies; and modification or repair of the products not authorized by Life Technologies. +Warranty Period Commencement Date. The applicable warranty period for software begins on the earlier of the date of installation or three (3) months from the date of shipment for software installed by Life Technologies personnel. For software installed by the purchaser or anyone other than Life Technologies, the warranty period begins on the date the software is delivered to you. The applicable warranty period for media begins on the date the media is delivered to the purchaser. + +LIFE TECHNOLOGIES MAKES NO OTHER WARRANTIES OF ANY KIND WHATSOEVER, EXPRESS OR IMPLIED, WITH RESPECT TO THE SOFTWARE, DATA GENERATED FROM THE USE OF THE SOFTWARE ("GENERATED DATA") OR DOCUMENTATION, INCLUDING BUT NOT LIMITED TO WARRANTIES OF FITNESS FOR A PARTICULAR PURPOSE OR MERCHANTABILITY, NON-INFRINGEMENT OR NON-MISSAPROPRIATION OF INTELLECTUAL PROPERTY RIGHTS OF A THIRD PARTY, CUSTOM, TRADE, QUIET ENJOYMENT, ACCURACY OF INFORMATIONAL CONTENT, OR SYSTEM INTEGRATION. ALL OTHER WARRANTIES ARE EXPRESSLY DISCLAIMED. WITHOUT LIMITING THE GENERALITY OF THE FOREGOING, LIFE TECHNOLOGIES MAKES NO WARRANTIES THAT THE SOFTWARE WILL MEET YOUR REQUIREMENTS, THAT OPERATION OF THE SOFTWARE WILL BE UNINTERRUPTED OR ERROR FREE OR COMPLETELY SECURE, WILL OPERATE IN COMBINATION WITH THIRD PARTY HARDWARE OR SOFTWARE PRODUCTS, OR WILL CONFORM EXACTLY TO THE DOCUMENTATION, OR THAT LIFE TECHNOLOGIES WILL CORRECT ALL PROGRAM ERRORS. LIFE TECHNOLOGIES SOLE LIABILITY AND RESPONSIBILITY FOR BREACH OF WARRANTY RELATING TO THE SOFTWARE OR DOCUMENTATION SHALL BE LIMITED, AT LIFE TECHNOLOGIES SOLE OPTION, TO (1) CORRECTION OF ANY ERROR IDENTIFIED TO LIFE TECHNOLOGIES IN A WRITING FROM YOU IN A SUBSEQUENT RELEASE OF THE SOFTWARE, WHICH SHALL BE SUPPLIED TO YOU FREE OF CHARGE, (2) ACCEPTING A RETURN OF THE PRODUCT, AND REFUNDING THE PURCHASE PRICE UPON RETURN OF THE PRODUCT AND REMOVAL OF ALL COPIES OF THE SOFTWARE FROM YOUR COMPUTERS AND STORAGE DEVICES, (3) REPLACEMENT OF THE DEFECTIVE SOFTWARE WITH A FUNCTIONALLY EQUIVALENT PROGRAM AT NO CHARGE TO YOU, OR (4) PROVIDING A REASONABLE WORK AROUND WITHIN A REASONABLE TIME. LIFE TECHNOLOGIES SOLE LIABILITY AND RESPONSIBILITY UNDER THIS AGREEMENT FOR BREACH OF WARRANTY RELATING TO MEDIA IS THE REPLACEMENT OF DEFECTIVE MEDIA RETURNED WITHIN 90 DAYS OF THE DELIVERY DATE. THESE ARE YOUR SOLE AND EXCLUSIVE REMEDIES FOR ANY BREACH OF WARRANTY. WARRANTY CLAIMS MUST BE MADE WITHIN THE APPLICABLE WARRANTY PERIOD. +YOU ACKNOWLEDGE THAT LIFE TECHNOLOGIES HAS NO CONTROL OVER THE SPECIFIC CONDITIONS UNDER WHICH YOU USE THE SOFTWARE. ACCORDINGLY, EXCEPT FOR THE FOREGOING EXPRESS WARRANTY, LICENSOR CANNOT AND DOES NOT WARRANT THE PERFORMANCE OF THE SOFTWARE OR ANY PARTICULAR RESULTS THAT MAY BE OBTAINED BY THE USE OF THE SOFTWARE. THE SOFTWARE DOES NOT REPLACE YOUR OBLIGATION TO EXERCISE YOUR INDEPENDENT JUDGMENT IN USING THE SOFTWARE. The warranties made by Life Technologies may be voided by abuse or misuse of the Software. + +LIMITATION OF LIABILITY + +IN NO EVENT SHALL LIFE TECHNOLOGIES OR ITS SUPPLIERS BE RESPONSIBLE OR LIABLE, WHETHER IN CONTRACT, TORT, WARRANTY OR UNDER ANY STATUTE (INCLUDING WITHOUT LIMITATION ANY TRADE PRACTICE, UNFAIR COMPETITION OR OTHER STATUTE OF SIMILAR IMPORT) OR ON ANY OTHER BASIS FOR DAMAGES ARISING FROM PERSONAL INJURY OR DEATH OR SPECIAL, INDIRECT, INCIDENTAL, MULTIPLE, PUNITIVE, OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE POSSESSION OR USE OF, OR THE INABILITY TO USE, THE SOFTWARE, THE GENERATED DATA OR DOCUMENTATION, EVEN IF LIFE TECHNOLOGIES IS ADVISED IN ADVANCE OF THE POSSIBILITY OF SUCH DAMAGES, INCLUDING WITHOUT LIMITATION DAMAGES OR EXPENSES ARISING FROM OR RELATED TO, OR ALLEGED TO HAVE ARISEN FROM OR BE RELATED TO, LOSS OF USE, LOSS OF DATA, DOWNTIME, OR FOR LOSS OF REVENUE, PROFITS, GOODWILL OR BUSINESS OR OTHER FINANCIAL LOSS. IN ANY CASE, THE ENTIRE LIABILITY OF LIFE TECHNOLOGIES AND ITS SUPPLIERS UNDER THIS LICENSE, OR ARISING OUT OF THE USE OF THE SOFTWARE OR DOCUMENTATION OR GENERATED DATA, SHALL NOT EXCEED, IN THE AGGREGATE, THE PURCHASE PRICE OF THE PRODUCT. +SOME STATES, COUNTRIES OR JURISDICTIONS LIMIT THE SCOPE OF OR PRECLUDE LIMITATIONS OR EXCLUSION OF REMEDIES OR DAMAGES, OR OF LIABILITY, SUCH AS LIABILITY FOR GROSS NEGLIGENCE OR WILLFUL MISCONDUCT, AS OR TO THE EXTENT SET FORTH ABOVE, OR DO NOT ALLOW IMPLIED WARRANTIES TO BE EXCLUDED. IN SUCH STATES, COUNTRIES OR JURISDICTIONS, THE LIMITATION OR EXCLUSION OF WARRANTIES, REMEDIES, DAMAGES OR LIABILITY SET FORTH ABOVE MAY NOT APPLY TO YOU. HOWEVER, ALTHOUGH THEY SHALL NOT APPLY TO THE EXTENT PROHIBITED BY LAW, THEY SHALL APPLY TO THE FULLEST EXTENT PERMITTED BY LAW. YOU MAY ALSO HAVE OTHER RIGHTS THAT VARY BY STATE, COUNTRY OR OTHER JURISDICTION. + +CONFIDENTIALITY + +You agree to protect Life Technologies Confidential Information with the same degree of care used to protect your own confidential information (but in no event less than a reasonable standard of care), and not to use or disclose any portion of such Confidential Information to third parties, except as expressly authorized in this Agreement. You acknowledge that the Software, including its content, structure, organization and design constitute proprietary and valuable trade secrets (and other intellectual property rights) of Life Technology and/or its licensors. 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IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, +INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING +OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY +YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER +PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. + + +END OF TERMS AND CONDITIONS + +Mozilla Public License, v. 2.0 + +DHCP + +Mozilla Public License +Version 2.0 + +1. Definitions + + 1.1. "Contributor" +means each individual or legal entity that creates, contributes to the creation of, or owns Covered +Software. + + + 1.2. "Contributor Version" +means the combination of the Contributions of others (if any) used by a Contributor and that particular +Contributor's Contribution. + + + 1.3. "Contribution" +means Covered Software of a particular Contributor. + + + 1.4. "Covered Software" +means Source Code Form to which the initial Contributor has attached the notice in Exhibit A, the Executable Form of such Source Code Form, and Modifications of such Source Code Form, in each case including portions thereof. + + + 1.5. "Incompatible With Secondary Licenses" +means +that the initial Contributor has attached the notice described in Exhibit B to the Covered Software; or that the Covered Software was made available under the terms of version 1.1 or earlier of the License, +but not also under the terms of a Secondary License. + + + 1.6. "Executable Form" +means any form of the work other than Source Code Form. + + + 1.7. "Larger Work" +means a work that combines Covered Software with other material, in a separate file or files, that is not +Covered Software. + + + 1.8. "License" +means this document. + + + 1.9. "Licensable" +means having the right to grant, to the maximum extent possible, whether at the time of the initial grant or subsequently, any and all of the rights conveyed by this License. + + + 1.10. "Modifications" +means any of the following: + + any file in Source Code Form that results from an addition to, deletion from, or modification of the +contents of Covered Software; or + + + any new file in Source Code Form that contains any Covered Software. + + + 1.11. "Patent Claims" of a Contributor +means any patent claim(s), including without limitation, method, process, and apparatus claims, in any patent Licensable by such Contributor that would be infringed, but for the grant of the License, by the making, using, selling, offering for sale, having made, import, or transfer of either its Contributions or its Contributor Version. + + + 1.12. "Secondary License" +means either the GNU General Public License, Version 2.0, the GNU Lesser General Public License, Version 2.1, the GNU Affero General Public License, Version 3.0, or any later versions of those licenses. + + + 1.13. "Source Code Form" +means the form of the work preferred for making modifications. + + + 1.14. "You" (or "Your") +means an individual or a legal entity exercising rights under this License. For legal entities, "You" includes any entity that controls, is controlled by, or is under common control with You. For purposes of this definition, "control" means (a) the power, direct or indirect, to cause the direction or management of such entity, whether by contract or otherwise, or (b) ownership of more than fifty percent (50%) of the outstanding shares or beneficial ownership of such entity. + + +2. License Grants and Conditions + + 2.1. Grants + + Each Contributor hereby grants You a world-wide, royalty-free, non-exclusive license: + under intellectual property rights (other than patent or trademark) Licensable by such Contributor to use, reproduce, make available, modify, display, perform, distribute, and otherwise exploit its Contributions, either on an unmodified basis, with Modifications, or as part of a Larger Work; and under Patent Claims of such Contributor to make, use, sell, offer for sale, have made, import, and otherwise transfer either its Contributions or its Contributor Version. + + + 2.2. Effective Date + + The licenses granted in Section 2.1 with respect to any Contribution become effective for each +Contribution on the date the Contributor first distributes such Contribution. + + + 2.3. Limitations on Grant Scope + + The licenses granted in this Section 2 are the only rights granted under this License. No additional rights or licenses will be implied from the distribution or licensing of Covered Software under this License. Notwithstanding Section 2.1(b) above, no patent license is granted by a Contributor: +for any code that a Contributor has removed from Covered Software; or for infringements caused by: (i) Your and any other third party's modifications of Covered Software, or (ii) the combination of its Contributions with other software (except as part of its Contributor Version); or +under Patent Claims infringed by Covered Software in the absence of its Contributions. +T. his License does not grant any rights in the trademarks, service marks, or logos of any Contributor +(except as may be necessary to comply with the notice requirements in Section 3.4). + + + 2.4. Subsequent Licenses + + No Contributor makes additional grants as a result of Your choice to distribute the Covered Software under a subsequent version of this License (see Section 10.2) or under the terms of a Secondary License (if permitted under the terms of Section 3.3). + + + 2.5. Representation + + Each Contributor represents that the Contributor believes its Contributions are its original creation(s) or it has sufficient rights to grant the rights to its Contributions conveyed by this License. + + + 2.6. Fair Use + + This License is not intended to limit any rights You have under applicable copyright doctrines of fair use, fair dealing, or other equivalents. + + + 2.7. Conditions + + Sections 3.1, 3.2, 3.3, and 3.4 are conditions of the licenses granted in Section 2.1. + + +3. Responsibilities + + + 3.1. Distribution of Source Form + + All distribution of Covered Software in Source Code Form, including any Modifications that You create or to which You contribute, must be under the terms of this License. You must inform recipients that the Source Code Form of the Covered Software is governed by the terms of this License, and how they can obtain a copy of this License. You may not attempt to alter or restrict the recipients' rights in the Source Code Form. + + 3.2. Distribution of Executable Form + + If You distribute Covered Software in Executable Form then: + such Covered Software must also be made available in Source Code Form, as described in Section 3.1, and You must inform recipients of the Executable Form how they can obtain a copy of such Source Code Form by reasonable means in a timely manner, at a charge no more than the cost of distribution to the recipient; and +You may distribute such Executable Form under the terms of this License, or sublicense it under different terms, provided that the license for the Executable Form does not attempt to limit or alter the recipients' rights in the Source Code Form under this License. + + 3.3. Distribution of a Larger Work + + You may create and distribute a Larger Work under terms of Your choice, provided that You also comply with the requirements of this License for the Covered Software. If the Larger Work is a combination of Covered Software with a work governed by one or more Secondary Licenses, and the Covered Software is not Incompatible With Secondary Licenses, this License permits You to additionally distribute such Covered Software under the terms of such Secondary License(s), so that the recipient of the Larger Work may, at their option, further distribute the Covered Software under the terms of either this License or such Secondary License(s). + + + 3.4. Notices + + You may not remove or alter the substance of any license notices (including copyright notices, patent notices, disclaimers of warranty, or limitations of liability) contained within the Source Code Form of the Covered Software, except that You may alter any license notices to the extent required to remedy known factual inaccuracies. + + + 3.5. Application of Additional Terms + + You may choose to offer, and to charge a fee for, warranty, support, indemnity or liability obligations +to one or more recipients of Covered Software. However, You may do so only on Your own behalf, and not on behalf of any Contributor. You must make it absolutely clear that any such warranty, support, indemnity, or liability obligation is offered by You alone, and You hereby agree to indemnify every Contributor for any liability incurred by such Contributor as a result of warranty, support, indemnity or liability terms You offer. You may include additional disclaimers of warranty and limitations of +liability specific to any jurisdiction. + + +4. Inability to Comply Due to Statute or Regulation + + + If it is impossible for You to comply with any of the terms of this License with respect to some or all of the Covered Software due to statute, judicial order, or regulation then You must: (a) comply with the terms of this License to the maximum extent possible; and (b) describe the limitations and the code they affect. Such description must be placed in a text file included with all distributions of the Covered Software under this License. Except to the extent prohibited by statute or regulation, such description must be sufficiently detailed for a recipient of ordinary skill to be able to understand it. + + +5. Termination + + + 5.1. The rights granted under this License will terminate automatically if You fail to comply with any of its terms. However, if You become compliant, then the rights granted under this License from a particular Contributor are reinstated (a) provisionally, unless and until such Contributor explicitly and finally terminates Your grants, and (b) on an ongoing basis, if such Contributor fails to notify You of the non-compliance by some reasonable means prior to 60 days after You have come back into compliance. Moreover, Your grants from a particular Contributor are reinstated on an ongoing basis if such Contributor notifies You of the non-compliance by some reasonable means, this is the first time +You have received notice of non-compliance with this License from such Contributor, and You become compliant prior to 30 days after Your receipt of the notice. + + + 5.2. If You initiate litigation against any entity by asserting a patent infringement claim (excluding declaratory judgment actions, counter-claims, and cross-claims) alleging that a Contributor Version directly or indirectly infringes any patent, then the rights granted to You by any and all Contributors for the Covered Software under Section 2.1 of this License shall terminate. + + + 5.3. In the event of termination under Sections 5.1 or 5.2 above, all end user license agreements (excluding distributors and resellers) which have been validly granted by You or Your distributors under this License prior to termination shall survive termination. + + +6. Disclaimer of Warranty + + Covered Software is provided under this License on an "as is" basis, without warranty of any kind, either expressed, implied, or statutory, including, without limitation, warranties that the Covered Software is free of defects, merchantable, fit for a particular purpose or non-infringing. The entire risk as to the quality and performance of the Covered Software is with You. Should any Covered Software prove defective in any respect, You (not any Contributor) assume the cost of any necessary servicing, repair, or correction. This disclaimer of warranty constitutes an essential part of this License. No use of any Covered Software is authorized under this License except under this disclaimer. + + +7. Limitation of Liability + + Under no circumstances and under no legal theory, whether tort (including negligence), contract, or otherwise, shall any Contributor, or anyone who distributes Covered Software as permitted above, be liable to You for any direct, indirect, special, incidental, or consequential damages of any character including, without limitation, damages for lost profits, loss of goodwill, work stoppage, computer failure or malfunction, or any and all other commercial damages or losses, even if such party shall have been informed of the possibility of such damages. This limitation of liability shall not apply to liability +for death or personal injury resulting from such party's negligence to the extent applicable law prohibits such limitation. Some jurisdictions do not allow the exclusion or limitation of incidental or consequential damages, so this exclusion and limitation may not apply to You. + + +8. Litigation + + Any litigation relating to this License may be brought only in the courts of a jurisdiction where the defendant maintains its principal place of business and such litigation shall be governed by laws of that jurisdiction, without reference to its conflict-of-law provisions. Nothing in this Section shall prevent a party's ability to bring cross-claims or counter-claims. + + +9. Miscellaneous + + This License represents the complete agreement concerning the subject matter hereof. If any provision of this License is held to be unenforceable, such provision shall be reformed only to the extent necessary to make it enforceable. Any law or regulation which provides that the language of a contract shall be construed against the drafter shall not be used to construe this License against a Contributor. + +10. Versions of the License + + + 10.1. New Versions + + Mozilla Foundation is the license steward. Except as provided in Section 10.3, no one other than the license steward has the right to modify or publish new versions of this License. Each version will be given a distinguishing version number. + + + 10.2. Effect of New Versions + + You may distribute the Covered Software under the terms of the version of the License under which You originally received the Covered Software, or under the terms of any subsequent version published by the license steward. + + + 10.3. Modified Versions + + If you create software not governed by this License, and you want to create a new license for such software, you may create and use a modified version of this License if you rename the license and remove any references to the name of the license steward (except to note that such modified license differs from this License). + + + 10.4. Distributing Source Code Form that is Incompatible With Secondary Licenses + + If You choose to distribute Source Code Form that is Incompatible With Secondary Licenses under the terms of this version of the License, the notice described in Exhibit B of this License must be attached. + + + Exhibit A - Source Code Form License Notice + + This Source Code Form is subject to the terms of the Mozilla Public License, v. 2.0. If a copy of the +MPL was not distributed with this file, You can obtain one at https://mozilla.org/MPL/2.0/. + + + If it is not possible or desirable to put the notice in a particular file, then You may include the notice in +a location (such as a LICENSE file in a relevant directory) where a recipient would be likely to look for such a notice. +You may add additional accurate notices of copyright ownership. Exhibit B - "Incompatible With Secondary Licenses" Notice +This Source Code Form is "Incompatible With Secondary Licenses", as defined by the Mozilla Public +License, v. 2.0. + + + + +## Private PTC CUSTOMER AGREEMENT Axeda Agent Embedded +======================================================================= + +PTC CUSTOMER AGREEMENT + +THIS PTC CUSTOMER AGREEMENT ("AGREEMENT") IS A LEGAL AGREEMENT BETWEEN THE INDIVIDUAL, OR +THE COMPANY OR OTHER ORGANIZATION ON WHOSE BEHALF SUCH INDIVIDUAL ACCEPTS THIS AGREEMENT, +THAT EITHER (A) CLICKS THE "I ACCEPT" BUTTON BELOW OR (B) INSTALLS, ACCESSES, +OR USES ANY +SOFTWARE OR DOCUMENTATION FROM PTC ("CUSTOMER"), AND PTC INC. OR, IF THE PURCHASE WAS MADE IN +A COUNTRY SPECIFIED ON SCHEDULE A TO THIS AGREEMENT, THE PTC AFFILIATE SPECIFIED ON SCHEDULE A +(AS APPLICABLE, "PTC"). +PLEASE READ THE TERMS AND CONDITIONS OF THIS AGREEMENT CAREFULLY BEFORE ACCEPTING THIS +AGREEMENT. BY CLICKING ON THE "I ACCEPT" BUTTON BELOW OR BY INSTALLING, ACCESSING, OR USING +ANY SOFTWARE OR DOCUMENTATION FROM PTC, CUSTOMER HEREBY AGREES TO BE BOUND BY THIS +AGREEMENT AND REPRESENTS THAT IT IS AUTHORIZED TO DO SO. +IF YOU DO NOT AGREE TO ALL OF THE TERMS OF THIS AGREEMENT OR IF YOU DO NOT HAVE AUTHORITY TO +BIND THE COMPANY OR OTHER ORGANIZATION ON WHOSE BEHALF YOU ARE ACCEPTING THIS AGREEMENT, +CLICK THE "I DECLINE" BUTTON AND RETURN TO PTC THE SOFTWARE AND DOCUMENTATION PRODUCTS +PROVIDED TOGETHER WITH THIS AGREEMENT IN ACCORDANCE WITH THE INSTRUCTIONS PROVIDED WHEN +YOU CLICK THE "I DECLINE" BUTTON. NOTE THAT FAILURE TO COMPLY WITH SUCH INSTRUCTIONS WITHIN +THE TIME PERIOD SPECIFIED WILL VOID ANY RIGHT YOU WOULD OTHERWISE HAVE HAD FOR A REFUND OF +ANY FEES PAID. EACH ORDER FOR LICENSED PRODUCTS MAY NOT BE CANCELLED ONCE THIS AGREEMENT +HAS BEEN ACCEPTED. +IF CUSTOMER DID NOT OBTAIN THE LICENSED PRODUCT FROM PTC DIRECTLY, FROM AN AUTHORIZED PTC +DISTRIBUTOR OR RESELLER OR FROM THE PTC ONLINE STORE (AT WWW.PTC.COM), CUSTOMER IS USING AN +ILLEGALLY OBTAINED UNLICENSED VERSION OF THE APPLICABLE LICENSED PRODUCT. PTC REGARDS +SOFTWARE PIRACY AS THE CRIME IT IS AND PURSUES (BOTH CIVILLY AND CRIMINALLY) THOSE WHO TAKE +PART IN THESE ACTIVITIES. AS PART OF THESE EFFORTS, PTC UTILIZES DATA MONITORING AND SCOURING +TECHNOLOGIES TO OBTAIN AND TRANSMIT TO PTC DATA ON USERS OF ILLEGAL COPIES OF LICENSED +PRODUCTS. IF CUSTOMER IS USING AN ILLEGAL COPY OF SOFTWARE, CEASE USING THE ILLEGAL VERSION +AND CONTACT PTC TO OBTAIN A LEGALLY LICENSED COPY. BY USING THIS SOFTWARE, YOU CONSENT TO THE +COLLECTION, USE, AND TRANSFER OF PERSONAL DATA (INCLUDING TO THE UNITED STATES) FOR THE +PURPOSES OF IDENTIFYING USERS OF ILLEGAL COPIES OF OUR SOFTWARE. SUCH CONSENT SHALL BE BINDING +ON ANY USERS OF THIS SOFTWARE, INCLUDING USERS OTHER THAN YOU. +IN ORDER TO UNDERSTAND THE PREFERENCES OF OUR SOFTWARE USERS, PTC USES DATA MONITORING +TECHNOLOGIES TO OBTAIN AND TRANSMIT DATA ON SYSTEM USE AND PERFORMANCE AND FOR GATHERING +USER DATA AND USE METRICS ON USERS OF OUR SOFTWARE. WE WILL SHARE THIS DATA WITHIN PTC, ITS +AFFILIATED COMPANIES AND OUR BUSINESS PARTNERS, INCLUDING WITHIN THE UNITED STATES AND +ELSEWHERE FOR TECHNICAL AND MARKETING PURPOSES AND WILL ENDEAVOR TO ENSURE THAT ANY SUCH +DATA TRANSFERRED IS APPROPRIATELY PROTECTED. OUR COMMERCIAL LICENSES PERMIT USERS TO OPT OUT OF THIS DATA COLLECTION AND OUR STUDENT/EDUCATIONAL VERSIONS ONLY COLLECT DATA ON +SYSTEM USE AND PERFORMANCE. OUR FREE AND TRIAL VERSIONS OF SOFTWARE DO NOT ALLOW USERS TO +OPT-OUT OF THIS DATA COLLECTION, INCLUDING USER DATA. +IF YOU ARE USING PTC SOFTWARE, VISITING A PTC WEBSITE OR COMMUNICATING ELECTRONICALLY WITH US +FROM A COUNTRY OTHER THAN THE UNITED STATES, VARIOUS COMMUNICATIONS WILL NECESSARILY +RESULT IN A TRANSFER OF THIS INFORMATION ACROSS INTERNATIONAL BOUNDARIES. +IF YOU DO NOT CONSENT TO THE COLLECTION AND/OR TRANSMISSION (INCLUDING TO THE UNITED STATES) +OF YOUR DATA AS DESCRIBED ABOVE, DO NOT DOWNLOAD OR USE PTC SOFTWARE. BY (I) USING FREE OR +TRIAL SOFTWARE OR (II) NOT OPTING-OUT OF THE COLLECTION OF CERTAIN PERSONAL DATA AS YOU ARE +ABLE TO WITH PTC COMMERCIAL SOFTWARE, YOU CONSENT TO PTC'S COLLECTION, USE, AND TRANSFER OF +YOUR PERSONAL DATA (INCLUDING TO THE UNITED STATES). +CAPITALIZED TERMS NOT DEFINED IN THE TEXT BELOW ARE DEFINED IN SCHEDULE B AT THE END OF THIS +AGREEMENT. +SCHEDULE A TO THIS AGREEMENT CONTAINS ADDITIONAL (OR ALTERNATIVE) TERMS APPLICABLE TO +SPECIFIC GEOGRAPHIES. + + + +### PTC Clickwrap Customer Agreement - Rev. 12/14 + +1. License. + + 1.1 License Grant. Subject to the terms and conditions of this Agreement, PTC hereby grants to Customer a non-exclusive, revocable, non-transferable license, without any right to sub-license, to install and use the Licensed +Products identified in the Quote +during the applicable License Term, solely for Customer's internal business purposes and solely in accordance with the applicable +usage and license-type restrictions identified in the Quote and in the Licensing Basis Webpage +("License"). Notwithstanding the foregoing: + + (a) If the Licensed Product is being provided by PTC on an "evaluation" or "trial" basis, such License will be instead to +install and use the Licensed Product solely to evaluate such Licensed Products, and Customer agrees not to use the +Licensed Product in any commercial applications or for productive purposes. + + (b) If the Licensed Software is Educational Software, Customer must be enrolled in, or employed by, an accredited, academic +institution, and shall use the Licensed Software solely for educational purposes in a degree-granting program. If Customer +does not meet one of these qualifications, Customer has no rights under this Agreement. Without limitation, non educational research or funded educational research conducted using the facilities of an academic institution or under an +academic name does not qualify as "educational purposes" and use of Educational Software for such purposes represents a +violation of the terms of this Agreement. + + (C) If the Licensed Software is sold on a "demo and test" or "non-production" basis (or similar designation), such Licensed +Software may not be used in a production environment. + + 1.2 Designated Country/Computers/Networks. Subject to Section 1.3, Customer may only install and operate Licensed Products on +the applicable Designated Computers or Designated Networks on computer systems and networks situated in the applicable +Designated Country. Customer may, from time to time, change the Designated Computer, Designated +Network, and/or the +Designated Country in which Customer seeks to install or operate a Licensed Product, provided that in each case (i) Customer shall +give prior written notice to PTC of any such change, and (ii) upon moving the Licensed Products to a different Designated Country, +Customer shall pay all applicable Uplift Fees. Notwithstanding the foregoing, Registered Users need not be located in the +Designated Country when accessing a Registered User Product. + + 1.3 Global/Restricted Global Licenses. If a Concurrent User Licensed Product is licensed by PTC on a +"Global" or "Restricted +Global" basis, Section 1.2 shall not apply to such Licensed Products and the following provisions shall apply instead: + + (i) Global Licenses. Subject to the other requirements of this Agreement, a Global License allows the +Customer to install, +operate and use such Licensed Product at any Customer site(s) throughout the world. + + (ii) Restricted Global Licenses. Subject to the other requirements of this Agreement, a Restricted +Global License allows the +Customer to install, operate and use such Licensed Product at any Customer site(s) located in the +Designated Country +and/or in any Permitted Country. "Permitted Countries" means China, India, Russia, the Czech +Republic, Poland, +Hungary, Malaysia, South Africa, Israel, Mexico, Brazil, Argentina, and Romania. + + 1.4 Additional Restrictions on Use. Customer shall not permit any persons who are not Permitted Users to access or use the +Licensed Products. Customer shall not and shall not permit any third party(ies) to: + + (i) modify or create any derivative work of any part of the Licensed Products; + + (ii) rent, lease, or loan the Licensed Products; + + (iii) use the Licensed Products, or permit them to be used, for third-party training, to deliver software implementation or +consulting services to any third parties, or for commercial time-sharing or service bureau use; + + + (iv) disassemble, decompile or reverse engineer the Licensed Products or the file format of the Licensed +Products, or otherwise +attempt to gain access to the source code or file format of the Licensed Products, except as expressly permitted in +Schedule A, if applicable; + + + (v) sell, license, sublicense, loan, assign, or otherwise transfer (whether by sale, exchange, gift, operation of law, or +otherwise) to any third party the Licensed Products, any copy thereof, or any License or other rights thereto, in whole or in +part, without in each case obtaining PTC's prior written consent, except to the extent that any of the foregoing are +explicitly authorized in the Quote and/or the Licensing Basis Webpage; + + (vi) alter, remove, or obscure any copyright, trade secret, patent, trademark, logo, proprietary and/or other legal notices on or +in any copies of the Licensed Products; and + + (vii) copy or otherwise reproduce the Licensed Products in whole or in part, except (a) as may be required for their installation +into computer memory for the purpose of executing the Licensed Products in accordance with this +Section 1, and/or (b) to +make a reasonable number of copies solely for back-up purposes (provided that any such permitted copies shall be the +property of PTC, and Customer shall reproduce thereon all PTC copyright, trade secret, patent, trademark, logo, +proprietary and/or other legal notices contained in the original copy of the Licensed Product obtained from PTC). +If Customer uses any unlicensed or unauthorized copies of any PTC software, Customer agrees that, +without limiting PTC's right to +terminate this Agreement for breach in accordance with Section 7 and without limiting any other remedies to which PTC may be entitled, Customer will pay to PTC the PTC then-current list price for all such unlicensed software, in addition to any fines or +penalties that may be imposed by law. + + 1.5 Additional Restrictions on Use Applicable to Concurrent User Products. If the Licensed Product is a +Concurrent User Product, +the following provisions apply: + + (i) The number of Permitted Users accessing or operating a Concurrent User Product at any point in time may not exceed the +number of Licenses in effect at such time for that particular Licensed Product. + + (ii) Except with respect to Integrity and Implementer Products, only Permitted Users physically located in the Designated +Country may access, operate and/or use the Licensed Products. Permitted Users who are not employees of Customer may +use the Licensed Products while physically located at Customer's site only. + + (iii) Where a Concurrent User Product is Licensed on a "fixed," "locked" or "node-locked" basis, or the +Licensed Product is +licensed as a "Designated Computer" product, such Licensed Product is licensed to operate solely on the Designated +Computer on which it is installed. + + 1.6 Additional Restrictions on Use Applicable to Registered User Products. A License is required for each individual who accesses +a Registered User product or the data contained therein, whether directly or through a web portal or other mechanism for "batching" +or otherwise achieving indirect access to the Licensed Product or such data. Generic or shared log-ins are not permitted. Customer +may add and/or substitute from time to time new Registered Users as long as the aggregate number of +Registered Users does not +exceed at any point in time the number of Licenses in effect at such time for that particular Licensed +Product and, provided further, +that if a person who was previously a Registered User returns to Registered User status, a new License fee must be paid to PTC at +PTC's then current rates. + + 1.7 Additional Restrictions on Use Applicable to Designated Server Products. Each Designated Server product may only be used on +the computer server that is designated by the Customer in connection with the initial installation of such product and that has one +unique instance of the applicable installed product application. In the event a computer server is partitioned in any manner +(physically, logically or otherwise), the reference in the preceding sentence to "computer server" shall mean each partition of such +server, and such Designated Server product may only be used on one of such partitions. Customer may, from time to time, change +the Designated Server(s) for a Designated Server Product, and/or the location thereof, provided that in each case (a) Customer shall +give prior written notice to PTC of any such change, and (b) upon transferring the Designated Server +Products to a different +Designated Country, Customer pays all applicable Uplift Fees. + + 1.8 Third Party Components and Bundled Third Party Products. Certain of the Licensed Products may contain third party software +components for which additional terms apply ("Third Party Components"). The current additional terms are set forth on the Schedule +of Third Party Terms available in the legal policies and guidelines section of http://www.ptc.com. Separately, third party software +products that PTC resells and/or bundles for distribution with the Licensed Products are licensed to +Customer directly by the +manufacturer of such third party software products ("Bundled Third Party Products"). Such Bundled +Third Party Products are also +described on the Schedule of Third Party Terms. Customer agrees that its use of Third Party +Components and/or Bundled Third +Party Products is subject to the terms of the Schedule of Third Party Terms. New Releases containing +Third Party Components or +Bundled Third Party Products may be subject to additional or different third party terms, of which PTC +shall notify the Customer at +the time such New Releases are delivered to the Customer. + + 1.9 Upgrades: If the Licensed Software was licensed as an upgrade from a previous version, Customer must first be licensed for the +Licensed Software identified by PTC as eligible for the upgrade and Customer must be active on +Support Services for such software. +After installing the upgrade, Licensed Software licensed as an upgrade replaces and/or supplements the product that formed the basis +of Customer's eligibility for the upgrade and Customer may no longer use the original Licensed +Software that formed the basis for +Customer's upgrade eligibility. + +2. Compliance. + + 2.1 License Usage Assessments. To confirm Customer's compliance with the terms and conditions hereof, Customer agrees that +PTC may perform a usage assessment with respect to Customer's use of the Licensed Products. Customer agrees to provide PTC +access to Customer's facilities and computer systems, and cooperation from Customer's employees and consultants, as reasonably +requested by PTC in order to perform such assessment, all during normal business hours, and after reasonable prior notice from PTC. +2.2 Reports. Upon written request from PTC, Customer agrees to provide to PTC an installation and/or usage report with respect to +the Licensed Products (and in the case of Registered User Products, such report shall include a list of all users for whom Customer +has issued a password or other unique identifier to enable such individual to use the Registered User +Product). Such report shall be +certified by an authorized representative of Customer as to its accuracy within ten (10) business days after receipt of any written +request from PTC. For any period in which Customer's use of the Licensed Products exceeds the number and/or the scope of the +Licenses in effect during such period for such Licensed Products, Customer agrees to pay for any such excess usage, including +applicable license and Support Services fees, and without limiting any other rights or remedies to which it is entitled, failure to pay +shall be grounds for termination in accordance with Section 7 hereof. + + +3. Intellectual Property. PTC and its licensors are the sole owners of the Licensed Products and of any copies of the Licensed +Products, and of all copyright, trade secret, patent, trademark and other intellectual or industrial property rights in and to the Licensed +Products. All copies of the Licensed Products, in whatever form provided by PTC or made by +Customer, shall remain the property of +PTC, and such copies shall be deemed to be on loan to Customer during the License Term. Customer acknowledges that the License +granted hereunder does not provide Customer with title to or ownership of the Licensed Products or any copies thereof, but only a +right of limited use consistent with the express terms and conditions of this Agreement. Customer shall have no rights to the source +code for the Licensed Products, and Customer agrees that only PTC shall have the right to maintain, enhance, or otherwise modify +the Licensed Products. + +4. Support Services; Warranty; Disclaimer of Warranties. +See Schedule A for a modified version of this Section 4 for Licensed Products licensed and used in +Germany, Austria or Switzerland. + + 4.1 Support Services. Upon PTC's acceptance of an order for Support Services or for Licensed +Products for which Usage License +Fees apply, PTC agrees that it or its designated service provider shall provide the applicable Support +Services in accordance with +Schedule C. + + 4.2 Warranty. PTC warrants to Customer that PTC is authorized to grant the License(s) and that, subject to Section 4.3, the +Licensed Products will be free from Errors for a period of ninety (90) days following PTC's initial shipment to Customer or +Customer's designee of such Licensed Products (the "Warranty Period"). + + 4.3 Warranty Exceptions. PTC shall have no warranty obligations hereunder with respect to any (i) +evaluation, "trial" or "express" +Licenses, (ii) New Releases, (iii) computer software provided to Customer in the course of PTC's delivery of Training Services, (iv) +Errors attributable to the use of the Licensed Product in an application or environment for which it was not designed or contemplated, +(v) Errors attributable to any modifications or customizations of the Licensed Products, (vi) Licensed +Products that are provided by +PTC free of charge to Customer, and/or (vii) Sun Software, Oracle Software and/or Bundled Third +Party Products. + + 4.4 Sole Remedy. PTC's and its licensors' entire liability and Customer's exclusive remedy for any breach by PTC of the warranty +given in Section 4.2 above shall be, at PTC's sole discretion, either to (a) replace the Licensed Product +(s) or (b) use diligent efforts to +repair the Error. PTC's obligations set forth in the preceding sentence shall apply only if notice of the +Error is received by PTC +within the Warranty Period and Customer supplies such additional information regarding the Error as +PTC may reasonably request. +If PTC does not replace the applicable Licensed Product(s) and/or does not repair the Error (either by providing a bug fix, a +workaround or otherwise) within a reasonable time after notice of the Error and associated information from Customer is received by +PTC, PTC will provide a refund of the license fees paid by Customer for the applicable Licensed +Product(s) upon return of such +Licensed Product(s) and any copies thereof. + + 4.5 No Additional Warranties. No third party, including any employee, partner, distributor (including any Reseller) or agent of PTC +or any of its resellers or sales agents, is authorized to give any representations, warranties or covenants greater or different than those +contained in this Agreement with respect to any Licensed Products or Services, except as specifically set forth in a written agreement +signed on behalf of Customer by an authorized officer and on behalf of PTC by its legal counsel or +Corporate Controller. + + 4.6 Disclaimer of Warranties. EXCEPT AS EXPRESSLY STATED IN SECTION 4, PTC DISCLAIMS (AND CUSTOMER +WAIVES) ALL WARRANTIES, WHETHER EXPRESS, IMPLIED, OR STATUTORY, WRITTEN OR ORAL, INCLUDING +ANY WARRANTY OF MERCHANTABILITY, SATISFACTORY QUALITY, FITNESS FOR A PARTICULAR PURPOSE, +NON-INFRINGEMENT, AND/OR ANY WARRANTY THAT CUSTOMER WILL ACHIEVE ANY PARTICULAR RETURN +ON INVESTMENT. THE LICENSED PRODUCTS ARE INTENDED TO BE USED BY TRAINED PROFESSIONALS AND +ARE NOT A SUBSTITUTE FOR PROFESSIONAL JUDGMENT, TESTING, SAFETY AND UTILITY. CUSTOMER IS +SOLELY RESPONSIBLE FOR ANY RESULTS OBTAINED FROM USING THE LICENSED +PRODUCTS, INCLUDING +THE ADEQUACY OF INDEPENDENT TESTING OF RELIABILITY AND ACCURACY OF ANY ITEM DESIGNED USING +LICENSED PRODUCTS. PTC does not warrant that the operation or other use of the Licensed +Products will be uninterrupted or +error free or will not cause damage or disruption to Customer's data, computers or networks. + +5. Indemnification; Infringement. + + 5.1 PTC's Obligation to Indemnify Customer. PTC, at its own expense, will defend any action brought against Customer based on a +claim that any Licensed Product infringes a United States, European Union or Japanese patent, copyright or trademark and, at its +option, will settle any such action or will pay any final judgment awarded against Customer, provided that: (a) PTC shall be notified +promptly in writing by Customer of any notice of any such claim; (b) PTC shall have the sole control of the defense of any action on +such claim and all negotiations for its settlement or compromise and shall bear the costs of the same +(save where one or more of the +exclusions in Section 5.3 applies); and (C) Customer shall cooperate fully at PTC's expense with PTC +in the defense, settlement or +compromise of such claim. This Section 5 states PTC's sole and exclusive liability, and Customer's sole remedy, for any and all +claims relating to infringement of any intellectual property right. + + 5.2 PTC's Right to Act to Prevent a Claim. If a claim described in Section 5.1 hereof occurs or, in +PTC's opinion, may occur, +Customer shall permit PTC, at PTC's option and expense to: (a) procure for Customer the right to continue using the Licensed +Product; (b) modify the Licensed Product so that it becomes non-infringing without materially impairing its functionality; or (C) +terminate the applicable Licenses, accept return of the Licensed Products and grant Customer a credit thereon. For Licenses purchased with a perpetual License Term, such credit shall be equal to the License fees paid by +Customer for such Licensed Product +depreciated on a straight-line, five year basis. For Licenses purchased on a term license or subscription basis, such credit shall be +equal to the prepaid license or subscription fees for the remainder of the License Term. + + 5.3 Exclusions from PTC's Obligation to Indemnify Customer. PTC shall have no liability to Customer under Section 5.1 hereof or +otherwise to the extent that any infringement or claim thereof is based upon: (a) use of the Licensed +Product in combination +with equipment or software not supplied hereunder where the Licensed Product itself would not be infringing; (b) use of the Licensed +Product in an application or environment for which it was not designed or not contemplated under this +Agreement; (C) use of other +than a current release of the Licensed Product(s) provided to Customer; (d) modification of the +Licensed Product by anyone other +than PTC or its employees or agents; or (e) any claims of infringement of any patent, copyright, trade secret, trademark or other +proprietary right in which Customer has an interest. + +6. Limitation of Liability. + + See Schedule A for a modified version of this Section 6 for Licensed Products licensed and used in +Germany, Austria or Switzerland. + + + 6.1 The warranty and indemnification provisions of Sections 4 and 5 hereof state the entire liability of +PTC, its subsidiaries and +affiliates, and each of their respective directors, officers, employees or agents, with respect to the +Licensed Products and Services, +including (without limitation) any liability for breach of warranty, or for infringement or alleged infringement of patent, copyrights, +trademarks, trade secrets and other intellectual or proprietary rights by the Licensed Products, or their use. + + 6.2 EXCEPT FOR PTC'S INDEMNIFICATION OBLIGATIONS IDENTIFIED IN SECTION 5.1 +ABOVE, THE MAXIMUM +LIABILITY OF PTC AND ITS LICENSORS ARISING OUT OF, OR RELATING TO, THE CREATION, LICENSE, +FUNCTIONING, USE OR SUPPLY OF THE LICENSED PRODUCTS OR THE PROVISION OF SERVICES OR OTHERWISE +RELATING TO THIS AGREEMENT, WHETHER BASED UPON WARRANTY, CONTRACT, TORT, OR OTHERWISE, +SHALL NOT, (I) FOR LICENSES PURCHASED ON A PERPETUAL BASIS, EXCEED THE FEES PAID BY CUSTOMER FOR +THE LICENSED PRODUCTS OR SERVICES THAT GAVE RISE TO THE CLAIM AND (II) FOR LICENSES PURCHASED +ON A TERM OR SUBSCRIPTION BASIS, EXCEED THE FEES PAID BY CUSTOMER IN THE TWELVE MONTH PERIOD +IMMEDIATELY PRECEDING THE EVENT GIVING RISE TO DAMAGES FOR THE LICENSED PRODUCTS OR SERVICES +THAT GAVE RISE TO THE CLAIM. + + 6.3 IN NO EVENT SHALL PTC, ITS LICENSORS, ITS AFFILIATES (INCLUDING ITS SUBSIDIARY COMPANIES), OR +ANY OF THEIR RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES OR AGENTS BE LIABLE FOR: (A) ANY LOSS OF +PROFIT, LOSS OF USE DAMAGES, LOSS OF GOODWILL, LOSS OF BUSINESS OPPORTUNITY, LOSS OF SALES, LOSS +OF REPUTATION OR LOSS OF ANTICIPATED SAVINGS; (B) ANY LOSS OR INACCURACY OF DATA OR BUSINESS +INFORMATION OR FAILURE OR INADEQUACY OF ANY SECURITY SYSTEM OR FEATURE; AND (C) SPECIAL, +INCIDENTAL, INDIRECT, PUNITIVE OR CONSEQUENTIAL LOSS OR DAMAGE +HOWSOEVER CAUSED; IN EACH +CASE EVEN IF PTC HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. + + 6.4 Customer agrees not to bring any suit or action against PTC, and/or its subsidiaries and affiliates, and/or any of their respective +directors, officers, employees or agents for any reason whatsoever more than one year after the cause of action arises. Customer +recognizes that fees paid by Customer for the Licensed Products and Services are based in part on the disclaimer of warranty and +limitation of liability provisions set forth herein and that, in the absence of Customer's agreement to such terms, the charges for the +Licensed Products would be significantly higher. The limitations and exclusions set forth in this Section +6 shall not apply to any +claim in respect of death or personal injury. + + +7. Term and Termination. + + 7.1 Events Causing Termination. This Agreement and all Licenses will terminate: + + (a) Automatically and without notice on the following events: (I) Customer's breach of any of clauses +(i) through (vii) of +Section 1.4 or Sections 3 or 8.4 hereof; (II) a receiver, trustee, liquidator, or such similar officer is appointed for Customer +or for any of Customer's properties or assets; (III) Customer makes a general assignment for the benefit of Customer's +creditors; (IV) Customer files a petition for its reorganization, dissolution or liquidation, or such a petition is filed against +Customer and is not dismissed within sixty (60) days thereafter; or (V) Customer ceases doing business or commence +dissolution or liquidation proceedings; or + + (b) Thirty (30) days after written notice from PTC specifying a breach (other than as listed in Section + + 7.1(a) above) of this +Agreement, including failure to make any payment due to either PTC or a Reseller in connection with the Licensed +Products in a timely manner, if that breach is not, within that thirty (30) day period, remedied to PTC's reasonable +satisfaction. + + 7.2 Effects of Expiration or Termination. Upon expiration of a given License Term and/or any expiration or termination of this +Agreement, Customer shall promptly pay all sums owed by Customer, return to PTC the original copies of all Licensed Products for +which the License Term has expired or has been terminated, destroy and/or delete all copies and backup copies thereof from Customer's computer libraries, storage facilities and/or hosting facilities, and certify in writing by an officer that Customer is in +compliance with the foregoing requirements and that such Licensed Products are no longer in +Customer's possession or in use. +7.3 Survival. Sections 2, 3, 4.6, 5, 6, 7.2, 7.3 and 8 shall survive expiration or termination of this +Agreement. + +8. General. + + 8.1 Governing Law and Jurisdiction. Unless otherwise stated in Schedule A, all disputes arising under, out of, or in any way +connected with this Agreement shall be governed by and construed in accordance with the laws of the +Commonwealth of +Massachusetts without reference to conflict of laws principles (and specifically excluding the Uniform +Computer Information +Transactions Act). The parties hereby expressly disclaim the application of the U.N. Convention for the +International Sale of Goods. +All disputes arising under, out of, or in any way connected with this Agreement shall be litigated exclusively in the state or federal +courts situated in the Commonwealth of Massachusetts, and in no other court or jurisdiction. Notwithstanding the foregoing or +anything to the contrary, PTC shall have the right to bring a claim in any court of competent jurisdiction to enforce any intellectual +property rights and/or protect any confidential information. Customer agrees that the state and federal courts situated in the +Commonwealth of Massachusetts shall have personal jurisdiction over its person, and Customer hereby irrevocably (i) submits to the +personal jurisdiction of said courts and (ii) consents to the service of process, pleadings, and notices in connection with any and all +actions initiated in said courts. The parties agree that a final judgment in any such action or proceeding shall be conclusive and +binding and may be enforced in any other jurisdiction. Each party waives its right to trial by jury in connection with any dispute +arising out of this Agreement. + + 8.2 Notices. Any notice or communication required or permitted under this Agreement shall be in writing. In the case of notice to +Customer, the notice shall be directed to the address set forth on the Customer's purchase order or to such other address as may be +provided to PTC in writing. In the case of notice to PTC, such notice shall be directed to PTC, 140 +Kendrick Street, Needham, MA +02494; Attn: Corporate Controller, with a copy to General Counsel. Any notice provided under this section shall be deemed to have +been received: (a) if given by hand, immediately; (b) if given by mail, five (5) business days after posting; (C) if given by express +courier service, the second business day following dispatch in the jurisdiction of the sender; or (d) if given by fax, upon receipt +thereof by the recipient's fax machine or as stated in the sender's transmission confirmation report as produced electronically by +sender's fax machine. + + 8.3 Assignment, Waiver, Modification. Customer may not assign, transfer, delegate or sublicense any +of Customer's rights or +obligations hereunder (including without limitation by operation of law or by sale of Customer assets, whether directly or by merger, +and a change in control of Customer shall be deemed to be an "assignment" for purposes of the foregoing) without PTC's prior +written consent, and any such attempted delegation, assignment, transfer or sublicense shall be void and a breach of this Agreement. +No waiver, consent, modification, amendment or change of the terms of this Agreement shall be binding unless in writing and signed +by PTC and Customer. PTC reserves the right to charge a transfer fee for any proposed assignment, transfer or sublicense of this +Agreement. + + 8.4 Compliance with Laws. Each party shall be responsible for its own compliance with applicable laws, regulations and other legal +requirements relating to the conduct of its business and this Agreement. Further Customer represents and warrants that it will use the +Licensed Products, as well as related technology and services, in full compliance with applicable laws and regulations. Customer +acknowledges and agrees that the Licensed Products and related technical data and services are subject to the export control laws and +regulations of the United States and any country in which the Licensed Products or related technical data or services are developed, +received, downloaded, used, or performed. Further, Customer understands and acknowledges that the release of software or +technology to a non-U.S. person within the United States or elsewhere abroad is deemed to be an export to the non-U.S. person's +home country or countries, and that the transfer of the Licensed Products or related technology to +Customer's employees, affiliates, +or any third party, may require a license from the United States Government and possibly other applicable authorities. Customer shall +be solely responsible for determining whether Customer's use or transfer of the Licensed Products or related technology or services +requires an export license or approval from U.S. or other authorities, and for securing all required authorizations. Customer hereby +warrants and represents that: (x) neither Customer nor any of Customer's directors, officers or affiliates is identified on the U.S. +Commerce Department's Denied Persons List, Entity List, or Unverified List, the U.S. State +Department's Nonproliferation +Sanctions List, the U.S. Treasury Department's List of Specially Designated Nationals and Blocked +Persons or any similar Export +Controls Division-Foreign Affairs and International Trade Canada listing that designates individuals or entities to which export +restrictions apply (collectively, the "Restricted Parties Lists"), (y) except as specifically authorized or licensed by the United States +Government and other applicable authorities, Customer will not sell, offer, transfer, deliver, release, either directly or indirectly, the +Licensed Products or related technology or services to any end-user: (A) that is either located in, a national of, or acting on behalf of +a country subject to U.S. economic embargoes, or (B) that have been designated as prohibited or restricted parties by the U.S. +Government, including but not limited to persons listed on the Restricted Parties Lists, or (C) engaged in activities related to the +design, development, stockpiling, or proliferation of nuclear, chemical, or biological weapons, or missiles or missile systems, or (D) +engaged in maritime nuclear propulsion activities. Customer represents and warrants that it will ensure that any person or entity to +which Customer has granted access to the Licensed Products or related technology or services has been made aware of, and will +comply with, this provision and U.S. and other applicable export control laws and regulations. Unless prohibited by applicable law +and without waiving sovereign immunity, Customer shall indemnify and hold harmless PTC and its employees against any damage, +loss, liability or expense (including attorneys' fees) that PTC may incur as a result of Customer's failure to comply with this Section + + 8.4. Such indemnification shall survive the expiration or termination of this Agreement. + + 8.5 Severability. It is intended that this Agreement shall not violate any applicable law and the unenforceability or invalidity of any +provision (other than the provisions obligating Customer to make payments to PTC) shall not affect the force and validity of the +remaining provisions and such provisions determined to be invalid shall be deemed severed from this +Agreement and, to the extent +possible, be replaced with terms which as closely as possible approximate the interest and economic intent of such invalid provisions. + + 8.6 Entire Agreement. This Agreement is the complete and exclusive statement of the contract between +PTC and Customer +with respect to the subject matter hereof. No waiver, consent, modification, amendment or change of this Agreement shall be binding +unless in writing and signed or otherwise expressly acknowledged by PTC and Customer. + + 8.7 Third Party Beneficiaries. It is agreed by the parties to this Agreement that PTC's third party licensors are intended +beneficiaries of this Agreement and have the right to rely upon and directly enforce its terms with respect to the products of such +licensors. + + 8.8 Marketing. Customer agrees that while this Agreement is in effect, PTC shall be authorized to identify Customer as a +customer/end-user of PTC software and services (as applicable) in public relations and marketing materials. + + 8.9 Government Licensees. If Customer is a United States Governmental entity, Customer agrees that the Licensed Products +are "commercial computer software" under the applicable federal acquisition regulations and are provided with the commercial +license rights and restrictions described elsewhere herein. If Customer is acquiring the Licensed +Product(s) under a United States +government contract, Customer agrees that Customer will include all necessary and applicable restricted rights legends on the +Licensed Products to protect PTC's proprietary rights under the FAR or other similar regulations of other federal agencies. Customer +agrees to always include such legends whenever the Licensed Products are, or are deemed to be, a deliverable under a government +contract. +Schedule A - Purchases from PTC Affiliates +If the Customer has obtained a License to any Licensed Products in one of the following countries, the entity granting the +License is specified below and, notwithstanding Section 8.1 of this Agreement, the governing law and jurisdiction shall be as set +forth below. +Country PTC Affiliate Licensing Entity Governing Law/Jurisdiction for +Disputes +Belgium, Netherlands, Luxembourg +Parametric Technology Nederland B.V. Netherlands +Austria, Germany Parametric Technology GmbH German Law*, Landgericht Munchen I, Germany +France Parametric Technology S.A. France Ireland PTC Software and Services (Ireland) Limited +Republic of Ireland +Italy Parametric Technology Italia S.r.L. Italy +Spain, Portugal Parametric Technology Espana, S.A. Spain +Switzerland Parametric Technology (Schweiz) AG German Law*, Landgericht Munchen I, Germany +United Kingdom Parametric Technology (UK) Limited United Kingdom +Remaining countries of the +European Union +PTC Software and Services (Ireland) Limited +Republic of Ireland Turkey, Kosovo, Serbia, Macedonia, Montenegro, Croatia, Bosnia and Herzegovina, and Albania +PTC Software and Services (Ireland) Limited +Republic of Ireland +The Russian Federation PTC International LLC Russian Law / International +Commercial Arbitration Court at the Chamber of Commerce and Industry of the Russian Federation in Moscow Belarus, Moldova, Ukraine, +Armenia, Georgia, Azerbaijan, Kazakhstan, Kyrgyzstan, Tajikistan, Turkmenistan, and Uzbekistan +PTC Software and Services (Ireland) Limited +Republic of Ireland +Norway, Sweden, and Denmark, Finland, Iceland, and the Faeroe Islands +PTC Sweden AB Sweden +Japan PTC Japan K.K. Japan / Tokyo District Court +Country PTC Affiliate Licensing Entity Governing Law/Jurisdiction for +Disputes +China Parametric Technology (Shanghai) Software Co., Ltd. +The People's Republic of China/China International Economic and Trade Arbitration Commission in Shanghai +Taiwan Parametric Technology Taiwan Limited Taiwan / Courts of Taipei, Taiwan +India Parametric Technology (India) Private +Limited +India +Korea Parametric Technology Korea Ltd. Republic of Korea +Other Asia Pacific Countries including Australia and New Zealand, but excluding China, Japan and Taiwan) +PTC Inc. Special Administrative Region of Hong +Kong / Hong Kong International +Arbitration Centre +Canada PTC (Canada) Inc. Ontario +Any other country PTC Inc., or such other affiliate of PTC as +PTC directs at the time of the order +Commonwealth of Massachusetts, +United States + +*Specific Provisions for Austria, Germany and Switzerland: +For Licensed Products licensed and used in Austria, Germany or Switzerland, the following provisions shall apply. The following +provisions shall have no applicability to any Licensed Products or Services purchased outside of +Austria, Germany or Switzerland. + +References to sections below are references to the applicable sections in the body of the Agreement. + +Section 1.4 (iv) above shall not apply to the extent that (i) the processes Customer undertakes are required to achieve +information necessary to achieve interoperability of an independently created computer program with other software +programs, (ii) the further requirements of Section 69e of the German Copyright Act are fulfilled and +(iii) PTC, upon +Customer's written request, has not made available the information required for this within a reasonable period. + +Sections 4.2 (Warranty), 4.4 (Sole Remedy), 4.5 (No Additional Warranties) and 4.6 (Disclaimer of +Warranties) are hereby +replaced by the following provisions: + +4.2 Warranty Period, Restarts and Investigation Duty. The limitation period for warranty claims shall be twelve (12) +months from delivery. Any replacement of the Licensed Product(s) and/or repair of Errors will not restart the warranty +period. The pre-requisite for the Customer's warranty claims (Mangelanspruche) is that: (i) the +Customer inspects the +Licensed Products according to Section 377 German Commercial Code, (ii) the defect is an Error as defined in this +Agreement, (iii) the Error already existed at the time of delivery and (iv) the Customer effects a proper notification of the +Error. Customer shall provide notifications of Errors to PTC in writing and Customer shall provide specific details of the +Error as deemed reasonable under the specific circumstances. Customer shall notify PTC of obvious +Errors in writing +within one week of delivery and of latent Errors within one week of discovery of such Error. The periods specified are +preclusion periods. + +4.4 Remedies. In the event of an Error, PTC in its sole discretion may: (a) replace the Licensed Product +(s) or (b) repair +the Error, provided that notice of the Error is received by PTC within the periods set forth in Section +4.2 and Customer +provides such additional information regarding the Error as PTC may reasonably request. If the repair +(either by providing +a bug fix, a workaround or otherwise) or replacement is not successful (after at least two repair attempts for the same Error +by PTC within a reasonable period of time), Customer shall be entitled, at Customer's choice, to either: +(i) rescission of the +affected order so that PTC provides a refund of the license fees paid by Customer for the applicable +Licensed Product(s) +upon return of such Licensed Product(s) and any copies made thereof or (ii) a reasonable reduction in the purchase price. +Replacements or repairs shall be made without acknowledgement of a legal obligation and shall not suspend the limitation +period for warranty claims related to the Licensed Products. + +4.5 No Additional Warranties. No employee, partner, distributor (including any Reseller) or agent of +PTC or any of its +resellers or sales agents is authorized to give representations, warranties or covenants greater or different than those +contained in this Agreement, except as specifically set forth in a written agreement signed on behalf of +Customer by an +authorized officer and on behalf of PTC by its legal counsel or Corporate Controller. Apart from claims for damages based +on Errors that are subject to the limitation of liability as set forth in Section 6, the obligations provided for in this Section 4 +shall be PTC's exclusive liability in case of warranty claims. + +4.6 Customer Responsibility. The Licensed Products are intended to be used by trained professionals and are not a +substitute for the exercise by Customer of professional judgement, testing, safety and utility in their use. Customer is +solely responsible for any results which were obtained by using the Licensed Products, including the adequacy of +independent testing of reliability and accuracy of any item designed using Licensed Products. + +4.7 Qualities (Beschaffenheit), Guarantees. Qualities of the Licensed Products stated in publications of +PTC or its sales +representatives, in particular in advertising, in drawings, brochures or other documents, including presentations in the +Internet, or on packaging and labeling of the Licensed Products, or which fall under trade usages, shall only be deemed to +be covered by the contractual quality of the Licensed Products if such qualities are expressly contained in an offer or an +order confirmation in writing. Guarantees, in particular guarantees as to quality, shall be binding on +PTC only to the extent +to which they (i) are contained in an offer or an order confirmation in writing, (ii) are expressly designated as "guarantee" +or "guarantee as to condition" (Beschaffenheitsgarantie), and (iii) expressly stipulate the obligations for +PTC resulting from such guarantee. + +Section 6 is hereby replaced by the following provisions: +6. Limitation of Liability + + 6.1 Liability Categories. PTC shall be liable for damages, regardless of the legal grounds, only if: (i) PTC breaches a +material contractual obligation (cardinal obligation) culpably (i.e., at least negligently), or (ii) the damage has been caused +by gross negligence or wilfull intent on the part of PTC or (iii) PTC has assumed a guarantee. + + 6.2 Predictability. PTC's liability shall be limited to the typical, foreseeable damage: (i) if PTC +breaches material +contractual obligations (cardinal obligations) with slight negligence, or (ii) if employees or agents of +PTC who are not +officers or executive staff have breached other obligations by gross negligence, or (iii) if PTC has assumed a guarantee, +unless such guarantee is expressly designated as guarantee as to condition (Beschaffenheitsgarantie). + + 6.3 Maximum Amount. In the cases of Section 6.2 (i) and (ii), PTC's liability shall be limited to a maximum amount of +EURO 1,000,000 or, in case of purely financial losses, to a maximum amount of EURO 100,000. + + 6.4 Indirect Damages. In the cases of Section 6.2, PTC shall not be liable for indirect damages, consequential damages or +loss of profit. + + 6.5 Liability Period. Customer's claims for damages against PTC and/or PTC's affiliates, regardless of the legal grounds, +shall expire at the latest one year from the time the Customer gains knowledge of the damage or, irrespective of this +knowledge, at the latest two years after the damaging event. For claims based on Errors of the Licensed +Product(s), the +warranty limitation period pursuant to Section 4.2 shall apply. + + 6.6 Mandatory Liability. PTC's liability pursuant to the German Product Liability Act +(Produkthaftungsgesetz), for injury +of life, body and health, for fraudulent concealment of a defect or for the assumption of a guarantee as to condition +(Beschaffenheitsgarantie) remains unaffected. + + 6.7 Employees. Sections 6.1 to 6.6 shall also apply in the case of any claims for damages of Customer against employees +or agents of PTC and/or PTC's affiliates. + + 6.8 Contributory Negligence. In the event of a guarantee or liability claim against PTC any contributory fault of +Customer must be taken into account accordingly, particularly in the event of inadequate fault notification or +inadequate data securing. It constitutes inadequate data securing if the client, among others, does not, by way of +appropriate state of the art security measures, take precautions against external influences, e.g. computer viruses and other +phenomena which could put individual data or an entire data stock at risk. Schedule B - Definitions + +"Concurrent User Products" means the Licensed Products licensed on a concurrent user basis, as +specified either in the Quote or at the Licensing Basis Webpage. + +"Designated Computer" means the central processing unit(s) designated in writing by Customer to PTC +at the time of installation of +the Licensed Products (as may be modified in accordance with Section 1.2 of this Agreement). + +"Designated Computer Product" means the Licensed Products licensed on a "Designated Computer" basis or otherwise designated as +"fixed," "locked" or "node-locked", as specified either in the Quote or at the Licensing Basis Webpage. Designated Computer +Products may not be remotely accessed or installed in a virtual environment. + +"Designated Country" means the country of installation specified in writing by Customer to PTC at the time Customer places its +order of the Licensed Products. The Designated Country may be changed only in accordance with +Section 1.2 of this Agreement. + +"Designated Network" means the network designated in writing by Customer to PTC at the time of installation of the Licensed +Products (as may be modified in accordance with Section 1.2 of this Agreement). + +"Designated Server" means a computer server designated in writing by Customer to PTC at the time of installation of the Licensed +Products (as may be modified in accordance with Section 1.2 of this Agreement) that has one unique instance of the applicable +installed Licensed Product application. + +"Designated Server Products" means the Licensed Products licensed on a Designated Server basis, as specified either in the Quote or +at the Licensing Basis Webpage. + +"Documentation" means the applicable Licensed Software user manuals provided or made available by electronic means by PTC at +the time of shipment of the Licensed Software. + +"Educational Software" means Licensed Products identified as "Priced for Education," "Student +Edition," "Schools Edition," + +"Schools Advanced Edition," "University Edition," "Professor's Edition/Version" or "Academic +Edition/Version," or otherwise +designated as educational or academic licenses. + +"Error" means a failure of the Licensed Software to conform substantially to the applicable +Documentation, provided that Customer +informs PTC of such failure in writing and PTC is able to replicate such failure after making reasonable efforts. + +"External User" means a Registered User who is a vendor or other third party external to the Customer and its affiliates. + +"License" shall have the meaning set out in Section 1.1 of the body of the Agreement. + +"License Term" means the time period during which the License for the applicable Licensed Products shall be in effect, as specified +in the name of the Licensed Product or in the applicable Quote (subject to earlier termination pursuant +to the terms hereof) or, if no +Quote was provided to Customer, as otherwise communicated by PTC to Customer. In the absence of a stated license term, the +License Term shall be perpetual, except that the License Term for evaluation Licenses shall be no longer than thirty days from the +date of Customer's request for an evaluation license, unless otherwise specifically designated by PTC, and the evaluation License +will cease to be operational after such term expires. The License Term of a "subscription" License is as specified in the Quote and/or +the invoice, and such License includes Support Services during such License Term at no additional fee. "License Locked Product" means a Licensed Product licensed for use with another PTC product to which the License Locked +Product is an extension. The License Locked Product will assume the licensing basis of such other product.. License Locked +Products are specified either in the Quote or at the Licensing Basis Webpage. + +"Licensed Products" means collectively the Licensed Software and the Documentation. + +"Licensed Software" means, collectively, the computer software product identified in the applicable +Quote, as well as (i) any +software product that is provided to operate with such computer software product (e.g., modules, software bundled with this software +product, etc.), but excluding any software that is a consulting services deliverable, (ii) any Error corrections pursuant to Section 4.4 +hereof, (iii) any updates, Error corrections and/or New Releases provided to Customer by PTC pursuant to Support Services +purchased by Customer and (iv) any computer software provided to Customer in the course of PTC's delivery of Training Services. + +"Licensing Basis Webpage" means the "Licensing Basis" document at http://www.ptc. com/support/customer_agreements/ +index.htm, which specifies the licensing basis of PTC's different products and states certain additional product-specific terms and +conditions. + +"Support Services" means the provision of New Releases and, depending on the level of Support +Services ordered, may also include +telephone support, web-based support tools, and correction of Errors, all in accordance with Schedule C +attached to this Agreement. + +"New Release" means a modified or enhanced version of a Licensed Product that is designated by PTC +as a new release of that +product and that PTC makes generally available to its Support Services customers. + +"Permitted User" means an individual who is authorized by Customer to use the Licensed Products, such use to be solely in +accordance with the terms and conditions of the Agreement. Permitted Users are limited to Customer's employees, consultants, +subcontractors, suppliers, business partners and customers who (i) are not competitors of PTC or employed by competitors of PTC +and (ii) are directly involved in the utilization of the Licensed Products solely in support of Customer's internal business purposes. +Customer shall at all times be responsible for its Permitted Users' compliance with this Agreement. + +"Per Instance Product" means a Licensed Product for which one License is required for each instance of a system to which the +applicable Licensed Product connects. For example, if an adapter that is licensed on a Per Instance basis enables Windchill to +connect to an ERP system and a CRM system, two licenses of such adapter will be required. The +Licensed Products that are Per +Instance Products are identified either in the Quote or at the Licensing Basis Webpage. + +"Quote" means the PTC product schedule, quote or order confirmation provided to Customer in connection with the purchase of the +applicable Licensed Product or, if no such document is provided, Customer's purchase order for such +Licensed Product, if any. + +"Registered User" means a Permitted User for whom Customer has purchased a License to use a +Registered User Product and for +whom Customer has issued a password or other unique identifier to enable such individual to use the +Registered User Product. + +"Registered User Products" means the Licensed Products licensed on a Registered User basis, as specified either in the Quote or at +the Licensing Basis Webpage. + +"Reseller" means a third-party appointed and authorized by PTC to resell or distribute any Licensed +Product. . + +"Services" means collectively Support Services and Training Services. + +"Site License" means a Licensed Product for which one License is required for each Customer location, as specified either in the +Quote or at the Licensing Basis Webpage. Multiple customer facilities located in the same city or town +(based on postal address) +shall be considered one "location," whereas locations located in different cities or towns will require multiple Site Licenses. + +"Training Services" means instruction or other training provided by PTC in the use of the Licensed +Products. "Training Services" +does not include PTC's e-Learning training products (e.g., "PTCU"), which are considered Licensed +Products for purposes of this +Agreement. + +"Uplift Fee" means a fee based upon the difference between the License fee applicable to installation of the applicable Licensed +Product in the original Designated Country and the License fee applicable to the installation of such +Licensed Product in the +Designated Country to which Customer wishes to move the Licensed Product. + +"Usage License Fee" means an ongoing fee that commences upon installation of the applicable +Licensed Product and that, during the +period for which the Usage License Fee is paid, entitles Customer to (i) continued use of the Licensed +Product in accordance with the +terms of the License and (ii) telephone support, Error corrections or workarounds, and New Releases for such software. + +Schedule C - PTC Support Services Terms and Conditions +The following additional terms and conditions apply to the provision of Support Services by PTC: Support Services Plan; Levels of Support Services. Upon PTC's acceptance of Customer's order for Support Services in respect of +the Licensed Products, PTC and/or its authorized subcontractors shall provide Support Services in accordance with these terms for a +time period of twelve (12) months or for such other period specified in Customer's order accepted by +PTC (a "Support Services +Plan"). All Support Services are provided subject to Customer's payment for such services at PTC's then-current rates, provided that +for Licensed Product licensed on a subscription basis, such License includes Support Services during such License Term at no +additional fee. If Customer does not order Support Services to commence on shipment of the Licensed +Product(s), or if Customer at +any time discontinues Support Services, and in either case subsequently wishes to obtain Support +Services, Customer must pay (i) the +then current fees for Support Services and (ii) the fees for Support Services for any period for which + +Customer has not purchased +Support Services. The then current levels of Support Services offered and the corresponding services provided thereunder are +described on http://www.ptc.com at http://www.ptc.com/support/maintenance/maintenance_support_policies.htm + +A Support Services Plan may not be cancelled by Customer following PTC's acceptance of an order for such Support Services Plan. +With respect to Registered User Products, e-Learning products and Integrity Concurrent User and +Server Licensed Products, Support +Services ordered by Customer must cover all Licenses granted to Customer for such Licensed Products. PTC is obligated to provide +Support Services only during periods for which Customer has paid the applicable Support Services fees and only in accordance with +the level of Support Services Customer has purchased. The services offered under any Support Services +Plan may change from time +to time, and PTC may cease to offer Support Services Plans at any time without notice, subject only to the obligation to refund to +Customer the unused portion of any previously paid applicable Support Services fee (on a prorated basis). + +(a) Telephone Support. If Customer purchases Support Services at a level that includes telephone support, Customer may utilize +PTC's telephone support service to report problems and seek assistance in use of the Licensed Products. The hours during which +PTC will provide telephone support will vary depending upon the level of Support Services ordered by +Customer. For all levels of +Support Services that include telephone support, PTC will provide telephone support in the languages, and during normal business +hours for the countries, listed on PTC's website at the website URL listed above. For levels of Support + +Services that include +telephone support during non-business hours, PTC will provide such support in the English language only. Regardless of the total +number of the Licensed Products licensed by Customer, Customer is entitled to telephone support only in direct connection with +Licenses that are covered by a Support Services Plan at a level that includes telephone support. + +(b) Repair of Errors. If Customer's Support Services Plan includes repair or workaround of Errors, PTC +shall use diligent efforts +to repair Errors or provide workarounds as required in such Support Services Plan, provided notice of the Error is received by PTC +during the term of a Support Services Plan and Customer supplies such additional information regarding the Error as PTC may +reasonably request. + +(C) New Releases. PTC will provide Customer with one copy of each New Release for each Licensed +Product for which +Customer is entitled to Support Services at the time the applicable language version of the New Release is made generally available. +Subject to different terms for particular products set forth at http://www.ptc.com/support/maintenance/maintenance_support_policies.htm, following shipment of the New Release, the previous +release shall remain "current" for purposes of this Agreement for a period of ninety (90) days; +thereafter only such New Release will be current. + +(d) Exclusions. + +(1) PTC is not obligated to perform investigation and/or repair of Errors (i) found by PTC to be in other than a current (as +described above), unaltered release of the Licensed Products; (ii) caused by changes to the Customer's operating systems, +environment, databases or other system components which adversely affect the Licensed Products; (iii) +caused by Customer's +modification of the Licensed Product or use thereof in combination or interconnection with software not provided by PTC; (iv) use of +the Licensed Product on a computer, operating system, software or peripherals other than a computer, operating system, software or +peripherals for which such Licensed Product was designed for and licensed for use on; (v) caused by improper or unauthorized use of +the Licensed Products; (vi) due to external causes such as, but not limited to, power failures or electric power surges; or (vii) due to a +failure by the Customer to implement recommendations in respect of solutions to Errors previously +provided by PTC to Customer. + +(2) PTC shall only be responsible for responding to problems reported by one of the two (2) technical contacts for +Customer's main location (which technical contacts and main location have previously been identified in writing to PTC by +Customer), and for sending New Releases to the "Central Support Location" designated by Customer in writing. Customer is +responsible for the distribution of New Releases to any of Customer's additional locations where +Licensed Products are authorized to +be used. Customer is responsible for providing to PTC in writing the name, address, phone number, fax number, and e-mail address +for each of Customer's designated contacts and Customer's Central Support Location. + +(3) PTC is not obligated to perform any Support Services with respect to modifications or customizations of the Licensed +Products, nor with respect to any developments resulting from Customer's use, development or customization of functionality +contained within the Licensed Products, all of which are Customer's sole responsibility + + + + +## MIT JsonCpp +============================ + + +The JsonCpp library's source code, including accompanying documentation, tests and demonstration applications, are licensed under the following conditions... + + +The author (Baptiste Lepilleur) explicitly disclaims copyright in all jurisdictions which recognize such a disclaimer. In such jurisdictions, this software is released into the Public Domain. + + +In jurisdictions which do not recognize Public Domain property (e.g. Germany as of +2010), this software is Copyright (C) 2007-2010 by Baptiste Lepilleur, and is released under the terms of the MIT License (see below). + + +In jurisdictions which recognize Public Domain property, the user of this software may choose to accept it either as 1) Public Domain, 2) under the conditions of the MIT License (see below), or 3) under the terms of dual Public Domain/MIT License conditions described here, as they choose. + + +The MIT License is about as close to Public Domain as a license can get, and is described in clear, concise terms at: + + +http://en.wikipedia.org/wiki/MIT_License + + +### The full text of the MIT License follows: +Copyright (C) 2007-2010 Baptiste Lepilleur + + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, +modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + + +The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. + + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. + +(END LICENSE TEXT) + + +The MIT license is compatible with both the GPL and commercial software, affording one all of the rights of Public Domain with the minor nuisance of being required to keep the above copyright notice and license text in the source code. Note also that by accepting the Public Domain "license" you can re-license your copy using whatever license you like. + + + +## Open source HPND License + +PIL +The Python Imaging Library (PIL) is + + +Copyright (C) 1997-2011 by Secret Labs AB Copyright (C) 1995-2011 by Fredrik Lundh + + +Pillow is the friendly PIL fork. It is + + +Copyright (C) 2010-2022 by Alex Clark and contributors +Like PIL, Pillow is licensed under the open source HPND License: + + +By obtaining, using, and/or copying this software and/or its associated documentation, you agree that you have read, understood, and will comply with the following terms and conditions: + + +Permission to use, copy, modify, and distribute this software and its associated documentation for any purpose and without fee is hereby granted, provided that the above copyright notice appears in all copies, and that +both that copyright notice and this permission notice appear in supporting documentation, and that the name of Secret Labs AB or the author not be used in advertising or publicity pertaining to distribution of the software without specific, written prior permission. + + +SECRET LABS AB AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS +SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. +IN NO EVENT SHALL SECRET LABS AB OR THE AUTHOR BE LIABLE FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM +LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE +OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. + + + + +END OF (3) ) Ion Chef(TM) Instrument Software Version 5.18 END USER LICENSE AGREEMENT +**************************************************** +**************************************************** +**************************************************** +**************************************************** +**************************************************** +(4) BEGINS: + +LIFE TECHNOLOGIES CORPORATION +END USER LICENSE AGREEMENT and LIMITED PRODUCT WARRANTY +FOR ION GENESTUDIOTM S5 INSTRUMENT SOFTWAREVERSION 5.18 INSTRUMENT OPERATING SOFTWARE +NOTICE TO USER: PLEASE READ THIS DOCUMENT CAREFULLY. THIS IS THE CONTRACT BETWEEN YOU AND LIFE TECHNOLOGIES CORPORATION ("LIFE TECHNOLOGIES") REGARDING THE OPERATING SOFTWARE FOR YOUR LIFE TECHNOLOGIES WORKSTATION OR OTHER INSTRUMENT AND BUNDLED SOFTWARE INSTALLED WITH YOUR OPERATING SOFTWARE. THIS AGREEMENT CONTAINS WARRANTY AND LIABILITY DISCLAIMERS AND LIMITATIONS. YOUR INSTALLATION AND USE OF THIS LIFE TECHNOLOGIES SOFTWARE IS SUBJECT TO THE TERMS AND CONDITIONS CONTAINED IN THIS END USER SOFTWARE LICENSE AGREEMENT, AND YOU WILL BE BOUND BY THESE TERMS AND CONDITIONS IF YOU INSTALL AND USE THE SOFTWARE. + +IF YOU DO NOT AGREE TO THESE TERMS AND CONDITIONS, YOU SHOULD PROMPTLY RETURN THIS SOFTWARE, TOGETHER WITH ALL PACKAGING, TO LIFE TECHNOLOGIES AND YOUR PURCHASE PRICE WILL BE REFUNDED. +This Life Technologies End User License Agreement accompanies a Life Technologies software product ("Software") and related explanatory materials ("Documentation"). The term "Software" also includes any upgrades, modified versions, updates, additions and copies of the Software licensed to you by Life Technologies. The term "License" or "Agreement" means this End User Software License Agreement. The term "you" or "Licensee" means the purchaser or user of this license to the Software. This Agreement includes herein by reference any additional use restrictions or Limited Use Label Licenses listed in or on user manuals, labeling, product inserts, technical notes, literature (including but not limited to Documentation) and/or splash screens related to this Software ("Supplemental Terms"). To the extent such Supplemental Terms are more restrictive than those contained herein, the more restrictive usage terms shall control. +This Software may use third-party software components from several sources. Portions of these software components are copyrighted and licensed by their respective owners. Various components require distribution of source code or if a URL is used to point the end-user to a source-code repository, and the source code is not available at such site, the distributor must, for a time determined by the license, offer to provide the source code. In such cases, please contact your Life Technologies representative. As well, various licenses require that the end-user receive a copy of the license. Such licenses, if any, may be found in Appendix 1 below. In order to use this Software, the end-user must abide by the terms and conditions of these third-party licenses. + +TITLE + +Title, ownership rights and intellectual property rights in and to the Software and Documentation shall at all times remain with Life Technologies and its subsidiaries, and their suppliers. All rights not specifically granted by this License, including Federal and international copyrights, are reserved by Life Technologies or their respective owners. + +COPYRIGHT + +The Software, including its structure, organization, code, user interface and associated Documentation, is a proprietary product of Life Technologies or its suppliers, and is protected by international laws of copyright. The law provides for civil and criminal penalties for anyone in violation of the laws of copyright. + +LICENSE + +USE OF THE SOFTWARE + +Subject to the terms and conditions of this Agreement, Life Technologies grants the purchaser of this product a non-exclusive, non-transferable (except in connection with the sale of the instrument on which it is hereby pre-installed) license, with no rights to sublicense, only to use the Software in object code (machine readable) format only on the single instrument on which it has been pre-installed by Life Technologies. + +RESTRICTIONS + +Unless permitted by applicable law, and in such cases only to the extent permitted by such law: + +7. You shall not copy, transfer (except temporarily in the event of a computer malfunction), rent, modify, distribute, electronically transmit, lend, lease, use, create derivative works based on the Software or merge the Software, or the associated Documentation, in whole or in part, whether alone or combined with any other products, except as expressly permitted in this Agreement. +8. You shall not reverse assemble, decompile, discover the source code or otherwise reverse engineer the Software. +9. You shall not remove any proprietary, copyright, trade secret or warning legend from the Software or any Documentation. +10. You agree to comply fully with all export laws and restrictions and regulations of the United States or applicable foreign agencies or authorities. You agree that you will not export or reexport, directly or indirectly, the Software and the Documentation into any country prohibited by the United States Export Administration Act and the regulations thereunder or other applicable United States law. +11. You may not use the Software or Documentation for the benefit of any third party by means of an outsourcing or service bureau relationship or for any similar commercial time-sharing or third-party training use. +12. You shall not sell, rent, transfer, resell for profit, or distribute this license or the Software, or any part thereof or any interest therein, unless the next user agrees to comply with the terms of this End User License Agreement. + +VERIFICATION + +At the written request of Life Technologies, not more frequently than annually, you shall furnish Life Technologies with a signed certification verifying that the Software is being used pursuant to the provisions of this License. + +TRIAL + +If this license is granted on a trial basis, you are hereby notified that license management software may be included to automatically cause the Software to cease functioning at the end of the trial period (and in any case you agree to discontinue usage at the end of the trial period or at the express written request of Life Technologies). + +TERMINATION + +You may terminate this Agreement by discontinuing use of the Software, removing all copies from your computers and storage media, and returning the Software and Documentation, and all copies thereof, to Life Technologies. Life Technologies may terminate this Agreement if you fail to comply with all of its terms, in which case you agree to discontinue using the Software, remove all copies from your computers and storage media, and return the Software and Documentation, and all copies thereof, to Life Technologies. + +U.S. GOVERNMENT END USERS + +The Software is a "commercial item," as that term is defined in 48 C.F.R. 2.101 (Oct. 1995), consisting of "commercial computer software" and "commercial computer software documentation," as such terms are used in 48 C.F.R. 12.212 (Sept. 1995). Consistent with 48 C.F.R. 12.212 and 48 C.F.R. 227.7202-1 through 227.7202-4 (June 1995), all U.S. Government End Users acquire the Software with only those rights set forth herein. + +EUROPEAN UNION END USERS + +If this Software is used within a country of the European Union, nothing in this Agreement shall be construed as restricting any rights available under Directive 2009/24/EC of the European Parliament and of the Council of 23 April 2009 on the legal protection of computer programs. + +LIMITED WARRANTY AND LIMITATION OF REMEDIES + +Limited Warranty. Life Technologies warrants that, except for Software provided on a trial basis, for a period of ninety days from the beginning of the applicable warranty period (as described below) the Software will, under normal use and as unmodified, function substantially in accordance with the functions and features described in the Documentation delivered with the Software when properly installed, and that for a period of ninety days from the beginning of the applicable warranty period (as described below) the tapes, CDs, diskettes or other media bearing the Software will be free of defects in materials and workmanship under normal use. +The above warranties do not apply to defects resulting from misuse, neglect, or accident, including without limitation: operation outside of the environmental or use specifications, or not in conformance with the instructions for any instrument system, software, or accessories; improper or inadequate maintenance by the user; installation of software or interfacing, or use in combination with software or products not supplied or authorized by Life Technologies; and modification or repair of the products not authorized by Life Technologies. +Warranty Period Commencement Date. The applicable warranty period for software begins on the earlier of the date of installation or three (3) months from the date of shipment for software installed by Life Technologies personnel. For software installed by the purchaser or anyone other than Life Technologies, the warranty period begins on the date the software is delivered to you. The applicable warranty period for media begins on the date the media is delivered to the purchaser. + +LIFE TECHNOLOGIES MAKES NO OTHER WARRANTIES OF ANY KIND WHATSOEVER, EXPRESS OR IMPLIED, WITH RESPECT TO THE SOFTWARE, DATA GENERATED FROM THE USE OF THE SOFTWARE ("GENERATED DATA") OR DOCUMENTATION, INCLUDING BUT NOT LIMITED TO WARRANTIES OF FITNESS FOR A PARTICULAR PURPOSE OR MERCHANTABILITY, NON-INFRINGEMENT OR NON-MISSAPROPRIATION OF INTELLECTUAL PROPERTY RIGHTS OF A THIRD PARTY, CUSTOM, TRADE, QUIET ENJOYMENT, ACCURACY OF INFORMATIONAL CONTENT, OR SYSTEM INTEGRATION. ALL OTHER WARRANTIES ARE EXPRESSLY DISCLAIMED. WITHOUT LIMITING THE GENERALITY OF THE FOREGOING, LIFE TECHNOLOGIES MAKES NO WARRANTIES THAT THE SOFTWARE WILL MEET YOUR REQUIREMENTS, THAT OPERATION OF THE SOFTWARE WILL BE UNINTERRUPTED OR ERROR FREE OR COMPLETELY SECURE, WILL OPERATE IN COMBINATION WITH THIRD PARTY HARDWARE OR SOFTWARE PRODUCTS, OR WILL CONFORM EXACTLY TO THE DOCUMENTATION, OR THAT LIFE TECHNOLOGIES WILL CORRECT ALL PROGRAM ERRORS. LIFE TECHNOLOGIES SOLE LIABILITY AND RESPONSIBILITY FOR BREACH OF WARRANTY RELATING TO THE SOFTWARE OR DOCUMENTATION SHALL BE LIMITED, AT LIFE TECHNOLOGIES SOLE OPTION, TO (1) CORRECTION OF ANY ERROR IDENTIFIED TO LIFE TECHNOLOGIES IN A WRITING FROM YOU IN A SUBSEQUENT RELEASE OF THE SOFTWARE, WHICH SHALL BE SUPPLIED TO YOU FREE OF CHARGE, (2) ACCEPTING A RETURN OF THE PRODUCT, AND REFUNDING THE PURCHASE PRICE UPON RETURN OF THE PRODUCT AND REMOVAL OF ALL COPIES OF THE SOFTWARE FROM YOUR COMPUTERS AND STORAGE DEVICES, (3) REPLACEMENT OF THE DEFECTIVE SOFTWARE WITH A FUNCTIONALLY EQUIVALENT PROGRAM AT NO CHARGE TO YOU, OR (4) PROVIDING A REASONABLE WORK AROUND WITHIN A REASONABLE TIME. LIFE TECHNOLOGIES SOLE LIABILITY AND RESPONSIBILITY UNDER THIS AGREEMENT FOR BREACH OF WARRANTY RELATING TO MEDIA IS THE REPLACEMENT OF DEFECTIVE MEDIA RETURNED WITHIN 90 DAYS OF THE DELIVERY DATE. THESE ARE YOUR SOLE AND EXCLUSIVE REMEDIES FOR ANY BREACH OF WARRANTY. WARRANTY CLAIMS MUST BE MADE WITHIN THE APPLICABLE WARRANTY PERIOD. +YOU ACKNOWLEDGE THAT LIFE TECHNOLOGIES HAS NO CONTROL OVER THE SPECIFIC CONDITIONS UNDER WHICH YOU USE THE SOFTWARE. ACCORDINGLY, EXCEPT FOR THE FOREGOING EXPRESS WARRANTY, LICENSOR CANNOT AND DOES NOT WARRANT THE PERFORMANCE OF THE SOFTWARE OR ANY PARTICULAR RESULTS THAT MAY BE OBTAINED BY THE USE OF THE SOFTWARE. THE SOFTWARE DOES NOT REPLACE YOUR OBLIGATION TO EXERCISE YOUR INDEPENDENT JUDGMENT IN USING THE SOFTWARE. The warranties made by Life Technologies may be voided by abuse or misuse of the Software. + +LIMITATION OF LIABILITY + +IN NO EVENT SHALL LIFE TECHNOLOGIES OR ITS SUPPLIERS BE RESPONSIBLE OR LIABLE, WHETHER IN CONTRACT, TORT, WARRANTY OR UNDER ANY STATUTE (INCLUDING WITHOUT LIMITATION ANY TRADE PRACTICE, UNFAIR COMPETITION OR OTHER STATUTE OF SIMILAR IMPORT) OR ON ANY OTHER BASIS FOR DAMAGES ARISING FROM PERSONAL INJURY OR DEATH OR SPECIAL, INDIRECT, INCIDENTAL, MULTIPLE, PUNITIVE, OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE POSSESSION OR USE OF, OR THE INABILITY TO USE, THE SOFTWARE, THE GENERATED DATA OR DOCUMENTATION, EVEN IF LIFE TECHNOLOGIES IS ADVISED IN ADVANCE OF THE POSSIBILITY OF SUCH DAMAGES, INCLUDING WITHOUT LIMITATION DAMAGES OR EXPENSES ARISING FROM OR RELATED TO, OR ALLEGED TO HAVE ARISEN FROM OR BE RELATED TO, LOSS OF USE, LOSS OF DATA, DOWNTIME, OR FOR LOSS OF REVENUE, PROFITS, GOODWILL OR BUSINESS OR OTHER FINANCIAL LOSS. IN ANY CASE, THE ENTIRE LIABILITY OF LIFE TECHNOLOGIES AND ITS SUPPLIERS UNDER THIS LICENSE, OR ARISING OUT OF THE USE OF THE SOFTWARE OR DOCUMENTATION OR GENERATED DATA, SHALL NOT EXCEED, IN THE AGGREGATE, THE PURCHASE PRICE OF THE PRODUCT. +SOME STATES, COUNTRIES OR JURISDICTIONS LIMIT THE SCOPE OF OR PRECLUDE LIMITATIONS OR EXCLUSION OF REMEDIES OR DAMAGES, OR OF LIABILITY, SUCH AS LIABILITY FOR GROSS NEGLIGENCE OR WILLFUL MISCONDUCT, AS OR TO THE EXTENT SET FORTH ABOVE, OR DO NOT ALLOW IMPLIED WARRANTIES TO BE EXCLUDED. IN SUCH STATES, COUNTRIES OR JURISDICTIONS, THE LIMITATION OR EXCLUSION OF WARRANTIES, REMEDIES, DAMAGES OR LIABILITY SET FORTH ABOVE MAY NOT APPLY TO YOU. HOWEVER, ALTHOUGH THEY SHALL NOT APPLY TO THE EXTENT PROHIBITED BY LAW, THEY SHALL APPLY TO THE FULLEST EXTENT PERMITTED BY LAW. YOU MAY ALSO HAVE OTHER RIGHTS THAT VARY BY STATE, COUNTRY OR OTHER JURISDICTION. +CONFIDENTIALITY + +You agree to protect Life Technologies Confidential Information with the same degree of care used to protect your own confidential information (but in no event less than a reasonable standard of care), and not to use or disclose any portion of such Confidential Information to third parties, except as expressly authorized in this Agreement. You acknowledge that the Software, including its content, structure, organization and design constitute proprietary and valuable trade secrets (and other intellectual property rights) of Life Technology and/or its licensors. The term "Confidential Information" means, collectively, non-public information that Life Technologies (and its licensors) provide and reasonably consider to be of a confidential, proprietary or trade secret nature, including but not limited to (i) the Software, and (ii) confidential elements of the Software and Life Technologies (and its licensors') technology and know-how, whether in tangible or intangible form, whether designated as confidential or not, and whether or not stored, compiled or memorialized physically, electronically, graphically, photographically, or in writing. Confidential Information does not include any information which you can demonstrate by credible evidence: (a) is, as of the time of its disclosure, or thereafter becomes part of the public domain through no fault of yours; (b) was rightfully known to you prior to the time of its disclosure, or to have been independently developed by you without use of Confidential Information; and/or (C) is subsequently learned from a third party not under a confidentiality obligation with respect to such Confidential Information. Confidential Information that is required to be disclosed by you pursuant to a duly authorized subpoena, court order, or government authority shall continue to be Confidential Information for all other purposes and you agree, prior to disclosing pursuant to a subpoena, court order, or government authority, to provide prompt written notice and assistance to Life Technologies prior to such disclosure, so that Life Technologies may seek a protective order or other appropriate remedy to protect against disclosure. + +SOFTWARE IMPROVEMENTS + +You acknowledge and agree that any ideas, enhancements, modifications, and the like disclosed by you to Life Technologies with respect to the Software ("Software Improvements and Feedback") will be the property of Life Technologies. You agree to assign, and hereby assign, all right, title, and interest worldwide in the Software Improvements and Feedback to Life Technologies and agree to assist Life Technologies, at Life Technologies' expense, in perfecting and enforcing Life Technologies rights thereto and ownership thereof. You acknowledge and agree that Life Technologies may use such Software Improvements and Feedback for its business purposes without restriction. + +GENERAL + +This Agreement shall be governed by laws of the State of California, exclusive of its conflict of laws provisions. This Agreement shall not be governed by the United Nations Convention on Contracts for the International Sale of Goods. This Agreement contains the complete agreement between the parties with respect to the subject matter hereof, and supersedes all prior or contemporaneous agreements or understandings, whether oral or written. If any provision of this Agreement is held by a court of competent jurisdiction to be contrary to law, that provision will be enforced to the maximum extent permissible and the remaining provisions of this Agreement will remain in full force and effect. The controlling language of this Agreement, and any proceedings relating to this Agreement, shall be English. You agree to bear any and all costs of translation, if necessary. The headings to the sections of this Agreement are used for convenience only and shall have no substantive meaning. All questions concerning this Agreement shall be directed to: Life Technologies Corporation, 5781 Van Allen Way, Carlsbad, CA 92008, Attention: Legal Department. +Unpublished rights reserved under the copyright laws of the United States. Life Technologies Corporation, 5781 Van Allen Way, Carlsbad, CA 92008. +Life Technologies is a trademark of Life Technologies Corporation or its subsidiaries in the U.S. and certain other countries. +All other trademarks are the sole property of their respective owners. + +May 26, 2022 + +Appendix 1 + +Life Technologies Corporation +Third Party Copyright Notices and Licenses + +Ion GeneStudioTM S5 Instrument Software VERSION 5.18 INSTRUMENT OPERATING SOFTWARE +This software uses third party software components from several sources. Portions of these software components are copyrighted and licensed by their respective owners as indicated below. Various licenses require distribution of source code or if a link is used to point the end-user to a source-code repository, and the source code is not available at such site, the distributor must, for a time determined by license, offer to provide source code. In such cases, please contact your Life Technologies representative. As well, various licenses require that the end-user receive a copy of the license or certain notices. Such licenses and notices may be found in this appendix. + +MIT/X derivate license libcurl +The curl license +COPYRIGHT AND PERMISSION NOTICE + + +Copyright (C) 1996 - 2022, Daniel Stenberg, daniel@haxx.se, and many contributors, see the THANKS +file. + + +All rights reserved. + + +Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. + + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT OF THIRD PARTY RIGHTS. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. + + +Except as contained in this notice, the name of a copyright holder shall not be used in advertising or otherwise to promote the sale, use or other dealings in this Software without prior written authorization of the copyright holder. + + + +## MIT +json library + +Copyright (C) 2007-2010 Baptiste Lepilleur and The JsonCpp Authors + + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, +modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + + +The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. + + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. + +======================================================================== +(END LICENSE TEXT) + + +The MIT license is compatible with both the GPL and commercial software, affording one all of the rights of Public Domain with the minor nuisance of being required to keep the above copyright notice and license text in the source code. Note also that by accepting the Public Domain "license" you can re-license your copy using whatever license you like. + + + +## LGPL-2.1 + +libjpeg + +Format-Specification: http://svn.debian.org/wsvn/dep/web/deps/dep5.mdwn?op=file&rev=135 + +Name: libjpeg8-empty + + +Files: * + +Copyright: 2011 Linaro Limited + +License: LGPL-2.1 + +This library is free software; you can redistribute it and/or modify it under the terms of the GNU Library General Public License (LGPL) as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. + +* This library is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Library General Public License for more details. +* You should have received a copy of the GNU Library General Public License along with this library; see the file COPYING.LIB. If not, write to +the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. +* On Debian systems, the complete text of the GNU Library General Public +License, version 2, can be found in /usr/share/common-licenses/LGPL-2.1. + + + +## LGPL-2.1 libpthread +This is the Debian prepackaged version of the Embedded GNU C Library version 2.19. + + +It was put together by the GNU Libc Maintainers +from + + +* Most of the GNU C library is under the following copyright: + + +Copyright (C) 1991,92,93,94,95,96,97,98,99,2000,2001,2002,2003,2004,2005, +2006,2007,2008,2009,2010,2011 Free Software Foundation, Inc. + + +The GNU C Library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. + + +The GNU C Library is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. + + +You should have received a copy of the GNU Lesser General Public License along with the GNU C Library; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA +02110-1301 USA + +On Debian systems, the complete text of the GNU Library +General Public License can be found in `/usr/share/common-licenses/LGPL-2.1'. + + +* The utilities associated with GNU C library is under the following copyright: + + +Copyright (C) 1991,92,93,94,95,96,97,98,99,2000,2001,2002,2003,2004,2005, +2006,2007,2008,2009,2010,2011 Free Software Foundation, Inc. + + +This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; version 2 of the License, or +(at your option) any later version. + + +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. + + +You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + + +On Debian systems, the complete text of the GNU Library +General Public License can be found in `/usr/share/common-licenses/GPL-2'. + + +* All code incorporated from 4.4 BSD is distributed under the following license: + + +Copyright (C) 1991 Regents of the University of California. All rights reserved. + + +Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: + + +1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. +2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. +3. [This condition was removed.] +4. Neither the name of the University nor the names of its contributors may be used to endorse or promote products derived from this software +without specific prior written permission. + + +THIS SOFTWARE IS PROVIDED BY THE REGENTS AND CONTRIBUTORS ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +PURPOSE +ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR +CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS +OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, +STRICT +LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +* The DNS resolver code, taken from BIND 4.9.5, is copyrighted both by UC Berkeley and by Digital Equipment Corporation. The DEC portions are under the following license: +Portions Copyright (C) 1993 by Digital Equipment Corporation. Permission to use, copy, modify, and distribute this software for any +purpose with or without fee is hereby granted, provided that the above +copyright notice and this permission notice appear in all copies, and that the name of Digital Equipment Corporation not be used in advertising or publicity pertaining to distribution of the document or software without specific, written prior permission. + + +THE SOFTWARE IS PROVIDED ``AS IS'' AND DIGITAL EQUIPMENT CORP. +DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. 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CARNEGIE MELLON DISCLAIMS ANY LIABILITY OF ANY KIND FOR ANY DAMAGES WHATSOEVER RESULTING FROM THE USE OF THIS SOFTWARE. + + +Carnegie Mellon requests users of this software to return to + + +Software Distribution Coordinator School of Computer Science Carnegie Mellon University Pittsburgh PA 15213-3890 + + +or Software.Distribution@CS.CMU.EDU any improvements or extensions that they make and grant Carnegie Mellon the rights to redistribute these changes. +* The file if_ppp.h is under the following CMU license: Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions +are met: +1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. +2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. +3. Neither the name of the University nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. + + +THIS SOFTWARE IS PROVIDED BY CARNEGIE MELLON UNIVERSITY AND CONTRIBUTORS ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE UNIVERSITY OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN +IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +* The following license covers the files from Intel's "Highly Optimized +Mathematical Functions for Itanium" collection: + +Intel License Agreement + + +Copyright (C) 2000, Intel Corporation + + +All rights reserved. + + +Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: + + +* Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. + + +* Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. + + +* The name of Intel Corporation may not be used to endorse or promote products derived from this software without specific prior written permission. + + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL INTEL OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +* The files inet/getnameinfo.c and sysdeps/posix/getaddrinfo.c are copyright +(C) by Craig Metz and are distributed under the following license: + + +* The Inner Net License, Version 2.00 + + +The author(s) grant permission for redistribution and use in source and +binary forms, with or without modification, of the software and documentation provided that the following conditions are met: + + +0. If you receive a version of the software that is specifically labelled +as not being for redistribution (check the version message and/or README), +you are not permitted to redistribute that version of the software in any way or form. +1. All terms of the all other applicable copyrights and licenses must be followed. +2. Redistributions of source code must retain the authors' copyright notice(s), this list of conditions, and the following disclaimer. +3. Redistributions in binary form must reproduce the authors' copyright notice(s), this list of conditions, and the following disclaimer in the documentation and/or other materials provided with the distribution. +4. [The copyright holder has authorized the removal of this clause.] +5. Neither the name(s) of the author(s) nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. + + +THIS SOFTWARE IS PROVIDED BY ITS AUTHORS AND CONTRIBUTORS ``AS IS'' AND ANY +EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +ARE +DISCLAIMED. IN NO EVENT SHALL THE AUTHORS OR CONTRIBUTORS BE LIABLE FOR ANY +DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES +(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; +LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON +ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS +SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. If these license terms cause you a real problem, contact the author. */ + +## MIT +libxml + +https://gitlab.gnome.org/GNOME/libxml2/-/wikis/home + + +The MIT License +OSI Approved License LogoLicense Copyright: Unknown. License License: Unknown. +License Contact: Unknown. + +SPDX short identifier: MIT Further resources... + +Begin license text. +Copyright + + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + + +The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. + + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. + + +End license text. + + + + +## LGPL-2.1+ +libudev + +Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: systemd +Upstream-Contact: systemd-devel@lists.freedesktop.org +Source: https://www.freedesktop.org/wiki/Software/systemd/ + + +Files: debian/* +Copyright: 2010-2013 Tollef Fog Heen +2013-2015 Michael Biebl +2013 Michael Stapelberg License: LGPL-2.1+ + + +Files: * + +Copyright: 2008-2015 Kay Sievers + +2010-2015 Lennart Poettering +2012-2015 Zbigniew Ja (TM) drzejewski-Szmek +2013-2015 Tom Gundersen +2013-2015 Daniel Mack +2010-2015 Harald Hoyer +2013-2015 David Herrmann +2013, 2014 Thomas H.P. Andersen +2013, 2014 Daniel Buch +2014 Susant Sahani +2009-2015 Intel Corporation +2000, 2005 Red Hat, Inc. +2009 Alan Jenkins +2010 ProFUSION embedded systems +2010 Maarten Lankhorst +1995-2004 Miquel van Smoorenburg +1999 Tom Tromey +2011 Michal Schmidt +2012 B. Poettering +2012 Holger Hans Peter Freyther +2012 Dan Walsh +2012 Roberto Sassu +2013 David Strauss +2013 Marius Vollmer +2013 Jan Janssen +2013 Simon Peeters +License: LGPL-2.1+ + + +Files: src/basic/siphash24.h src/basic/siphash24.c +Copyright: 2012 Jean-Philippe Aumasson +2012 Daniel J. Bernstein License: CC0-1.0 + + +Files: src/basic/securebits.h +Copyright: Linus Torvalds License: GPL-2 + + +Files: src/basic/ioprio.h +Copyright: Jens Axboe License: GPL-2 + + +Files: src/shared/linux/auto_dev-ioctl.h +Copyright: 2008 Red Hat, Inc. +2008 Ian Kent License: GPL-2+ + + +Files: src/basic/sparse-endian.h +Copyright: 2012 Josh Triplett License: Expat + + +Files: src/journal/lookup3.c src/journal/lookup3.h +Copyright: none +License: public-domain +You can use this free for any purpose. It's in the public domain. It has no warranty. + + +Files: src/udev/* +Copyright: 2003-2012 Kay Sievers +2003-2004 Greg Kroah-Hartman +2004 Chris Friesen +2004, 2009, 2010 David Zeuthen +2005, 2006 SUSE Linux Products GmbH +2003 IBM Corp. +2007 Hannes Reinecke +2009 Canonical Ltd. +2009 Scott James Remnant +2009 Martin Pitt +2009 Piter Punk +2009, 2010 Lennart Poettering +2009 Filippo Argiolas +2010 Maxim Levitsky +2011 ProFUSION embedded systems +2011 Karel Zak +2014 Zbigniew Ja (TM) drzejewski-Szmek +2014 David Herrmann +2014 Carlos Garnacho License: GPL-2+ + + +Files: src/udev/udev-ctrl.c src/udev/udevadm-hwdb.c src/udev/udev-builtin.c src/udev/udev-builtin-net_id.c +src/udev/udev-builtin-net_setup_link.c src/udev/udev-builtin-hwdb.c src/udev/udev-builtin-btrfs.c src/udev/udev-builtin-keyboard.c +src/udev/net/link-config.h src/udev/net/link-config.c src/udev/net/ethtool-util.c src/udev/net/ethtool-util.h +Copyright: 2007-2013 Kay Sievers +2013 Tom Gundersen License: LGPL-2.1+ + + +Files: src/udev/scsi_id/scsi.h Copyright: 2003 IBM Corp. License: GPL-2 + + +License: Expat + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to +deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + +* The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. +* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS +IN THE SOFTWARE. + + +## License: GPL-2 +This program is free software; you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by the Free Software Foundation; version 2 of the License. +* This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. +You should have received a copy of the GNU General Public License +along with this program; if not, write to the Free Software Foundation, Inc., +51 Franklin St, Fifth Floor, Boston, MA 02110-1301, USA. +*On Debian and systems the full text of the GNU General Public +License version 2 can be found in the file +`/usr/share/common-licenses/GPL-2` + + +## License: GPL-2+ +This program is free software; you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2, or (at your option) +any later version. + +* This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. +* You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, +Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. +* On Debian systems, the complete text of the GNU General Public License version 2 can be found in `/usr/share/common-licenses/GPL-2` (TM) . + + +## License: LGPL-2.1+ +This program is free software; you can redistribute it and/or modify +it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1, or (at your option) +any later version. + +* This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. +* You should have received a copy of the GNU Lesser General Public License along with this program; if not, write to the Free Software Foundation, +Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. +* On Debian systems, the complete text of the GNU Lesser General Public +License version 2.1 can be found in `/usr/share/common-licenses/LGPL-2.1`(TM) . + +## License: CC0-1.0 +To the extent possible under law, the author(s) have dedicated all copyright and related and neighboring rights to this software to the public domain worldwide. This software is distributed without any warranty. + +* You should have received a copy of the CC0 Public Domain Dedication along with this software. If not, see . +* On Debian systems, the complete text of the CC0 1.0 Universal license can be found in `/usr/share/common-licenses/CC0-1.0` (TM) . + + +## Libpng license libpng12 + +COPYRIGHT NOTICE, DISCLAIMER, and LICENSE + + +### PNG Reference Library License version 2 + + +* Copyright (C) 1995-2019 The PNG Reference Library Authors. +* Copyright (C) 2018-2019 Cosmin Truta. +* Copyright (C) 2000-2002, 2004, 2006-2018 Glenn Randers-Pehrson. +* Copyright (C) 1996-1997 Andreas Dilger. +* Copyright (C) 1995-1996 Guy Eric Schalnat, Group 42, Inc. + + +The software is supplied "as is", without warranty of any kind, express or implied, including, without limitation, the warranties of merchantability, fitness for a particular purpose, title, and +non-infringement. In no event shall the Copyright owners, or anyone distributing the software, be liable for any damages or other liability, whether in contract, tort or otherwise, arising from, out of, or in connection with the software, or the use or other dealings in the software, even if advised of the possibility of such damage. + + +Permission is hereby granted to use, copy, modify, and distribute this software, or portions hereof, for any purpose, without fee, subject to the following restrictions: + + +1. The origin of this software must not be misrepresented; you must not claim that you wrote the original software. If you +use this software in a product, an acknowledgment in the product documentation would be appreciated, but is not required. +2. Altered source versions must be plainly marked as such, and must not be misrepresented as being the original software. + + +3. This Copyright notice may not be removed or altered from any source or altered source distribution. + + + +## PNG Reference Library License version 1 (for libpng 0.5 through 1.6.35) + + +libpng versions 1.0.7, July 1, 2000, through 1.6.35, July 15, 2018 are Copyright (C) 2000-2002, 2004, 2006-2018 Glenn Randers-Pehrson, are derived from libpng-1.0.6, and are distributed according to the same disclaimer and license as libpng-1.0.6 with the following individuals added to the list of Contributing Authors: + + +Simon-Pierre Cadieux +Eric S. Raymond Mans Rullgard Cosmin Truta Gilles Vollant James Yu +Mandar Sahastrabuddhe +Google Inc. Vadim Barkov + + +and with the following additions to the disclaimer: + + +There is no warranty against interference with your enjoyment of the library or against infringement. There is no warranty that our efforts or the library will fulfill any of your particular purposes +or needs. This library is provided with all faults, and the entire risk of satisfactory quality, performance, accuracy, and effort is with the user. + + +Some files in the "contrib" directory and some configure-generated files that are distributed with libpng have other copyright owners, and are released under other open source licenses. + + +libpng versions 0.97, January 1998, through 1.0.6, March 20, 2000, are Copyright (C) 1998-2000 Glenn Randers-Pehrson, are derived from libpng-0.96, and are distributed according to the same disclaimer and license as libpng-0.96, with the following individuals added to the list of Contributing Authors: + +Tom Lane +Glenn Randers-Pehrson +Willem van Schaik + + +libpng versions 0.89, June 1996, through 0.96, May 1997, are +Copyright (C) 1996-1997 Andreas Dilger, are derived from libpng-0.88, and are distributed according to the same disclaimer and license as libpng-0.88, with the following individuals added to the list of Contributing Authors: + + +John Bowler Kevin Bracey Sam Bushell +Magnus Holmgren +Greg Roelofs +Tom Tanner + + +Some files in the "scripts" directory have other copyright owners, but are released under this license. + + +libpng versions 0.5, May 1995, through 0.88, January 1996, are +Copyright (C) 1995-1996 Guy Eric Schalnat, Group 42, Inc. + + +For the purposes of this copyright and license, "Contributing Authors" is defined as the following set of individuals: + + +Andreas Dilger Dave Martindale Guy Eric Schalnat Paul Schmidt +Tim Wegner + +The PNG Reference Library is supplied "AS IS". The Contributing Authors and Group 42, Inc. disclaim all warranties, expressed or implied, including, without limitation, the warranties of merchantability and of fitness for any purpose. The Contributing Authors and Group 42, Inc. assume no liability for direct, indirect, incidental, special, exemplary, or consequential damages, which may result from the use of the PNG Reference Library, even if advised of the possibility of such damage. + + +Permission is hereby granted to use, copy, modify, and distribute this source code, or portions hereof, for any purpose, without fee, subject to the following restrictions: + + +1. The origin of this source code must not be misrepresented. + + +2. Altered versions must be plainly marked as such and must not be misrepresented as being the original source. + + +3. This Copyright notice may not be removed or altered from any source or altered source distribution. + + +The Contributing Authors and Group 42, Inc. specifically permit, without fee, and encourage the use of this source code as a component to supporting the PNG file format in commercial products. If you use +this source code in a product, acknowledgment is not required but would be appreciated. + + +LGPL-2.1 libnuma +This package was debianized by Ian Wienand +on Wed, 15 Dec 2004. + + +libnuma sources are available from https://github.com/numactl/numactl + + +Upstream Authors: +Andi Kleen Copyright (C) 2004 Andi Kleen +numactl and the demo programs are under the GNU General Public License, v.2 libnuma is under the GNU Lesser General Public License, v2.1. +The manpages are under the same license as the Linux manpages (see the files) + + +This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, +or (at your option) any later version. 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See the GNU General Public License for more details. + + +Parts of the numademo program are derived from the STREAM benchmark, available from + +http://www.cs.virginia.edu/stream/ + + +Proprietary license from PTC Axeda Agent Embedded +PTC CUSTOMER AGREEMENT + +THIS PTC CUSTOMER AGREEMENT ("AGREEMENT") IS A LEGAL AGREEMENT BETWEEN THE INDIVIDUAL, OR THE COMPANY OR OTHER ORGANIZATION ON WHOSE BEHALF SUCH INDIVIDUAL ACCEPTS THIS AGREEMENT, THAT EITHER (A) CLICKS THE "I ACCEPT" BUTTON BELOW OR (B) INSTALLS, ACCESSES, OR USES ANY SOFTWARE OR DOCUMENTATION FROM PTC ("CUSTOMER"), AND PTC INC. OR, IF THE PURCHASE WAS MADE IN A COUNTRY SPECIFIED ON SCHEDULE A TO THIS AGREEMENT, THE PTC AFFILIATE SPECIFIED ON SCHEDULE A (AS APPLICABLE, "PTC"). + +PLEASE READ THE TERMS AND CONDITIONS OF THIS AGREEMENT CAREFULLY BEFORE ACCEPTING THIS AGREEMENT. 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SUCH CONSENT SHALL BE BINDING ON ANY USERS OF THIS SOFTWARE, INCLUDING USERS OTHER THAN YOU. + +IN ORDER TO UNDERSTAND THE PREFERENCES OF OUR SOFTWARE USERS, PTC USES DATA MONITORING TECHNOLOGIES TO OBTAIN AND TRANSMIT DATA ON SYSTEM USE AND PERFORMANCE AND FOR GATHERING USER DATA AND USE METRICS ON USERS OF OUR SOFTWARE. WE WILL SHARE THIS DATA WITHIN PTC, ITS AFFILIATED COMPANIES AND OUR BUSINESS PARTNERS, INCLUDING WITHIN THE UNITED STATES AND ELSEWHERE FOR TECHNICAL AND MARKETING PURPOSES AND WILL ENDEAVOR TO ENSURE THAT ANY SUCH DATA TRANSFERRED IS APPROPRIATELY PROTECTED. OUR COMMERCIAL LICENSES PERMIT USERS TO OPT- OUT OF THIS DATA COLLECTION AND OUR STUDENT/EDUCATIONAL VERSIONS ONLY COLLECT DATA ON SYSTEM USE AND PERFORMANCE. OUR FREE AND TRIAL VERSIONS OF SOFTWARE DO NOT ALLOW USERS TO OPT-OUT OF THIS DATA COLLECTION, INCLUDING USER DATA. +IF YOU ARE USING PTC SOFTWARE, VISITING A PTC WEBSITE OR COMMUNICATING ELECTRONICALLY WITH US FROM A COUNTRY OTHER THAN THE UNITED STATES, VARIOUS COMMUNICATIONS WILL NECESSARILY RESULT IN A TRANSFER OF THIS INFORMATION ACROSS INTERNATIONAL BOUNDARIES. +IF YOU DO NOT CONSENT TO THE COLLECTION AND/OR TRANSMISSION (INCLUDING TO THE UNITED STATES) OF YOUR DATA AS DESCRIBED ABOVE, DO NOT DOWNLOAD OR USE PTC SOFTWARE. BY (I) USING FREE OR TRIAL SOFTWARE OR (II) NOT OPTING-OUT OF THE COLLECTION OF CERTAIN PERSONAL DATA AS YOU ARE ABLE TO WITH PTC COMMERCIAL SOFTWARE, YOU CONSENT TO PTC'S COLLECTION, USE, AND TRANSFER OF YOUR PERSONAL DATA (INCLUDING TO THE UNITED STATES). + +CAPITALIZED TERMS NOT DEFINED IN THE TEXT BELOW ARE DEFINED IN SCHEDULE B AT THE END OF THIS AGREEMENT. + +SCHEDULE A TO THIS AGREEMENT CONTAINS ADDITIONAL (OR ALTERNATIVE) TERMS APPLICABLE TO SPECIFIC GEOGRAPHIES. + + +1. License. + + 1.1 License Grant. Subject to the terms and conditions of this Agreement, PTC hereby grants to Customer a non-exclusive, revocable, non-transferable license, without any right to sub-license, to install and use the Licensed Products identified in the Quote during the applicable License Term, solely for Customer's internal business purposes and solely in accordance with the applicable usage and license-type restrictions identified in the Quote and in the Licensing Basis Webpage ("License"). Notwithstanding the foregoing: + + (a) If the Licensed Product is being provided by PTC on an "evaluation" or "trial" basis, such License will be instead to install and use the Licensed Product solely to evaluate such Licensed Products, and Customer agrees not to use the Licensed Product in any commercial applications or for productive purposes. + + (b) If the Licensed Software is Educational Software, Customer must be enrolled in, or employed by, an accredited, academic institution, and shall use the Licensed Software solely for educational purposes in a degree-granting program. If Customer does not meet one of these qualifications, Customer has no rights under this Agreement. Without limitation, non- educational research or funded educational research conducted using the facilities of an academic institution or under an academic name does not qualify as "educational purposes" and use of Educational Software for such purposes represents a violation of the terms of this Agreement. + + (C) If the Licensed Software is sold on a "demo and test" or "non-production" basis (or similar designation), such Licensed +Software may not be used in a production environment. + + 1.2 Designated Country/Computers/Networks. Subject to Section 1.3, Customer may only install and operate Licensed Products on the applicable Designated Computers or Designated Networks on computer systems and networks situated in the applicable Designated Country. Customer may, from time to time, change the Designated Computer, Designated Network, and/or the Designated Country in which Customer seeks to install or operate a Licensed Product, provided that in each case (i) Customer shall give prior written notice to PTC of any such change, and (ii) upon moving the Licensed Products to a different Designated Country, Customer shall pay all applicable Uplift Fees. Notwithstanding the foregoing, Registered Users need not be located in the Designated Country when accessing a Registered User Product. + + 1.3 Global/Restricted Global Licenses. If a Concurrent User Licensed Product is licensed by PTC on a "Global" or "Restricted +Global" basis, Section 1.2 shall not apply to such Licensed Products and the following provisions shall apply instead: + + (i) Global Licenses. Subject to the other requirements of this Agreement, a Global License allows the Customer to install, operate and use such Licensed Product at any Customer site(s) throughout the world. + + (ii) Restricted Global Licenses. Subject to the other requirements of this Agreement, a Restricted Global License allows the Customer to install, operate and use such Licensed Product at any Customer site(s) located in the Designated Country and/or in any Permitted Country. "Permitted Countries" means China, India, Russia, the Czech Republic, Poland, Hungary, Malaysia, South Africa, Israel, Mexico, Brazil, Argentina, and Romania. + + 1.4 Additional Restrictions on Use. Customer shall not permit any persons who are not Permitted Users to access or use the +Licensed Products. Customer shall not and shall not permit any third party(ies) to: + + (i) modify or create any derivative work of any part of the Licensed Products; (ii) rent, lease, or loan the Licensed Products; + + (iii) use the Licensed Products, or permit them to be used, for third-party training, to deliver software implementation or consulting services to any third parties, or for commercial time-sharing or service bureau use; + + (iv) disassemble, decompile or reverse engineer the Licensed Products or the file format of the Licensed Products, or otherwise attempt to gain access to the source code or file format of the Licensed Products, except as expressly permitted in Schedule A, if applicable; + + (v) sell, license, sublicense, loan, assign, or otherwise transfer (whether by sale, exchange, gift, operation of law, or otherwise) to any third party the Licensed Products, any copy thereof, or any License or other rights thereto, in whole or in part, without in each case obtaining PTC's prior written consent, except to the extent that any of the foregoing are explicitly authorized in the Quote and/or the Licensing Basis Webpage; + + (vi) alter, remove, or obscure any copyright, trade secret, patent, trademark, logo, proprietary and/or other legal notices on or in any copies of the Licensed Products; and + + (vii) copy or otherwise reproduce the Licensed Products in whole or in part, except (a) as may be required for their installation into computer memory for the purpose of executing the Licensed Products in accordance with this Section 1, and/or (b) to make a reasonable number of copies solely for back-up purposes (provided that any such permitted copies shall be the property of PTC, and Customer shall reproduce thereon all PTC copyright, trade secret, patent, trademark, logo, proprietary and/or other legal notices contained in the original copy of the Licensed Product obtained from PTC). + + If Customer uses any unlicensed or unauthorized copies of any PTC software, Customer agrees that, without limiting PTC's right to terminate this Agreement for breach in accordance with Section 7 and without limiting any other remedies to which PTC may be +entitled, Customer will pay to PTC the PTC then-current list price for all such unlicensed software, in addition to any fines or penalties that may be imposed by law. + + 1.5 Additional Restrictions on Use Applicable to Concurrent User Products. If the Licensed Product is a Concurrent User Product, the following provisions apply: + + (i) The number of Permitted Users accessing or operating a Concurrent User Product at any point in time may not exceed the number of Licenses in effect at such time for that particular Licensed Product. + + (ii) Except with respect to Integrity and Implementer Products, only Permitted Users physically located in the Designated Country may access, operate and/or use the Licensed Products. Permitted Users who are not employees of Customer may use the Licensed Products while physically located at Customer's site only. + + (iii) Where a Concurrent User Product is Licensed on a "fixed," "locked" or "node-locked" basis, or the Licensed Product is licensed as a "Designated Computer" product, such Licensed Product is licensed to operate solely on the Designated Computer on which it is installed. + + 1.6 Additional Restrictions on Use Applicable to Registered User Products. A License is required for each individual who accesses a Registered User product or the data contained therein, whether directly or through a web portal or other mechanism for "batching" or otherwise achieving indirect access to the Licensed Product or such data. Generic or shared log-ins are not permitted. Customer may add and/or substitute from time to time new Registered Users as long as the aggregate number of Registered Users does not exceed at any point in time the number of Licenses in effect at such time for that particular Licensed Product and, provided further, that if a person who was previously a Registered User returns to Registered User status, a new License fee must be paid to PTC at PTC's then current rates. + + 1.7 Additional Restrictions on Use Applicable to Designated Server Products. Each Designated Server product may only be used on the computer server that is designated by the Customer in connection with the initial installation of such product and that has one unique instance of the applicable installed product application. In the event a computer server is partitioned in any manner (physically, logically or otherwise), the reference in the preceding sentence to "computer server" shall mean each partition of such server, and such Designated Server product may only be used on one of such partitions. Customer may, from time to time, change the Designated Server(s) for a Designated Server Product, and/or the location thereof, provided that in each case +(a) Customer shall give prior written notice to PTC of any such change, and (b) upon transferring the Designated Server Products to a different Designated Country, Customer pays all applicable Uplift Fees. + + 1.8 Third Party Components and Bundled Third Party Products. Certain of the Licensed Products may contain third party software components for which additional terms apply ("Third Party Components"). The current additional terms are set forth on the Schedule of Third Party Terms available in the legal policies and guidelines section of http://www.ptc.com. Separately, third party software products that PTC resells and/or bundles for distribution with the Licensed Products are licensed to Customer directly by the manufacturer of such third party software products ("Bundled Third Party Products"). Such Bundled Third Party Products are also described on the Schedule of Third Party Terms. Customer agrees that its use of Third Party Components and/or Bundled Third Party Products is subject to the terms of the Schedule of Third Party Terms. New Releases containing Third Party Components or Bundled Third Party Products may be subject to additional or different third party terms, of which PTC shall notify the Customer at the time such New Releases are delivered to the Customer. + + 1.9 Upgrades: If the Licensed Software was licensed as an upgrade from a previous version, Customer must first be licensed for the Licensed Software identified by PTC as eligible for the upgrade and Customer must be active on Support Services for such software. After installing the upgrade, Licensed Software licensed as an upgrade replaces and/or supplements the product that formed the basis of Customer's eligibility for the upgrade and Customer may no longer use the original Licensed Software that formed the basis for Customer's upgrade eligibility. + +2. Compliance. + + 2.1 License Usage Assessments. To confirm Customer's compliance with the terms and conditions hereof, Customer agrees that PTC may perform a usage assessment with respect to Customer's use of the Licensed Products. Customer agrees to provide PTC access to Customer's facilities and computer systems, and cooperation from Customer's employees and consultants, as reasonably requested by PTC in order to perform such assessment, all during normal business hours, and after reasonable prior notice from PTC. + + 2.2 Reports. Upon written request from PTC, Customer agrees to provide to PTC an installation and/or usage report with respect to the Licensed Products (and in the case of Registered User Products, such report shall include a list of all users for whom Customer has issued a password or other unique identifier to enable such individual to use the Registered User Product). Such report shall be certified by an authorized representative of Customer as to its accuracy within ten (10) business days after receipt of any written request from PTC. For any period in which Customer's use of the Licensed Products exceeds the number and/or the scope of the Licenses in effect during such period for such Licensed Products, Customer agrees to pay for any such excess usage, including applicable license and Support Services fees, and without limiting any other rights or remedies to which it is entitled, failure to pay shall be grounds for termination in accordance with Section 7 hereof. + +3. Intellectual Property. PTC and its licensors are the sole owners of the Licensed Products and of any copies of the Licensed Products, and of all copyright, trade secret, patent, trademark and other intellectual or industrial property rights in and to the Licensed Products. All copies of the Licensed Products, in whatever form provided by PTC or made by Customer, shall remain the property of PTC, and such copies shall be deemed to be on loan to Customer during the License Term. Customer acknowledges that the License granted hereunder does not provide Customer with title to or ownership of the Licensed Products or any copies thereof, but only a right of limited use consistent with the express terms and conditions of this Agreement. Customer shall have no rights to the source code for the Licensed Products, and Customer agrees that only PTC shall have the right to maintain, enhance, or otherwise modify the Licensed Products. + +4. Support Services; Warranty; Disclaimer of Warranties. + + See Schedule A for a modified version of this Section 4 for Licensed Products licensed and used in Germany, Austria or Switzerland. + + 4.1 Support Services. Upon PTC's acceptance of an order for Support Services or for Licensed Products for which Usage License Fees apply, PTC agrees that it or its designated service provider shall provide the applicable Support Services in accordance with Schedule C. + + 4.2 Warranty. PTC warrants to Customer that PTC is authorized to grant the License(s) and that, subject to Section 4.3, the Licensed Products will be free from Errors for a period of ninety (90) days following PTC's initial shipment to Customer or Customer's designee of such Licensed Products (the "Warranty Period"). + + 4.3 Warranty Exceptions. PTC shall have no warranty obligations hereunder with respect to any (i) evaluation, "trial" or "express" Licenses, (ii) New Releases, (iii) computer software provided to Customer in the course of PTC's delivery of Training Services, (iv) Errors attributable to the use of the Licensed Product in an application or environment for which it was not designed or contemplated, (v) Errors attributable to any modifications or customizations of the Licensed Products, (vi) Licensed Products that are provided by PTC free of charge to Customer, and/or (vii) Sun Software, Oracle Software and/or Bundled Third Party Products. + + 4.4 Sole Remedy. PTC's and its licensors' entire liability and Customer's exclusive remedy for any breach by PTC of the warranty given in Section 4.2 above shall be, at PTC's sole discretion, either to (a) replace the Licensed Product(s) or (b) use diligent efforts to repair the Error. PTC's obligations set forth in the preceding sentence shall apply only if notice of the Error is received by PTC within the Warranty Period and Customer supplies such additional information regarding the Error as PTC may reasonably request. If PTC does not replace the applicable Licensed Product(s) and/or does not repair the Error (either by providing a bug fix, a workaround or otherwise) within a reasonable time after notice of the Error and associated information from Customer is received by PTC, PTC will provide a refund of the license fees paid by Customer for the applicable Licensed Product(s) upon return of such Licensed Product(s) and any copies thereof. + + 4.5 No Additional Warranties. No third party, including any employee, partner, distributor (including any Reseller) or agent of PTC or any of its resellers or sales agents, is authorized to give any representations, warranties or covenants greater or different than those contained in this Agreement with respect to any Licensed Products or Services, except as specifically set forth in a written agreement signed on behalf of Customer by an authorized officer and on behalf of PTC by its legal counsel or Corporate Controller. + + 4.6 Disclaimer of Warranties. EXCEPT AS EXPRESSLY STATED IN SECTION 4, PTC DISCLAIMS (AND CUSTOMER WAIVES) ALL WARRANTIES, WHETHER EXPRESS, IMPLIED, OR STATUTORY, WRITTEN OR ORAL, INCLUDING ANY WARRANTY OF MERCHANTABILITY, SATISFACTORY QUALITY, FITNESS FOR A PARTICULAR PURPOSE, NON-INFRINGEMENT, AND/OR ANY WARRANTY THAT CUSTOMER WILL ACHIEVE ANY PARTICULAR RETURN ON INVESTMENT. THE LICENSED PRODUCTS ARE INTENDED TO BE USED BY TRAINED PROFESSIONALS AND ARE NOT A SUBSTITUTE FOR PROFESSIONAL JUDGMENT, TESTING, SAFETY AND UTILITY. CUSTOMER IS SOLELY RESPONSIBLE FOR ANY RESULTS OBTAINED FROM USING THE LICENSED PRODUCTS, INCLUDING THE ADEQUACY OF INDEPENDENT TESTING OF RELIABILITY AND ACCURACY OF ANY ITEM DESIGNED USING LICENSED PRODUCTS. PTC does not warrant that the operation or other use of the Licensed Products will be uninterrupted or error free or will not cause damage or disruption to Customer's data, computers or networks. + +5. Indemnification; Infringement. + + 5.1 P TC's Ob li gati on to Ind emn ify C u sto mer . PTC, at its own expense, will defend any action brought against Customer based on a claim that any Licensed Product infringes a United States, European Union or Japanese patent, copyright or trademark and, at its option, will settle any such action or will pay any final judgment awarded against Customer, provided that: (a) PTC shall be notified promptly in writing by Customer of any notice of any such claim; (b) PTC shall have the sole control of the defense of any action on such claim and all negotiations for its settlement or compromise and shall bear the costs of the same (save where one or more of the exclusions in Section 5.3 applies); and (C) Customer shall cooperate fully at PTC's expense with PTC in the defense, settlement or compromise of such claim. This Section 5 states PTC's sole and exclusive liability, and Customer's sole remedy, for any and all claims relating to infringement of any intellectual property right. + + 5.2 P TC's Righ t to Act to P reven t a Clai m + + + If a claim described in Section 5.1 hereof occurs or, in PTC's opinion, may occur, +Customer shall permit PTC, at PTC's option and expense to: (a) procure for Customer the right to continue using the Licensed Product; (b) modify the Licensed Product so that it becomes non-infringing without materially impairing its functionality; or (C) terminate the applicable Licenses, accept return of the Licensed Products and grant Customer a credit thereon. For Licenses purchased with a perpetual License Term, such credit shall be equal to the License fees paid by Customer for such Licensed Product depreciated on a straight-line, five year basis. For Licenses purchased on a term license or subscription basis, such credit shall be equal to the prepaid license or subscription fees for the remainder of the License Term. + + 5.3 Exclu sio n s fro m P TC's Ob li gati o n to In d emn ify Cu sto mer . PTC shall have no liability to Customer under Section 5.1 hereof or otherwise to the extent that any infringement or claim thereof is based upon: (a) use of the Licensed Product in combination with equipment or software not supplied hereunder where the Licensed Product itself would not be infringing; (b) use of the Licensed Product in an application or environment for which it was not designed or not contemplated under this Agreement; (C) use of other than a current release of the Licensed Product(s) provided to Customer; (d) modification of the Licensed Product by anyone other than PTC or its employees or agents; or (e) any claims of infringement of any patent, copyright, trade secret, trademark or other proprietary right in which Customer has an interest. + + +6. Limitation of Liability. + + See Schedule A for a modified version of this Section 6 for Licensed Products licensed and used in Germany, Austria or Switzerland. + + 6.1 The warranty and indemnification provisions of Sections 4 and 5 hereof state the entire liability of PTC, its subsidiaries and affiliates, and each of their respective directors, officers, employees or agents, with respect to the Licensed Products and Services, including (without limitation) any liability for breach of warranty, or for infringement or alleged infringement of patent, copyrights, trademarks, trade secrets and other intellectual or proprietary rights by the Licensed Products, or their use. + + 6.2 EXCEPT FOR PTC'S INDEMNIFICATION OBLIGATIONS IDENTIFIED IN SECTION 5.1 ABOVE, THE MAXIMUM LIABILITY OF PTC AND ITS LICENSORS ARISING OUT OF, OR RELATING TO, THE CREATION, LICENSE, FUNCTIONING, USE OR SUPPLY OF THE LICENSED PRODUCTS OR THE PROVISION OF SERVICES OR OTHERWISE RELATING TO THIS AGREEMENT, WHETHER BASED UPON WARRANTY, CONTRACT, TORT, OR OTHERWISE, SHALL NOT, (I) FOR LICENSES PURCHASED ON A PERPETUAL BASIS, EXCEED THE FEES PAID BY CUSTOMER FOR THE LICENSED PRODUCTS OR SERVICES THAT GAVE RISE TO THE CLAIM AND (II) FOR LICENSES PURCHASED ON A TERM OR SUBSCRIPTION BASIS, EXCEED THE FEES PAID BY CUSTOMER IN THE TWELVE MONTH PERIOD IMMEDIATELY PRECEDING THE EVENT GIVING RISE TO DAMAGES FOR THE LICENSED PRODUCTS OR SERVICES THAT GAVE RISE TO THE CLAIM. + + 6.3 IN NO EVENT SHALL PTC, ITS LICENSORS, ITS AFFILIATES (INCLUDING ITS SUBSIDIARY COMPANIES), OR ANY OF THEIR RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES OR AGENTS BE LIABLE FOR: (A) ANY LOSS OF PROFIT, LOSS OF USE DAMAGES, LOSS OF GOODWILL, LOSS OF BUSINESS OPPORTUNITY, LOSS OF SALES, LOSS OF REPUTATION OR LOSS OF ANTICIPATED SAVINGS; (B) ANY LOSS OR INACCURACY OF DATA OR BUSINESS INFORMATION OR FAILURE OR INADEQUACY OF ANY SECURITY SYSTEM OR FEATURE; AND (C) SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE OR CONSEQUENTIAL LOSS OR DAMAGE HOWSOEVER CAUSED; IN EACH CASE EVEN IF PTC HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. + + 6.4 Customer agrees not to bring any suit or action against PTC, and/or its subsidiaries and affiliates, and/or any of their respective directors, officers, employees or agents for any reason whatsoever more than one year after the cause of action arises. Customer recognizes that fees paid by Customer for the Licensed Products and Services are based in part on the disclaimer of warranty and limitation of liability provisions set forth herein and that, in the absence of Customer's agreement to such terms, the charges for the Licensed Products would be significantly higher. The limitations and exclusions set forth in this Section 6 shall not apply to any claim in respect of death or personal injury. + +7. Term and Termination. + + 7.1 Events Causing Termination. This Agreement and all Licenses will terminate: + + (a) Automatically and without notice on the following events: (I) Customer's breach of any of clauses (i) through (vii) of Section 1.4 or Sections 3 or 8.4 hereof; (II) a receiver, trustee, liquidator, or such similar officer is appointed for Customer or for any of Customer's properties or assets; (III) Customer makes a general assignment for the benefit of Customer's creditors; (IV) Customer files a petition for its reorganization, dissolution or liquidation, or such a petition is filed against Customer and is not dismissed within sixty (60) days thereafter; or (V) Customer ceases doing business or commence dissolution or liquidation proceedings; or + + (b) Thirty (30) days after written notice from PTC specifying a breach (other than as listed in Section 7.1(a) above) of this Agreement, including failure to make any payment due to either PTC or a Reseller in connection with the Licensed Products in a timely manner, if that breach is not, within that thirty (30) day period, remedied to PTC's reasonable satisfaction. + + 7.2 Effects of Expiration or Termination. Upon expiration of a given License Term and/or any expiration or termination of this Agreement, Customer shall promptly pay all sums owed by Customer, return to PTC the original copies of all Licensed Products for which the License Term has expired or has been terminated, destroy and/or delete all copies and backup copies thereof from Customer's computer libraries, storage facilities and/or hosting facilities, and certify in writing by an officer that Customer is in +compliance with the foregoing requirements and that such Licensed Products are no longer in Customer's possession or in use. + + 7.3 Survival. Sections 2, 3, 4.6, 5, 6, 7.2, 7.3 and 8 shall survive expiration or termination of this Agreement. + +8. General. + + 8.1 Governing Law and Jurisdiction. Unless otherwise stated in Schedule A, all disputes arising under, out of, or in any way connected with this Agreement shall be governed by and construed in accordance with the laws of the Commonwealth of Massachusetts without reference to conflict of laws principles (and specifically excluding the Uniform Computer Information Transactions Act). The parties hereby expressly disclaim the application of the U.N. Convention for the International Sale of Goods. All disputes arising under, out of, or in any way connected with this Agreement shall be litigated exclusively in the state or federal courts situated in the Commonwealth of Massachusetts, and in no other court or jurisdiction. Notwithstanding the foregoing or anything to the contrary, PTC shall have the right to bring a claim in any court of competent jurisdiction to enforce any intellectual property rights and/or protect any confidential information. Customer agrees that the state and federal courts situated in the Commonwealth of Massachusetts shall have personal jurisdiction over its person, and Customer hereby irrevocably (i) submits to the personal jurisdiction of said courts and (ii) consents to the service of process, pleadings, and notices in connection with any and all actions initiated in said courts. The parties agree that a final judgment in any such action or proceeding shall be conclusive and binding and may be enforced in any other jurisdiction. Each party waives its right to trial by jury in connection with any dispute arising out of this Agreement. + + 8.2 Notices. Any notice or communication required or permitted under this Agreement shall be in writing. In the case of notice to Customer, the notice shall be directed to the address set forth on the Customer's purchase order or to such other address as may be provided to PTC in writing. In the case of notice to PTC, such notice shall be directed to PTC, 140 Kendrick Street, Needham, MA +02494; Attn: Corporate Controller, with a copy to General Counsel. Any notice provided under this section shall be deemed to have been received: (a) if given by hand, immediately; (b) if given by mail, five (5) business days after posting; (C) if given by express courier service, the second business day following dispatch in the jurisdiction of the sender; or (d) if given by fax, upon receipt +thereof by the recipient's fax machine or as stated in the sender's transmission confirmation report as produced electronically by sender's fax machine. + + 8.3 Assignment, Waiver, Modification. Customer may not assign, transfer, delegate or sublicense any of Customer's rights or obligations hereunder (including without limitation by operation of law or by sale of Customer assets, whether directly or by merger, and a change in control of Customer shall be deemed to be an "assignment" for purposes of the foregoing) without PTC's prior written consent, and any such attempted delegation, assignment, transfer or sublicense shall be void and a breach of this Agreement. No waiver, consent, modification, amendment or change of the terms of this Agreement shall be binding unless in writing and signed by PTC and Customer. PTC reserves the right to charge a transfer fee for any proposed assignment, transfer or sublicense of this Agreement. + + 8.4 Compliance with Laws. Each party shall be responsible for its own compliance with applicable laws, regulations and other legal requirements relating to the conduct of its business and this Agreement. Further Customer represents and warrants that it will use the Licensed Products, as well as related technology and services, in full compliance with applicable laws and regulations. Customer acknowledges and agrees that the Licensed Products and related technical data and services are subject to the export control laws and regulations of the United States and any country in which the Licensed Products or related technical data or services are developed, received, downloaded, used, or performed. Further, Customer understands and acknowledges that the release of software or technology to a non-U.S. person within the United States or elsewhere abroad is deemed to be an export to the non-U.S. person's home country or countries, and that the transfer of the Licensed Products or related technology to Customer's employees, affiliates, or any third party, may require a license from the United States Government and possibly other applicable authorities. Customer shall be solely responsible for determining whether Customer's use or transfer of the Licensed Products or related technology or services requires an export license or approval from U.S. or other authorities, and for securing all required authorizations. Customer hereby warrants and represents that: (x) neither Customer nor any of Customer's directors, officers or affiliates is identified on the U.S. Commerce Department's Denied Persons List, Entity List, or Unverified List, the U.S. State Department's Nonproliferation Sanctions List, the U.S. Treasury Department's List of Specially Designated Nationals and Blocked Persons or any similar Export Controls Division-Foreign Affairs and International Trade Canada listing that designates individuals or entities to which export restrictions apply (collectively, the "Restricted Parties Lists"), (y) except as specifically authorized or licensed by the United States Government and other applicable authorities, Customer will not sell, offer, transfer, deliver, release, either directly or indirectly, the Licensed Products or related technology or services to any end-user: (A) that is either located in, a national of, or acting on behalf of a country subject to U.S. economic embargoes, or (B) that have been designated as prohibited or restricted parties by the U.S. Government, including but not limited to persons listed on the Restricted Parties Lists, or (C) engaged in activities related to the design, development, stockpiling, or proliferation of nuclear, chemical, or biological weapons, or missiles or missile systems, or (D) engaged in maritime nuclear propulsion activities. Customer represents and warrants that it will ensure that any person or entity to which Customer has granted access to the Licensed Products or related technology or services has been made aware of, and will comply with, this provision and U.S. and other applicable export control laws and regulations. Unless prohibited by applicable law and without waiving sovereign immunity, Customer shall indemnify and hold harmless PTC and its employees against any damage, loss, liability or expense (including attorneys' fees) that PTC may incur as a result of Customer's failure to comply with this Section + + 8.4. Such indemnification shall survive the expiration or termination of this Agreement. + + 8.5 Severability. It is intended that this Agreement shall not violate any applicable law and the unenforceability or invalidity of any provision (other than the provisions obligating Customer to make payments to PTC) shall not affect the force and validity of the remaining provisions and such provisions determined to be invalid shall be deemed severed from this Agreement and, to the extent possible, be replaced with terms which as closely as possible approximate the interest and economic intent of such invalid provisions. + + 8.6 Entire Agreement. This Agreement is the complete and exclusive statement of the contract between PTC and Customer with respect to the subject matter hereof. No waiver, consent, modification, amendment or change of this Agreement shall be binding unless in writing and signed or otherwise expressly acknowledged by PTC and Customer. + + 8.7 Third Party Beneficiaries. It is agreed by the parties to this Agreement that PTC's third party licensors are intended beneficiaries of this Agreement and have the right to rely upon and directly enforce its terms with respect to the products of such licensors. + + 8.8 Marketing. Customer agrees that while this Agreement is in effect, PTC shall be authorized to identify Customer as a customer/end-user of PTC software and services (as applicable) in public relations and marketing materials. + + 8.9 Government Licensees. If Customer is a United States Governmental entity, Customer agrees that the Licensed Products are "commercial computer software" under the applicable federal acquisition regulations and are provided with the commercial license rights and restrictions described elsewhere herein. If Customer is acquiring the Licensed Product(s) under a United States government contract, Customer agrees that Customer will include all necessary and applicable restricted rights legends on the Licensed Products to protect PTC's proprietary rights under the FAR or other similar regulations of other federal agencies. Customer agrees to always include such legends whenever the Licensed Products are, or are deemed to be, a deliverable under a government contract. + + +Schedule A - Purchases from PTC Affiliates + +If the Customer has obtained a License to any Licensed Products in one of the following countries, the entity granting the License is specified below and, notwithstanding Section 8.1 of this Agreement, the governing law and jurisdiction shall be as set forth below. + +Country PTC Affiliate Licensing Entity Governing Law/Jurisdiction for + Disputes +Belgium, Netherlands, Parametric Technology Nederland B.V. Netherlands +Luxembourg +Austria, Germany Parametric Technology GmbH German Law*, Landgericht Munchen I, +Germany +France Parametric Technology S.A. France +Ireland PTC Software and Services (Ireland) +Limited Republic of Ireland +Italy Parametric Technology Italia S.r.L. Italy +Spain, Portugal Parametric Technology Espana, S.A. Spain +Switzerland Parametric Technology (Schweiz) AG German Law*, Landgericht Munchen I, +Germany +United Kingdom Parametric Technology (UK) Limited United Kingdom +Remaining countries of the PTC Software and Services (Ireland) +Limited Republic of Ireland +European Union +Turkey, Kosovo, Serbia, PTC Software and Services (Ireland) +Limited Republic of Ireland +Macedonia, Montenegro, Croatia, Bosnia and Herzegovina, and +Albania +The Russian Federation PTC International LLC Russian Law / International +Commercial Arbitration Court at the +Chamber of Commerce and Industry of the Russian Federation in Moscow + +Belarus Moldova, Ukraine, PTC Software and Services (Ireland) +Limited Republic of Ireland +Armenia, Georgia, Azerbaijan, +Kazakhstan, Kyrgyz stan, +Tajikistan, Turkmenistan, and +Uzbekistan +Norway, Sweden, and Denmark, PTC Sweden AB Sweden +Finland, Iceland, and the Faeroe +Islands +Japan PTC Japan K.K. Japan / Tokyo District Court + + +Country PTC Affiliate Licensing Entity Governing Law/Jurisdiction for + Disputes +China Parametric Technology (Shanghai) The People's Republic of China/China +International Economic and Trade +Arbitration Commission in Shanghai + Software Co., Ltd. +Taiwan Parametric Technology Taiwan Limited Taiwan / Courts of Taipei, Taiwan +India Parametric Technology (India) Private +Limited India +Korea Parametric Technology Korea Ltd. Republic of Korea +Other Asia Pacific Countries PTC Inc. Special Administrative Region of Hong +Kong / Hong Kong International +Arbitration Centre +including Australia and New +Zealand, but excluding China, +Japan and Taiwan) +Canada PTC (Canada) Inc. Ontario +Any other country PTC Inc., or such other affiliate of PTC as +PTC directs at the time of the order Commonwealth of Massachu setts, + United States + +* Specific Provisions for Austria, Germany and Switzerland: + +For Licensed Products licensed and used in Austria, Germany or Switzerland, the following provisions shall apply. The following provisions shall have no applicability to any Licensed Products or Services purchased outside of Austria, Germany or Switzerland. References to sections below are references to the applicable sections in the body of the Agreement. + +* Section 1.4 (iv) above shall not apply to the extent that (i) the processes Customer undertakes are required to achieve information necessary to achieve interoperability of an independently created computer program with other software programs, (ii) the further requirements of Section 69e of the German Copyright Act are fulfilled and (iii) PTC, upon Customer's written request, has not made available the information required for this within a reasonable period. + +* Sections 4.2 (Warranty), 4.4 (Sole Remedy), 4.5 (No Additional Warranties) and 4.6 (Disclaimer of Warranties) are hereby replaced by the following provisions: + +4.2 Warranty Period, Restarts and Investigation Duty. The limitation period for warranty claims shall be twelve (12) months from delivery. Any replacement of the Licensed Product(s) and/or repair of Errors will not restart the warranty period. The pre-requisite for the Customer's warranty claims (Mangelanspruche) is that: (i) the Customer inspects the Licensed Products according to Section 377 German Commercial Code, (ii) the defect is an Error as defined in this Agreement, (iii) the Error already existed at the time of delivery and (iv) the Customer effects a proper notification of the Error. Customer shall provide notifications of Errors to PTC in writing and Customer shall provide specific details of the Error as deemed reasonable under the specific circumstances. Customer shall notify PTC of obvious Errors in writing within one week of delivery and of latent Errors within one week of discovery of such Error. The periods specified are preclusion periods. + +4.4 Remedies. In the event of an Error, PTC in its sole discretion may: (a) replace the Licensed Product(s) or (b) repair the Error, provided that notice of the Error is received by PTC within the periods set forth in Section 4.2 and Customer provides such additional information regarding the Error as PTC may reasonably request. If the repair (either by providing a bug fix, a workaround or otherwise) or replacement is not successful (after at least two repair attempts for the same Error by PTC within a reasonable period of time), Customer shall be entitled, at Customer's choice, to either: (i) rescission of the affected order so that PTC provides a refund of the license fees paid by Customer for the applicable Licensed Product(s) upon return of such Licensed Product(s) and any copies made thereof or (ii) a reasonable reduction in the purchase price. Replacements or repairs shall be made without acknowledgement of a legal obligation and shall not suspend the limitation period for warranty claims related to the Licensed Products. + +4.5 No Additional Warranties. No employee, partner, distributor (including any Reseller) or agent of PTC or any of its resellers or sales agents is authorized to give representations, warranties or covenants greater or different than those contained in this Agreement, except as specifically set forth in a written agreement signed on behalf of Customer by an authorized officer and on behalf of PTC by its legal counsel or Corporate Controller. Apart from claims for damages based on Errors that are subject to the limitation of liability as set forth in Section 6, the obligations provided for in this Section 4 shall be PTC's exclusive liability in case of warranty claims. + +4.6 Customer Responsibility. The Licensed Products are intended to be used by trained professionals and are not a substitute for the exercise by Customer of professional judgement, testing, safety and utility in their use. Customer is solely responsible for any results which were obtained by using the Licensed Products, including the adequacy of independent testing of reliability and accuracy of any item designed using Licensed Products. + +4.7 Qualities (Beschaffenheit), Guarantees. Qualities of the Licensed Products stated in publications of PTC or its sales representatives, in particular in advertising, in drawings, brochures or other documents, including presentations in the Internet, or on packaging and labeling of the Licensed Products, or which fall under trade usages, shall only be deemed to be covered by the contractual quality of the Licensed Products if such qualities are expressly contained in an offer or an order confirmation in writing. Guarantees, in particular guarantees as to quality, shall be binding on PTC only to the extent to which they (i) are contained in an offer or an order confirmation in writing, (ii) are expressly designated as "guarantee" or "guarantee as to condition" (Beschaffenheitsgarantie), and (iii) expressly stipulate the obligations for PTC resulting from such guarantee. + +* Section 6 is hereby replaced by the following provisions: + +6.Limitation of Liability + +6.1 Liability Categories. PTC shall be liable for damages, regardless of the legal grounds, only if: (i) PTC breaches a material contractual obligation (cardinal obligation) culpably (i.e., at least negligently), or (ii) the damage has been caused by gross negligence or wilfull intent on the part of PTC or (iii) PTC has assumed a guarantee. + +6.2 Predictability. PTC's liability shall be limited to the typical, foreseeable damage: (i) if PTC breaches material contractual obligations (cardinal obligations) with slight negligence, or (ii) if employees or agents of PTC who are not officers or executive staff have breached other obligations by gross negligence, or (iii) if PTC has assumed a guarantee, unless such guarantee is expressly designated as guarantee as to condition (Beschaffenheitsgarantie). + +6.3 Maximum Amount. In the cases of Section 6.2 (i) and (ii), PTC's liability shall be limited to a maximum amount of +EURO 1,000,000 or, in case of purely financial losses, to a maximum amount of EURO 100,000. + +6.4 Indirect Damages. In the cases of Section 6.2, PTC shall not be liable for indirect damages, consequential damages or loss of profit. + +6.5 Liability Period. Customer's claims for damages against PTC and/or PTC's affiliates, regardless of the legal grounds, shall expire at the latest one year from the time the Customer gains knowledge of the damage or, irrespective of this knowledge, at the latest two years after the damaging event. For claims based on Errors of the Licensed Product(s), the warranty limitation period pursuant to Section 4.2 shall apply. + +6.6 Mandatory Liability. PTC's liability pursuant to the German Product Liability Act (Produkthaftungsgesetz), for injury of life, body and health, for fraudulent concealment of a defect or for the assumption of a guarantee as to condition (Beschaffenheitsgarantie) remains unaffected. + +6.7 Employees. Sections 6.1 to 6.6 shall also apply in the case of any claims for damages of Customer against employees +or agents of PTC and/or PTC's affiliates. + +6.8 Contributory Negligence. In the event of a guarantee or liability claim against PTC any contributory fault of Customer must be taken into account accordingly, particularly in the event of inadequate fault notification or inadequate data securing. It constitutes inadequate data securing if the client, among others, does not, by way of appropriate state of the art security measures, take precautions against external influences, e.g. computer viruses and other phenomena which could put individual data or an entire data stock at risk. + +Schedule B - Definitions + +"Concurrent User Products" means the Licensed Products licensed on a concurrent user basis, as specified either in the Quote or at +the Licensing Basis Webpage. + +"Designated Computer" means the central processing unit(s) designated in writing by Customer to PTC at the time of installation of the Licensed Products (as may be modified in accordance with Section 1.2 of this Agreement). + +"Designated Computer Product" means the Licensed Products licensed on a "Designated Computer" basis or otherwise designated as "fixed," "locked" or "node-locked", as specified either in the Quote or at the Licensing Basis Webpage. Designated Computer Products may not be remotely accessed or installed in a virtual environment. + +"Designated Country" means the country of installation specified in writing by Customer to PTC at the time Customer places its +order of the Licensed Products. The Designated Country may be changed only in accordance with Section 1.2 of this Agreement. + +"Designated Network" means the network designated in writing by Customer to PTC at the time of installation of the Licensed +Products (as may be modified in accordance with Section 1.2 of this Agreement). + +"Designated Server" means a computer server designated in writing by Customer to PTC at the time of installation of the Licensed Products (as may be modified in accordance with Section 1.2 of this Agreement) that has one unique instance of the applicable installed Licensed Product application. + +"Designated Server Products" means the Licensed Products licensed on a Designated Server basis, as specified either in the Quote or +at the Licensing Basis Webpage. + +"Documentation" means the applicable Licensed Software user manuals provided or made available by electronic means by PTC at the time of shipment of the Licensed Software. + +"Educational Software" means Licensed Products identified as "Priced for Education," "Student Edition," "Schools Edition," "Schools Advanced Edition," "University Edition," "Professor's Edition/Version" or "Academic Edition/Version," or otherwise designated as educational or academic licenses. + +"Error" means a failure of the Licensed Software to conform substantially to the applicable Documentation, provided that Customer informs PTC of such failure in writing and PTC is able to replicate such failure after making reasonable efforts. + +"External User" means a Registered User who is a vendor or other third party external to the Customer and its affiliates. "License" shall have the meaning set out in Section 1.1 of the body of the Agreement. +"License Term" means the time period during which the License for the applicable Licensed Products shall be in effect, as specified in the name of the Licensed Product or in the applicable Quote (subject to earlier termination pursuant to the terms hereof) or, if no Quote was provided to Customer, as otherwise communicated by PTC to Customer. In the absence of a stated license term, the License Term shall be perpetual, except that the License Term for evaluation Licenses shall be no longer than thirty days from the date of Customer's request for an evaluation license, unless otherwise specifically designated by PTC, and the evaluation License will cease to be operational after such term expires. The License Term of a "subscription" License is as specified in the Quote and/or the invoice, and such License includes Support Services during such License Term at no additional fee. + +"License Locked Product" means a Licensed Product licensed for use with another PTC product to which the License Locked Product is an extension. The License Locked Product will assume the licensing basis of such other product.. License Locked Products are specified either in the Quote or at the Licensing Basis Webpage. + +"Licensed Products" means collectively the Licensed Software and the Documentation. + +"Licensed Software" means, collectively, the computer software product identified in the applicable Quote, as well as (i) any software product that is provided to operate with such computer software product (e.g., modules, software bundled with this software product, etc.), but excluding any software that is a consulting services deliverable, (ii) any Error corrections pursuant to Section 4.4 hereof, (iii) any updates, Error corrections and/or New Releases provided to Customer by PTC pursuant to Support Services purchased by Customer and (iv) any computer software provided to Customer in the course of PTC's delivery of Training Services. + +"Licensing Basis Webpage" means the "Licensing Basis" document at http://www.ptc.com/support/customer_agreements/ +index.htm, which specifies the licensing basis of PTC's different products and states certain additional product-specific terms and conditions. + +"Support Services" means the provision of New Releases and, depending on the level of Support Services ordered, may also include telephone support, web-based support tools, and correction of Errors, all in accordance with Schedule C attached to this Agreement. + +"New Release" means a modified or enhanced version of a Licensed Product that is designated by PTC as a new release of that +product and that PTC makes generally available to its Support Services customers. + +"Permitted User" means an individual who is authorized by Customer to use the Licensed Products, such use to be solely in accordance with the terms and conditions of the Agreement. Permitted Users are limited to Customer's employees, consultants, subcontractors, suppliers, business partners and customers who (i) are not competitors of PTC or employed by competitors of PTC and (ii) are directly involved in the utilization of the Licensed Products solely in support of Customer's internal business purposes. Customer shall at all times be responsible for its Permitted Users' compliance with this Agreement. + +"Per Instance Product" means a Licensed Product for which one License is required for each instance of a system to which the applicable Licensed Product connects. For example, if an adapter that is licensed on a Per Instance basis enables Windchill to connect to an ERP system and a CRM system, two licenses of such adapter will be required. The Licensed Products that are Per Instance Products are identified either in the Quote or at the Licensing Basis Webpage. + +"Quote" means the PTC product schedule, quote or order confirmation provided to Customer in connection with the purchase of the applicable Licensed Product or, if no such document is provided, Customer's purchase order for such Licensed Product, if any. + +"Registered User" means a Permitted User for whom Customer has purchased a License to use a Registered User Product and for +whom Customer has issued a password or other unique identifier to enable such individual to use the Registered User Product. + +"Registered User Products" means the Licensed Products licensed on a Registered User basis, as specified either in the Quote or at +the Licensing Basis Webpage. + +"Reseller" means a third-party appointed and authorized by PTC to resell or distribute any Licensed Product. . + +"Services" means collectively Support Services and Training Services. + +"Site License" means a Licensed Product for which one License is required for each Customer location, as specified either in the Quote or at the Licensing Basis Webpage. Multiple customer facilities located in the same city or town (based on postal address) shall be considered one "location," whereas locations located in different cities or towns will require multiple Site Licenses. + +"Training Services" means instruction or other training provided by PTC in the use of the Licensed Products. "Training Services" does not include PTC's e-Learning training products (e.g., "PTCU"), which are considered Licensed Products for purposes of this Agreement. + +"Uplift Fee" means a fee based upon the difference between the License fee applicable to installation of the applicable Licensed Product in the original Designated Country and the License fee applicable to the installation of such Licensed Product in the Designated Country to which Customer wishes to move the Licensed Product. + +"Usage License Fee" means an ongoing fee that commences upon installation of the applicable Licensed Product and that, during the period for which the Usage License Fee is paid, entitles Customer to (i) continued use of the Licensed Product in accordance with the terms of the License and (ii) telephone support, Error corrections or workarounds, and New Releases for such software. + + +Schedule C - PTC Support Services Terms and Conditions +The following additional terms and conditions apply to the provision of Support Services by PTC: + +Support Services Plan; Levels of Support Services. Upon PTC's acceptance of Customer's order for Support Services in respect of the Licensed Products, PTC and/or its authorized subcontractors shall provide Support Services in accordance with these terms for a time period of twelve (12) months or for such other period specified in Customer's order accepted by PTC (a "Support Services Plan"). All Support Services are provided subject to Customer's payment for such services at PTC's then-current rates, provided that for Licensed Product licensed on a subscription basis, such License includes Support Services during such License Term at no additional fee. If Customer does not order Support Services to commence on shipment of the Licensed Product(s), or if Customer at any time discontinues Support Services, and in either case subsequently wishes to obtain Support Services, Customer must pay (i) the then current fees for Support Services and (ii) the fees for Support Services for any period for which Customer has not purchased Support Services. The then current levels of Support Services offered and the corresponding services provided thereunder are described on http://www.ptc.com at + +http://www.ptc.com/support/maintenance/maintenance_support_policies.htm + +A Support Services Plan may not be cancelled by Customer following PTC's acceptance of an order for such Support Services Plan. With respect to Registered User Products, e-Learning products and Integrity Concurrent User and Server Licensed Products, Support Services ordered by Customer must cover all Licenses granted to Customer for such Licensed Products. PTC is obligated to provide Support Services only during periods for which Customer has paid the applicable Support Services fees and only in accordance with the level of Support Services Customer has purchased. The services offered under any Support Services Plan may change from time to time, and PTC may cease to offer Support Services Plans at any time without notice, subject only to the obligation to refund to Customer the unused portion of any previously paid applicable Support Services fee (on a prorated basis). + +(a) Telephone Support. If Customer purchases Support Services at a level that includes telephone support, Customer may utilize PTC's telephone support service to report problems and seek assistance in use of the Licensed Products. The hours during which PTC will provide telephone support will vary depending upon the level of Support Services ordered by Customer. For all levels of Support Services that include telephone support, PTC will provide telephone support in the languages, and during normal business hours for the countries, listed on PTC's website at the website URL listed above. For levels of Support Services that include telephone support during non-business hours, PTC will provide such support in the English language only. Regardless of the total number of the Licensed Products licensed by Customer, Customer is entitled to telephone support only in direct connection with Licenses that are covered by a Support Services Plan at a level that includes telephone support. + +(b) Repair of Errors. If Customer's Support Services Plan includes repair or workaround of Errors, PTC shall use diligent efforts to repair Errors or provide workarounds as required in such Support Services Plan, provided notice of the Error is received by PTC during the term of a Support Services Plan and Customer supplies such additional information regarding the Error as PTC may reasonably request. + +(C) New Releases. PTC will provide Customer with one copy of each New Release for each Licensed Product for which Customer is entitled to Support Services at the time the applicable language version of the New Release is made generally available. Subject to different terms for particular products set forth at http://www.ptc.com/support/maintenance/maintenance_support_policies.htm, following shipment of the New Release, the previous release shall remain "current" for purposes of this Agreement for a period of ninety (90) days; thereafter only such New Release will be current. + +(d) Exclusions. + +(1) PTC is not obligated to perform investigation and/or repair of Errors (i) found by PTC to be in other than a current (as described above), unaltered release of the Licensed Products; (ii) caused by changes to the Customer's operating systems, environment, databases or other system components which adversely affect the Licensed Products; (iii) caused by Customer's modification of the Licensed Product or use thereof in combination or interconnection with software not provided by PTC; (iv) use of the Licensed Product on a computer, operating system, software or peripherals other than a computer, operating system, software or peripherals for which such Licensed Product was designed for and licensed for use on; (v) caused by improper or unauthorized use of the Licensed Products; (vi) due to external causes such as, but not limited to, power failures or electric power surges; or (vii) due to a failure by the Customer to implement recommendations in respect of solutions to Errors previously provided by PTC to Customer. + +(2) PTC shall only be responsible for responding to problems reported by one of the two (2) technical contacts for Customer's main location (which technical contacts and main location have previously been identified in writing to PTC by Customer), and for sending New Releases to the "Central Support Location" designated by Customer in writing. Customer is responsible for the distribution of New Releases to any of Customer's additional locations where Licensed Products are authorized to be used. Customer is responsible for providing to PTC in writing the name, address, phone number, fax number, and e-mail address for each of Customer's designated contacts and Customer's Central Support Location. + +(3) PTC is not obligated to perform any Support Services with respect to modifications or customizations of the Licensed Products, nor with respect to any developments resulting from Customer's use, development or customization of functionality contained within the Licensed Products, all of which are Customer's sole responsibility. + + +END OF (4) Ion GeneStudio(TM) S5 V5.18 END USER LICENSE AGREEMENT +**************************************************** + diff --git a/dbReports/iondb/bin/add_or_update_systemPlanTemplates.py b/dbReports/iondb/bin/add_or_update_systemPlanTemplates.py index 9a77339b..d277dbf6 100755 --- a/dbReports/iondb/bin/add_or_update_systemPlanTemplates.py +++ b/dbReports/iondb/bin/add_or_update_systemPlanTemplates.py @@ -101,11 +101,16 @@ def __init__(self, templateName, instrument, runType="GENS"): self.libraryReadLength = 0 self.samplePrepProtocol = "" self.irworkflow = "" + self.usableSequenceThreshold = "" + self.keySignal = "" + self.beadLoading = "" + # Experiment self.chipType = "" self.flows = 0 self.sequencekitname = "" self.flowOrder = "" + self.metaData = {} # EAS self.barcodeKitName = "" self.libraryKey = "TCAG" @@ -117,6 +122,16 @@ def __init__(self, templateName, instrument, runType="GENS"): self.libraryKitName = "" self.selectedPlugins = "" self.endBarcodeKitName = "" + self.sseBedFile = "" + self.mixedTypeRNA_reference = "" + self.mixedTypeRNA_targetRegionBedFile = "" + self.mixedTypeRNA_hotSpotRegionBedFile = "" + self.chipTecDfltAmbient = None + self.chipTecSlope = None + self.chipTecMinThreshold = None + self.manTecDfltAmbient = None + self.manTecSlope = None + self.manTecMinThreshold = None if instrument == PGM: self.instrumentType = "PGM" @@ -188,9 +203,16 @@ def finish_creating_sys_template(currentTime, sysTemplate, templateParams): sysTemplate.save() + threshold = 30 for qcType in models.QCType.objects.all(): + if 'Usable Sequence' in qcType.qcName and templateParams.usableSequenceThreshold: + threshold = templateParams.usableSequenceThreshold + if 'Key Signal' in qcType.qcName and templateParams.keySignal: + threshold = templateParams.keySignal + if 'Bead Loading' in qcType.qcName and templateParams.beadLoading: + threshold = templateParams.beadLoading sysDefaultQC, isQcCreated = models.PlannedExperimentQC.objects.get_or_create( - plannedExperiment=sysTemplate, qcType=qcType, threshold=30 + plannedExperiment=sysTemplate, qcType=qcType, threshold=threshold ) sysTemplate.plannedexperimentqc_set.add(sysDefaultQC) @@ -228,6 +250,11 @@ def create_sys_template_experiment(currentTime, sysTemplate, templateParams): "storageHost": "", "notes": "", "status": templateParams.planStatus, + "chipTecDfltAmbient": templateParams.chipTecDfltAmbient, + "chipTecSlope": templateParams.chipTecSlope, + "manTecDfltAmbient": templateParams.manTecDfltAmbient, + "manTecSlope": templateParams.manTecSlope, + "metaData": templateParams.metaData or {} } experiment = models.Experiment(**exp_kwargs) @@ -261,6 +288,7 @@ def create_sys_template_eas( "targetRegionBedFile": templateParams.targetRegionBedFile, "threePrimeAdapter": templateParams.threePrimeAdapter, "tfKey": templateParams.tfKey, + "sseBedFile": templateParams.sseBedFile } eas = models.ExperimentAnalysisSettings(**eas_kwargs) @@ -276,6 +304,14 @@ def create_sys_template_eas( return sysTemplate +def orderedJson(obj): + if isinstance(obj, dict): + return sorted((k, orderedJson(v)) for k, v in obj.items()) + if isinstance(obj, list): + return sorted(orderedJson(x) for x in obj) + else: + return obj + @cache_plugin_config def finish_sys_template(sysTemplate, isCreated, templateParams, plugins={}): # when debug, do nothing @@ -365,6 +401,69 @@ def finish_sys_template(sysTemplate, isCreated, templateParams, plugins={}): exp.flowsInOrder = templateParams.flowOrder hasChanges = True + if exp.chipTecDfltAmbient != templateParams.chipTecDfltAmbient: + print( + ">>> DIFF: orig exp.chipTecDfltAmbient=%s for system template.id=%d; name=%s" + % (exp.chipTecDfltAmbient, sysTemplate.id, sysTemplate.planName) + ) + + exp.chipTecDfltAmbient = templateParams.chipTecDfltAmbient + hasChanges = True + + if exp.chipTecSlope != templateParams.chipTecSlope: + print( + ">>> DIFF: orig exp.chipTecSlope=%s for system template.id=%d; name=%s" + % (exp.chipTecSlope, sysTemplate.id, sysTemplate.planName) + ) + + exp.chipTecSlope = templateParams.chipTecSlope + hasChanges = True + + if exp.chipTecMinThreshold != templateParams.chipTecMinThreshold: + print( + ">>> DIFF: orig exp.chipTecMinThreshold=%s for system template.id=%d; name=%s" + % (exp.chipTecMinThreshold, sysTemplate.id, sysTemplate.planName) + ) + + exp.chipTecMinThreshold = templateParams.chipTecMinThreshold + hasChanges = True + + if exp.manTecDfltAmbient != templateParams.manTecDfltAmbient: + print( + ">>> DIFF: orig exp.manTecDfltAmbient=%s for system template.id=%d; name=%s" + % (exp.manTecDfltAmbient, sysTemplate.id, sysTemplate.planName) + ) + + exp.manTecDfltAmbient = templateParams.manTecDfltAmbient + hasChanges = True + + if exp.manTecSlope != templateParams.manTecSlope: + print( + ">>> DIFF: orig exp.manTecSlope=%s for system template.id=%d; name=%s" + % (exp.manTecSlope, sysTemplate.id, sysTemplate.planName) + ) + + exp.manTecSlope = templateParams.manTecSlope + hasChanges = True + + if exp.manTecMinThreshold != templateParams.manTecMinThreshold: + print( + ">>> DIFF: orig exp.manTecMinThreshold=%s for system template.id=%d; name=%s" + % (exp.manTecMinThreshold, sysTemplate.id, sysTemplate.planName) + ) + + exp.manTecMinThreshold = templateParams.manTecMinThreshold + hasChanges = True + + if orderedJson(exp.metaData) != orderedJson(templateParams.metaData): + print( + ">>> DIFF: orig exp.metaData=%s for system template.id=%d; name=%s" + % (exp.metaData, sysTemplate.id, sysTemplate.planName) + ) + + exp.metaData = templateParams.metaData + hasChanges = True + if hasChanges: exp.date = currentTime exp.save() @@ -487,6 +586,33 @@ def finish_sys_template(sysTemplate, isCreated, templateParams, plugins={}): eas.tfKey = templateParams.tfKey hasChanges = True + if eas.mixedTypeRNA_reference != templateParams.mixedTypeRNA_reference: + print( + ">>> DIFF: orig eas.mixedTypeRNA_reference=%s for system template.id=%d; name=%s" + % (eas.mixedTypeRNA_reference, sysTemplate.id, sysTemplate.planName) + ) + + eas.mixedTypeRNA_reference = templateParams.mixedTypeRNA_reference + hasChanges = True + + if eas.mixedTypeRNA_targetRegionBedFile != templateParams.mixedTypeRNA_targetRegionBedFile: + print( + ">>> DIFF: orig eas.mixedTypeRNA_targetRegionBedFile=%s for system template.id=%d; name=%s" + % (eas.mixedTypeRNA_targetRegionBedFile, sysTemplate.id, sysTemplate.planName) + ) + + eas.mixedTypeRNA_targetRegionBedFile = templateParams.mixedTypeRNA_targetRegionBedFile + hasChanges = True + + if eas.mixedTypeRNA_hotSpotRegionBedFile != templateParams.mixedTypeRNA_hotSpotRegionBedFile: + print( + ">>> DIFF: orig eas.mixedTypeRNA_hotSpotRegionBedFile=%s for system template.id=%d; name=%s" + % (eas.mixedTypeRNA_hotSpotRegionBedFile, sysTemplate.id, sysTemplate.planName) + ) + + eas.mixedTypeRNA_hotSpotRegionBedFile = templateParams.mixedTypeRNA_hotSpotRegionBedFile + hasChanges = True + if sysTemplate.latestEAS != eas: print( ">>> DIFF: orig eas.latestEAS=%s for system template.id=%d; name=%s" @@ -531,6 +657,38 @@ def _get_plugin_dict(pluginName, userInput={}): return pluginDict +def get_plugin_user_input_from_custom_json(configFileName = None): + pluginUserInput = {} + if configFileName: + with open(configFileName) as fileInput: + data = json.load(fileInput) + if data: + pluginUserInput = data + return pluginUserInput + +def _get_plugin_dict_custom(pluginName, customUserInputJson=None): + try: + userInput = get_plugin_user_input_from_custom_json(customUserInputJson) + selectedPlugin = models.Plugin.objects.get( + name=pluginName, selected=True, active=True + ) + pluginDict = { + "id": selectedPlugin.id, + "name": selectedPlugin.name, + "version": selectedPlugin.version, + "userInput": userInput, + "ampliSeqVariantCallerConfig": userInput, + "features": [], + } + except models.Plugin.DoesNotExist: + pluginDict = { + "name": pluginName, + "version": "1.0", + "userInput": userInput, + "features": [], + } + + return pluginDict def get_tvc_plugin_dict(configuration): """tvc: variantCaller""" @@ -616,7 +774,7 @@ def add_or_update_sys_template(templateParams, isSystemDefault=False): "templatingKitName": templateParams.templatingKitName, "controlSequencekitname": templateParams.controlSequencekitname, "samplePrepKitName": templateParams.samplePrepKitName, - "metaData": "", + "metaData": templateParams.metaData or {}, "date": currentTime, "applicationGroup": applicationGroup_obj, "sampleGrouping": sampleGrouping_obj, @@ -946,7 +1104,7 @@ def add_or_update_genericseq_system_templates(): finish_sys_template(sysTemplate, isCreated, templateParams) # 14 - templateParams = TemplateParams("System Generic Seq Template", PGM, "GENS") + templateParams = TemplateParams("System Generic Seq Template", S5, "GENS") templateParams.update({"flows": 500, "reference": "hg19"}) sysTemplate, isCreated, isUpdated = add_or_update_sys_template(templateParams) finish_sys_template(sysTemplate, isCreated, templateParams) @@ -1355,7 +1513,7 @@ def add_or_update_reproseq_system_templates(): DEFAULT_P1_3_PRIME_ADAPTER_SEQUENCE = "ATCACCGACTGCCCATAGAGAGGAAAGCGG" BARCODE_KIT_PGM = "Ion SingleSeq Barcode set 1-24" BARCODE_KIT_S5 = "Ion SingleSeq Barcode set 1-96" - CATEGORIES = "repro" + CATEGORIES = "repro;multi_ir_workflow_support" LIBRARY_KIT = "IonPicoPlex" LIBRARY_READ_LENGTH = 0 REFERENCE = "hg19" @@ -1365,6 +1523,7 @@ def add_or_update_reproseq_system_templates(): plugins = {} plugins["FilterDuplicates"] = _get_plugin_dict("FilterDuplicates") + metaData = {"lockAssayParams": ["applicationGroupName", "runType", "chipType", "flows", "sequenceKit", "libraryKitType", "templateKit"]} # 32 templateParams = TemplateParams( "Ion ReproSeq Aneuploidy - Ion PGM System", PGM, RUN_TYPE @@ -1378,6 +1537,7 @@ def add_or_update_reproseq_system_templates(): "sequencekitname": "IonPGMHiQView", "libraryKitName": LIBRARY_KIT, "barcodeKitName": BARCODE_KIT_PGM, + "metaData": metaData, "reference": REFERENCE, "threePrimeAdapter": DEFAULT_P1_3_PRIME_ADAPTER_SEQUENCE, "categories": CATEGORIES, @@ -1412,6 +1572,7 @@ def add_or_update_reproseq_system_templates(): "reference": REFERENCE, "threePrimeAdapter": PGS_S5_3PrimeAdapter, "categories": CATEGORIES, + "metaData": metaData, } ) sysTemplate, isCreated, isUpdated = add_or_update_sys_template(templateParams) @@ -2554,25 +2715,53 @@ def add_or_update_ocp_myeloid_s5_system_templates(): def add_or_update_ocp_myeloid_mrd_550_s5_system_templates(): + # These templates has the 550 chef protocol auto selected for 5.18. BARCODE_KIT_NAME = "Ion AmpliSeq HD Dual Barcode Kit 1-24" - CATEGORIES_DNA = "Oncomine;barcodes_12;onco_liquidBiopsy;onco_heme;mrd;" - CATEGORIES_RNA_FUSIONS = "Oncomine;barcodes_48;onco_liquidBiopsy;onco_heme;" - CATEGORIES_DNA_n_FUSIONS = "Oncomine;barcodes_24;onco_liquidBiopsy;onco_heme;mrd;" + CATEGORIES_DNA = "Oncomine;barcodes_6;onco_liquidBiopsy;onco_heme;mrd;" + CATEGORIES_RNA_FUSIONS = "Oncomine;barcodes_18;onco_liquidBiopsy;onco_heme;" + CATEGORIES_DNA_n_FUSIONS = "Oncomine;barcodes_8;onco_liquidBiopsy;onco_heme;mrd;" + CATEGORIES_MHT = "Oncomine;barcodes_18;onco_liquidBiopsy;onco_heme;mrd;" + CATEGORIES_DNA_MHT = "Oncomine;barcodes_5;onco_liquidBiopsy;onco_heme;mrd;" + CATEGORIES_DNA_n_FUSIONS_MHT = "Oncomine;barcodes_6;onco_liquidBiopsy;onco_heme;mrd;" + CHIP_NAME = "550" FLOWS = 550 LIB_KIT_NAME = "Ion AmpliSeq HD Library Kit" LIBRARY_READ_LENGTH = 200 REFERENCE = "hg19" SAMPLE_GROUPING = "Self" - SAMPLE_PREP_PROTOCOL = "" + SAMPLE_PREP_PROTOCOL = "cerebro_550" SEQ_KIT_NAME = "Ion S5 Sequencing Kit" TEMPLATE_KIT_NAME = "Ion Chef S550 V1" - PLAN_STATUS = "inactive" + BEDFILE = "Oncomine_Myeloid_MRD_DNA_Regions_v1.2.bed" + HOTSPOT_FILE = "Oncomine_Myeloid_MRD_DNA_Hotspots_v1.2.bed" + FUSION_REFERENCE = "Oncomine_Myeloid_MRD_RNA_Fusions_v1.2_Reference" + FUSION_BEDFILE = "Oncomine_Myeloid_MRD_RNA_Fusions_v1.2_Reference.bed" + MICROHAPLOTYPE_DNA_BEDFILE = "Oncomine_Myeloid_MRD_DNA_Microhaplotype_Regions_v1.2.bed" + MICROHAPLOTYPE_DNA_HOTSPOT_FILE = "Oncomine_Myeloid_MRD_DNA_Microhaplotype_Hotspots_v1.2.bed" + MICROHAPLOTYPE_BEDFILE = "Oncomine_Myeloid_MRD_Microhaplotype_Regions_v1.2.bed" + MICROHAPLOTYPE_HOTSPOT_FILE = "Oncomine_Myeloid_MRD_Microhaplotype_Hotspots_v1.2.bed" # pre-select plugins - plugins = {} - plugins["molecularCoverageAnalysis"] = get_mca_plugin_dict("ampliseq_hd_cfdna") - plugins["sampleID"] = _get_plugin_dict("sampleID") + # Add custom param to MCA plugin - TS-18359 + CUSTOM_PLUGIN_CONFIG_FILENAME_TVC = "rundb/fixtures/systemtemplateparams/cerebro_mrd_parameters.json" + CUSTOM_PLUGIN_CONFIG_FILENAME_MCA = "rundb/fixtures/systemtemplateparams/cerebro_mrd_mca_parameters.json" + plugins = { + "coverageAnalysis": _get_plugin_dict("coverageAnalysis"), + "molecularCoverageAnalysis": _get_plugin_dict_custom("molecularCoverageAnalysis", CUSTOM_PLUGIN_CONFIG_FILENAME_MCA), + } + plugins_with_custom_tvc = dict(plugins) + plugins_with_custom_tvc.update({"variantCaller": _get_plugin_dict_custom("variantCaller", CUSTOM_PLUGIN_CONFIG_FILENAME_TVC)}) + + plugins_microaplotype = dict(plugins) + plugins_microaplotype.update({"microhaplotype_analysis" : _get_plugin_dict("microhaplotype_analysis")}) + + plugins_microaplotype_custom_tvc = dict(plugins_with_custom_tvc) + plugins_microaplotype_custom_tvc.update({"microhaplotype_analysis": _get_plugin_dict("microhaplotype_analysis")}) + + fusion_plugins = { + "coverageAnalysis": _get_plugin_dict("coverageAnalysis") + } templateParams = TemplateParams( "Oncomine Myeloid MRD DNA for 550", S5, "AMPS_HD_DNA" @@ -2587,15 +2776,16 @@ def add_or_update_ocp_myeloid_mrd_550_s5_system_templates(): "libraryKitName": LIB_KIT_NAME, "libraryReadLength": LIBRARY_READ_LENGTH, "reference": REFERENCE, + "targetRegionBedFile": BEDFILE, + "hotSpotRegionBedFile": HOTSPOT_FILE, "sampleGrouping": SAMPLE_GROUPING, "samplePrepProtocol": SAMPLE_PREP_PROTOCOL, "sequencekitname": SEQ_KIT_NAME, "templatingKitName": TEMPLATE_KIT_NAME, - "planStatus": PLAN_STATUS, } ) sysTemplate, isCreated, isUpdated = add_or_update_sys_template(templateParams) - finish_sys_template(sysTemplate, isCreated, templateParams, plugins) + finish_sys_template(sysTemplate, isCreated, templateParams, plugins_with_custom_tvc) templateParams = TemplateParams( "Oncomine Myeloid MRD Fusions for 550", S5, "AMPS_HD_RNA" @@ -2609,19 +2799,19 @@ def add_or_update_ocp_myeloid_mrd_550_s5_system_templates(): "flows": FLOWS, "libraryKitName": LIB_KIT_NAME, "libraryReadLength": LIBRARY_READ_LENGTH, - "reference": "", + "reference": FUSION_REFERENCE, + "targetRegionBedFile": FUSION_BEDFILE, "sampleGrouping": "Single Fusions", "samplePrepProtocol": SAMPLE_PREP_PROTOCOL, "sequencekitname": SEQ_KIT_NAME, "templatingKitName": TEMPLATE_KIT_NAME, - "planStatus": PLAN_STATUS, } ) sysTemplate, isCreated, isUpdated = add_or_update_sys_template(templateParams) - finish_sys_template(sysTemplate, isCreated, templateParams, plugins) + finish_sys_template(sysTemplate, isCreated, templateParams, fusion_plugins) templateParams = TemplateParams( - "Oncomine Myeloid MRD DNA and Fusions for 550", S5, "AMPS_HD_DNA_RNA_1" + "Oncomine Myeloid MRD DNA and Fusions for 550", S5, "AMPS_HD_DNA_RNA" ) templateParams.update( { @@ -2633,22 +2823,102 @@ def add_or_update_ocp_myeloid_mrd_550_s5_system_templates(): "libraryKitName": LIB_KIT_NAME, "libraryReadLength": LIBRARY_READ_LENGTH, "reference": REFERENCE, + "targetRegionBedFile": BEDFILE, + "hotSpotRegionBedFile": HOTSPOT_FILE, + "mixedTypeRNA_reference": FUSION_REFERENCE, + "mixedTypeRNA_targetRegionBedFile": FUSION_BEDFILE, "sampleGrouping": "DNA and Fusions", "samplePrepProtocol": SAMPLE_PREP_PROTOCOL, "sequencekitname": SEQ_KIT_NAME, "templatingKitName": TEMPLATE_KIT_NAME, - "planStatus": PLAN_STATUS, } ) sysTemplate, isCreated, isUpdated = add_or_update_sys_template(templateParams) - finish_sys_template(sysTemplate, isCreated, templateParams, plugins) + finish_sys_template(sysTemplate, isCreated, templateParams, plugins_with_custom_tvc) + #Microhaplotype templates + templateParams = TemplateParams( + "Oncomine Myeloid MRD Microhaplotype for 550", S5, "AMPS_HD_DNA" + ) + templateParams.update( + { + "applicationGroup": "DNA", + "barcodeKitName": BARCODE_KIT_NAME, + "categories": CATEGORIES_MHT, + "chipType": CHIP_NAME, + "flows": FLOWS, + "libraryKitName": LIB_KIT_NAME, + "libraryReadLength": LIBRARY_READ_LENGTH, + "reference": REFERENCE, + "targetRegionBedFile": MICROHAPLOTYPE_BEDFILE, + "hotSpotRegionBedFile": MICROHAPLOTYPE_HOTSPOT_FILE, + "sampleGrouping": SAMPLE_GROUPING, + "samplePrepProtocol": SAMPLE_PREP_PROTOCOL, + "sequencekitname": SEQ_KIT_NAME, + "templatingKitName": TEMPLATE_KIT_NAME, + } + ) + sysTemplate, isCreated, isUpdated = add_or_update_sys_template(templateParams) + finish_sys_template(sysTemplate, isCreated, templateParams, plugins_microaplotype) + + templateParams = TemplateParams( + "Oncomine Myeloid MRD DNA and Microhaplotype for 550", S5, "AMPS_HD_DNA" + ) + templateParams.update( + { + "applicationGroup": "DNA", + "barcodeKitName": BARCODE_KIT_NAME, + "categories": CATEGORIES_DNA_MHT, + "chipType": CHIP_NAME, + "flows": FLOWS, + "libraryKitName": LIB_KIT_NAME, + "libraryReadLength": LIBRARY_READ_LENGTH, + "reference": REFERENCE, + "targetRegionBedFile": MICROHAPLOTYPE_DNA_BEDFILE, + "hotSpotRegionBedFile": MICROHAPLOTYPE_DNA_HOTSPOT_FILE, + "sampleGrouping": SAMPLE_GROUPING, + "samplePrepProtocol": SAMPLE_PREP_PROTOCOL, + "sequencekitname": SEQ_KIT_NAME, + "templatingKitName": TEMPLATE_KIT_NAME, + } + ) + sysTemplate, isCreated, isUpdated = add_or_update_sys_template(templateParams) + finish_sys_template(sysTemplate, isCreated, templateParams, plugins_microaplotype_custom_tvc) + + templateParams = TemplateParams( + "Oncomine Myeloid MRD DNA Fusions and Microhaplotype for 550", S5, "AMPS_HD_DNA_RNA" + ) + templateParams.update( + { + "applicationGroup": "DNA + RNA", + "barcodeKitName": BARCODE_KIT_NAME, + "categories": CATEGORIES_DNA_n_FUSIONS_MHT, + "chipType": CHIP_NAME, + "flows": FLOWS, + "libraryKitName": LIB_KIT_NAME, + "libraryReadLength": LIBRARY_READ_LENGTH, + "reference": REFERENCE, + "targetRegionBedFile": MICROHAPLOTYPE_DNA_BEDFILE, + "hotSpotRegionBedFile": MICROHAPLOTYPE_DNA_HOTSPOT_FILE, + "mixedTypeRNA_reference": FUSION_REFERENCE, + "mixedTypeRNA_targetRegionBedFile": FUSION_BEDFILE, + "sampleGrouping": "DNA and Fusions", + "samplePrepProtocol": SAMPLE_PREP_PROTOCOL, + "sequencekitname": SEQ_KIT_NAME, + "templatingKitName": TEMPLATE_KIT_NAME, + } + ) + sysTemplate, isCreated, isUpdated = add_or_update_sys_template(templateParams) + finish_sys_template(sysTemplate, isCreated, templateParams, plugins_microaplotype_custom_tvc) def add_or_update_ocp_myeloid_mrd_540_s5_system_templates(): BARCODE_KIT_NAME = "Ion AmpliSeq HD Dual Barcode Kit 1-24" - CATEGORIES_DNA = "Oncomine;barcodes_12;onco_liquidBiopsy;onco_heme;mrd" - CATEGORIES_RNA_FUSIONS = "Oncomine;barcodes_48;onco_liquidBiopsy;onco_heme;" - CATEGORIES_DNA_n_FUSIONS = "Oncomine;barcodes_24;onco_liquidBiopsy;onco_heme;mrd" + CATEGORIES_DNA = "Oncomine;barcodes_4;onco_liquidBiopsy;onco_heme;mrd" + CATEGORIES_RNA_FUSIONS = "Oncomine;barcodes_12;onco_liquidBiopsy;onco_heme;" + CATEGORIES_DNA_n_FUSIONS = "Oncomine;barcodes_4;onco_liquidBiopsy;onco_heme;mrd" + CATEGORIES_MHT = "Oncomine;barcodes_12;onco_liquidBiopsy;onco_heme;mrd" + CATEGORIES_DNA_MHT = "Oncomine;barcodes_3;onco_liquidBiopsy;onco_heme;mrd" + CHIP_NAME = "540" FLOWS = 550 LIB_KIT_NAME = "Ion AmpliSeq HD Library Kit" @@ -2658,12 +2928,36 @@ def add_or_update_ocp_myeloid_mrd_540_s5_system_templates(): SAMPLE_PREP_PROTOCOL = "" SEQ_KIT_NAME = "Ion S5 Sequencing Kit" TEMPLATE_KIT_NAME = "Ion Chef S540 V1" - PLAN_STATUS = "inactive" + BEDFILE = "Oncomine_Myeloid_MRD_DNA_Regions_v1.2.bed" + HOTSPOT_FILE = "Oncomine_Myeloid_MRD_DNA_Hotspots_v1.2.bed" + FUSION_REFERENCE = "Oncomine_Myeloid_MRD_RNA_Fusions_v1.2_Reference" + FUSION_BEDFILE = "Oncomine_Myeloid_MRD_RNA_Fusions_v1.2_Reference.bed" + MICROHAPLOTYPE_DNA_BEDFILE = "Oncomine_Myeloid_MRD_DNA_Microhaplotype_Regions_v1.2.bed" + MICROHAPLOTYPE_DNA_HOTSPOT_FILE = "Oncomine_Myeloid_MRD_DNA_Microhaplotype_Hotspots_v1.2.bed" + MICROHAPLOTYPE_BEDFILE = "Oncomine_Myeloid_MRD_Microhaplotype_Regions_v1.2.bed" + MICROHAPLOTYPE_HOTSPOT_FILE = "Oncomine_Myeloid_MRD_Microhaplotype_Hotspots_v1.2.bed" + # pre-select plugins - plugins = {} - plugins["molecularCoverageAnalysis"] = get_mca_plugin_dict("ampliseq_hd_cfdna") - plugins["sampleID"] = _get_plugin_dict("sampleID") + # Add custom param to MCA plugin - TS-18359 + CUSTOM_PLUGIN_CONFIG_FILENAME_TVC = "rundb/fixtures/systemtemplateparams/cerebro_mrd_parameters.json" + CUSTOM_PLUGIN_CONFIG_FILENAME_MCA = "rundb/fixtures/systemtemplateparams/cerebro_mrd_mca_parameters.json" + plugins = { + "coverageAnalysis": _get_plugin_dict("coverageAnalysis"), + "molecularCoverageAnalysis": _get_plugin_dict_custom("molecularCoverageAnalysis", CUSTOM_PLUGIN_CONFIG_FILENAME_MCA), + } + plugins_with_custom_tvc = dict(plugins) + plugins_with_custom_tvc.update({"variantCaller": _get_plugin_dict_custom("variantCaller", CUSTOM_PLUGIN_CONFIG_FILENAME_TVC)}) + + plugins_microaplotype = dict(plugins) + plugins_microaplotype.update({"microhaplotype_analysis" : _get_plugin_dict("microhaplotype_analysis")}) + + plugins_microaplotype_custom_tvc = dict(plugins_with_custom_tvc) + plugins_microaplotype_custom_tvc.update({"microhaplotype_analysis": _get_plugin_dict("microhaplotype_analysis")}) + + fusion_plugins = { + "coverageAnalysis": _get_plugin_dict("coverageAnalysis") + } templateParams = TemplateParams( "Oncomine Myeloid MRD DNA for 540", S5, "AMPS_HD_DNA" @@ -2678,15 +2972,16 @@ def add_or_update_ocp_myeloid_mrd_540_s5_system_templates(): "libraryKitName": LIB_KIT_NAME, "libraryReadLength": LIBRARY_READ_LENGTH, "reference": REFERENCE, + "targetRegionBedFile": BEDFILE, + "hotSpotRegionBedFile": HOTSPOT_FILE, "sampleGrouping": SAMPLE_GROUPING, "samplePrepProtocol": SAMPLE_PREP_PROTOCOL, "sequencekitname": SEQ_KIT_NAME, "templatingKitName": TEMPLATE_KIT_NAME, - "planStatus": PLAN_STATUS, } ) sysTemplate, isCreated, isUpdated = add_or_update_sys_template(templateParams) - finish_sys_template(sysTemplate, isCreated, templateParams, plugins) + finish_sys_template(sysTemplate, isCreated, templateParams, plugins_with_custom_tvc) templateParams = TemplateParams( "Oncomine Myeloid MRD Fusions for 540", S5, "AMPS_HD_RNA" @@ -2700,19 +2995,19 @@ def add_or_update_ocp_myeloid_mrd_540_s5_system_templates(): "flows": FLOWS, "libraryKitName": LIB_KIT_NAME, "libraryReadLength": LIBRARY_READ_LENGTH, - "reference": "", + "reference": FUSION_REFERENCE, + "targetRegionBedFile": FUSION_BEDFILE, "sampleGrouping": "Single Fusions", "samplePrepProtocol": SAMPLE_PREP_PROTOCOL, "sequencekitname": SEQ_KIT_NAME, "templatingKitName": TEMPLATE_KIT_NAME, - "planStatus": PLAN_STATUS, } ) sysTemplate, isCreated, isUpdated = add_or_update_sys_template(templateParams) - finish_sys_template(sysTemplate, isCreated, templateParams, plugins) + finish_sys_template(sysTemplate, isCreated, templateParams, fusion_plugins) templateParams = TemplateParams( - "Oncomine Myeloid MRD DNA and Fusions for 540", S5, "AMPS_HD_DNA_RNA_1" + "Oncomine Myeloid MRD DNA and Fusions for 540", S5, "AMPS_HD_DNA_RNA" ) templateParams.update( { @@ -2724,15 +3019,93 @@ def add_or_update_ocp_myeloid_mrd_540_s5_system_templates(): "libraryKitName": LIB_KIT_NAME, "libraryReadLength": LIBRARY_READ_LENGTH, "reference": REFERENCE, + "targetRegionBedFile": BEDFILE, + "hotSpotRegionBedFile": HOTSPOT_FILE, + "mixedTypeRNA_reference": FUSION_REFERENCE, + "mixedTypeRNA_targetRegionBedFile": FUSION_BEDFILE, "sampleGrouping": "DNA and Fusions", "samplePrepProtocol": SAMPLE_PREP_PROTOCOL, "sequencekitname": SEQ_KIT_NAME, "templatingKitName": TEMPLATE_KIT_NAME, - "planStatus": PLAN_STATUS, } ) sysTemplate, isCreated, isUpdated = add_or_update_sys_template(templateParams) - finish_sys_template(sysTemplate, isCreated, templateParams, plugins) + finish_sys_template(sysTemplate, isCreated, templateParams, plugins_with_custom_tvc) + + # Microhaplotype templates for Cerebro + templateParams = TemplateParams( + "Oncomine Myeloid MRD Microhaplotype for 540", S5, "AMPS_HD_DNA" + ) + templateParams.update( + { + "applicationGroup": "DNA", + "barcodeKitName": BARCODE_KIT_NAME, + "categories": CATEGORIES_MHT, + "chipType": CHIP_NAME, + "flows": FLOWS, + "libraryKitName": LIB_KIT_NAME, + "libraryReadLength": LIBRARY_READ_LENGTH, + "reference": REFERENCE, + "targetRegionBedFile": MICROHAPLOTYPE_BEDFILE, + "hotSpotRegionBedFile": MICROHAPLOTYPE_HOTSPOT_FILE, + "sampleGrouping": SAMPLE_GROUPING, + "samplePrepProtocol": SAMPLE_PREP_PROTOCOL, + "sequencekitname": SEQ_KIT_NAME, + "templatingKitName": TEMPLATE_KIT_NAME, + } + ) + sysTemplate, isCreated, isUpdated = add_or_update_sys_template(templateParams) + finish_sys_template(sysTemplate, isCreated, templateParams, plugins_microaplotype) + + templateParams = TemplateParams( + "Oncomine Myeloid MRD DNA and Microhaplotype for 540", S5, "AMPS_HD_DNA" + ) + templateParams.update( + { + "applicationGroup": "DNA", + "barcodeKitName": BARCODE_KIT_NAME, + "categories": CATEGORIES_DNA_MHT, + "chipType": CHIP_NAME, + "flows": FLOWS, + "libraryKitName": LIB_KIT_NAME, + "libraryReadLength": LIBRARY_READ_LENGTH, + "reference": REFERENCE, + "targetRegionBedFile": MICROHAPLOTYPE_DNA_BEDFILE, + "hotSpotRegionBedFile": MICROHAPLOTYPE_DNA_HOTSPOT_FILE, + "sampleGrouping": SAMPLE_GROUPING, + "samplePrepProtocol": SAMPLE_PREP_PROTOCOL, + "sequencekitname": SEQ_KIT_NAME, + "templatingKitName": TEMPLATE_KIT_NAME, + } + ) + sysTemplate, isCreated, isUpdated = add_or_update_sys_template(templateParams) + finish_sys_template(sysTemplate, isCreated, templateParams, plugins_microaplotype_custom_tvc) + + templateParams = TemplateParams( + "Oncomine Myeloid MRD DNA Fusions and Microhaplotype for 540", S5, "AMPS_HD_DNA_RNA" + ) + templateParams.update( + { + "applicationGroup": "DNA + RNA", + "barcodeKitName": BARCODE_KIT_NAME, + "categories": CATEGORIES_DNA_n_FUSIONS, + "chipType": CHIP_NAME, + "flows": FLOWS, + "libraryKitName": LIB_KIT_NAME, + "libraryReadLength": LIBRARY_READ_LENGTH, + "reference": REFERENCE, + "targetRegionBedFile": MICROHAPLOTYPE_DNA_BEDFILE, + "hotSpotRegionBedFile": MICROHAPLOTYPE_DNA_HOTSPOT_FILE, + "mixedTypeRNA_reference": FUSION_REFERENCE, + "mixedTypeRNA_targetRegionBedFile": FUSION_BEDFILE, + "sampleGrouping": "DNA and Fusions", + "samplePrepProtocol": SAMPLE_PREP_PROTOCOL, + "sequencekitname": SEQ_KIT_NAME, + "templatingKitName": TEMPLATE_KIT_NAME, + } + ) + sysTemplate, isCreated, isUpdated = add_or_update_sys_template(templateParams) + finish_sys_template(sysTemplate, isCreated, templateParams, plugins_microaplotype_custom_tvc) def add_or_update_proton_PQ_system_template(): @@ -3031,7 +3404,7 @@ def add_or_update_tagseq_cfdna_s5_540_chef_system_template(templateName): def add_or_update_immune_repertoire_clonality_s5_system_templates(): APPLICATION_GROUP = "immune_repertoire" BARCODE_KIT_NAME = "Ion Dual Barcode Kit 1-96" - CATEGORIES = "onco_immune;immunology" + CATEGORIES = "onco_immune;immunology;multi_ir_workflow_support" CHIP = "540" END_BARCODE_KIT_NAME = "" LIBRARY_KIT_NAME = "Ion AmpliSeq Library Kit Plus" @@ -3041,19 +3414,17 @@ def add_or_update_immune_repertoire_clonality_s5_system_templates(): SEQ_KIT_NAME = "Ion S5 Sequencing Kit" TEMPLATE_KIT_NAME = "Ion Chef S540 V1" PLAN_STATUS = "planned" + FLOWS = 550 # the follow templates will be create with same settings. template_names = [ - "Oncomine BCR IGHKL-SR - DNA", - "Oncomine BCR IGH FR3-J RF1 Assay", - "Oncomine BCR IGH FR2-J RF2 Assay", + "Oncomine BCR Pan-Clonality Assay", + "Oncomine IGH FR3(d)-J Assay", + "Oncomine IGH FR2-J Assay", "Oncomine TCR Pan-Clonality Assay" ] for template_name in template_names: - FLOWS = 500 if template_name in ["Oncomine BCR IGHKL-SR - DNA", - "Oncomine TCR Pan-Clonality Assay"] else 550 - templateParams = TemplateParams(template_name, S5, "MIXED") templateParams.update( { @@ -3100,7 +3471,7 @@ def add_or_update_immune_repertoire_clonality_s5_system_templates(): def add_or_update_immune_repertoire_SHM_s5_system_templates(): APPLICATION_GROUP = "immune_repertoire" BARCODE_KIT_NAME = "Ion Dual Barcode Kit 1-96" - CATEGORIES = "onco_immune;immunology" + CATEGORIES = "onco_immune;immunology;multi_ir_workflow_support" CHIP = "530" END_BARCODE_KIT_NAME = "" FLOWS = 1100 @@ -3112,13 +3483,23 @@ def add_or_update_immune_repertoire_SHM_s5_system_templates(): TEMPLATE_KIT_NAME = "Ion Chef S530 V2" SAMPLE_PREP_PROTOCOL = "pcr400bp" PLAN_STATUS = "planned" + USABLE_SEQ_THRESHOLD = 30 # the follow templates will be create with same settings. template_names = [ "Oncomine BCR IGH FR1-J RF3 Assay", "Oncomine BCR IGHV SHM Leader-J Assay" ] + + # the follow templates will be create with same settings. + template_names = [ + "Oncomine IGH FR1-J Assay", + "Oncomine IGHV Leader-J Assay" + ] for template_name in template_names: + if template_name in "Oncomine IGHV Leader-J Assay": + LIBRARY_READ_LENGTH = 400 + USABLE_SEQ_THRESHOLD = 20 templateParams = TemplateParams(template_name, S5, "MIXED") templateParams.update( { @@ -3136,6 +3517,7 @@ def add_or_update_immune_repertoire_SHM_s5_system_templates(): "templatingKitName": TEMPLATE_KIT_NAME, "samplePrepProtocol": SAMPLE_PREP_PROTOCOL, "planStatus": PLAN_STATUS, + "usableSequenceThreshold": USABLE_SEQ_THRESHOLD, } ) sysTemplate, isCreated, isUpdated = add_or_update_sys_template(templateParams) @@ -3146,7 +3528,7 @@ def add_or_update_immune_repertoire_s5_system_templates(): APPLICATION_GROUP = "immune_repertoire" BARCODE_KIT_NAME = "Ion Select BC Set-1" BARCODE_KIT_NAME_DUAL = "Ion Dual Barcode Kit 1-96" - CATEGORIES = "onco_immune;immunology" + CATEGORIES = "onco_immune;immunology;multi_ir_workflow_support" CHIP = "530" FLOWS = 850 LIBRARY_KIT_NAME = "Ion AmpliSeq Library Kit Plus" @@ -3205,7 +3587,7 @@ def add_or_update_immune_repertoire_s5_system_templates(): def add_or_update_immune_repertoire_long_igh_s5_system_templates(): APPLICATION_GROUP = "immune_repertoire" BARCODE_KIT_NAME = "Ion Dual Barcode Kit 1-96" - CATEGORIES = "onco_immune;immunology" + CATEGORIES = "onco_immune;immunology;multi_ir_workflow_support" CHIP = "530" FLOWS = 1100 LIBRARY_KIT_NAME = "Ion AmpliSeq Library Kit Plus" @@ -3243,7 +3625,7 @@ def add_or_update_immune_repertoire_long_igh_s5_system_templates(): def add_or_update_immune_repertoire_pgm_system_templates(): APPLICATION_GROUP = "immune_repertoire" BARCODE_KIT_NAME = "Ion Select BC Set-1" - CATEGORIES = "onco_immune;immunology" + CATEGORIES = "onco_immune;immunology;multi_ir_workflow_support" CHIP = "318" FLOWS = 800 LIBRARY_KIT_NAME = "Ion AmpliSeq Library Kit Plus" @@ -3335,7 +3717,7 @@ def add_or_update_tagseq_cfdna_s5_550_chef_system_template(templateName): def add_or_update_immune_repertoire_short_s5_system_templates(): APPLICATION_GROUP = "immune_repertoire" BARCODE_KIT_NAME = "Ion Dual Barcode Kit 1-96" - CATEGORIES = "onco_immune;immunology" + CATEGORIES = "onco_immune;immunology;multi_ir_workflow_support" CHIP = "540" END_BARCODE_KIT_NAME = "" # TODO: replace with the real barcode kit FLOWS = 500 @@ -3373,7 +3755,7 @@ def add_or_update_immune_repertoire_short_s5_system_templates(): def add_or_update_immune_repertoire_short_igh_mouse_s5_system_templates(): APPLICATION_GROUP = "immune_repertoire" BARCODE_KIT_NAME = "Ion Dual Barcode Kit 1-96" - CATEGORIES = "onco_immune;immunology" + CATEGORIES = "onco_immune;immunology;multi_ir_workflow_support" CHIP = "540" END_BARCODE_KIT_NAME = "" # TODO: replace with the real barcode kit FLOWS = 500 @@ -3846,8 +4228,8 @@ def add_or_update_carrierseq_system_templates(): def add_or_update_oncomine_ocav4_550_system_templates(): # OCAv4 550 OCAV4_BARCODE_KIT_NAME = "IonXpress" - OCAV4_CATEGORIES = "Oncomine;onco_solidTumor;onco_immune;ocav4" - OCAV4_CATEGORIES_2 = "Oncomine;barcodes_8;onco_solidTumor;onco_immune;ocav4" + OCAV4_CATEGORIES = "Oncomine;onco_solidTumor;onco_immune;ocav4;tecParam" + OCAV4_CATEGORIES_2 = "Oncomine;barcodes_8;onco_solidTumor;onco_immune;ocav4;tecParam" OCAV4_CHIP_NAME = "550" OCAV4_FLOWS = 500 OCAV4_FUSION_LIB_KIT_NAME = "Ion AmpliSeq Library Kit Plus" @@ -3857,6 +4239,13 @@ def add_or_update_oncomine_ocav4_550_system_templates(): OCAV4_SEQ_KIT_NAME = "Ion S5 Sequencing Kit" OCAV4_TEMPLATE_KIT_NAME = "Ion Chef S550 V1" OCAV4_STATUS = "planned" + # PlaceHolder : Get below final values from R&D and update all OCA4(DNA, DNA&Fusion and Fusion only) templates + CHIP_TEC_DFLTAMBIENT = 0.0 + CHIP_TEC_SLOPE = 0.0 + CHIP_TEC_MINTHRESHOLD = 0.0 + MAN_TEC_DFLTAMBIENT = 26.90 + MAN_TEC_SLOPE = 1.47 + MAN_TEC_MINTHRESHOLD = 40 # pre-select plugins plugins = {} @@ -3879,6 +4268,12 @@ def add_or_update_oncomine_ocav4_550_system_templates(): "sequencekitname": OCAV4_SEQ_KIT_NAME, "templatingKitName": OCAV4_TEMPLATE_KIT_NAME, "planStatus": OCAV4_STATUS, + "chipTecDfltAmbient": CHIP_TEC_DFLTAMBIENT, + "chipTecSlope": CHIP_TEC_SLOPE, + "chipTecMinThreshold": CHIP_TEC_MINTHRESHOLD, + "manTecDfltAmbient": MAN_TEC_DFLTAMBIENT, + "manTecSlope": MAN_TEC_SLOPE, + "manTecMinThreshold": MAN_TEC_MINTHRESHOLD, } ) sysTemplate, isCreated, isUpdated = add_or_update_sys_template(templateParams) @@ -3902,6 +4297,12 @@ def add_or_update_oncomine_ocav4_550_system_templates(): "sequencekitname": OCAV4_SEQ_KIT_NAME, "templatingKitName": OCAV4_TEMPLATE_KIT_NAME, "planStatus": OCAV4_STATUS, + "chipTecDfltAmbient": CHIP_TEC_DFLTAMBIENT, + "chipTecSlope": CHIP_TEC_SLOPE, + "chipTecMinThreshold": CHIP_TEC_MINTHRESHOLD, + "manTecDfltAmbient": MAN_TEC_DFLTAMBIENT, + "manTecSlope": MAN_TEC_SLOPE, + "manTecMinThreshold": MAN_TEC_MINTHRESHOLD, } ) sysTemplate, isCreated, isUpdated = add_or_update_sys_template(templateParams) @@ -3925,11 +4326,55 @@ def add_or_update_oncomine_ocav4_550_system_templates(): "sequencekitname": OCAV4_SEQ_KIT_NAME, "templatingKitName": OCAV4_TEMPLATE_KIT_NAME, "planStatus": OCAV4_STATUS, + "chipTecDfltAmbient": CHIP_TEC_DFLTAMBIENT, + "chipTecSlope": CHIP_TEC_SLOPE, + "chipTecMinThreshold": CHIP_TEC_MINTHRESHOLD, + "manTecDfltAmbient": MAN_TEC_DFLTAMBIENT, + "manTecSlope": MAN_TEC_SLOPE, + "manTecMinThreshold": MAN_TEC_MINTHRESHOLD, } ) sysTemplate, isCreated, isUpdated = add_or_update_sys_template(templateParams) finish_sys_template(sysTemplate, isCreated, templateParams) +def add_or_update_hiv_drug_system_templates(): + HIV_DRUG_CHIP = "520" + HIV_DRUG_FLOWS = 850 + HIV_DRUG_REFERENCE = "HXB2" + HIV_DRUG_BARCODE = "IonCode" + HIV_DRUG_SEQ_KIT_NAME = "Ion S5 Sequencing Kit" + HIV_DRUG_TEMPLATE_KIT_NAME = "Ion Chef S530 V2" + HIV_DRUG_LIBRARY_KIT_NAME = "Ampliseq DNA V1" + HIV_DRUG_STATUS = "planned" + HIV_DRUG_BEDFILE = "WG00248.3.20170122.designed.bed" + + # pre-select plugins + plugins = {} + plugins["ARUPHIVGenotyper"] = _get_plugin_dict("ARUPHIVGenotyper") + plugins["coverageAnalysis"] = _get_plugin_dict("coverageAnalysis") + + templateParams = TemplateParams( + templateName="Ion Ampliseq HIV Drug Resistance Research Panel", instrument=S5, runType="AMPS" + ) + + templateParams.update( + { + "applicationGroup": "DNA", + "barcodeKitName": HIV_DRUG_BARCODE, + "categories": "", + "chipType": HIV_DRUG_CHIP, + "flows": HIV_DRUG_FLOWS, + "reference": HIV_DRUG_REFERENCE, + "targetRegionBedFile": HIV_DRUG_BEDFILE, + "sequencekitname": HIV_DRUG_SEQ_KIT_NAME, + "templatingKitName": HIV_DRUG_TEMPLATE_KIT_NAME, + "libraryKitName": HIV_DRUG_LIBRARY_KIT_NAME, + "planStatus": HIV_DRUG_STATUS, + } + ) + sysTemplate, isCreated, isUpdated = add_or_update_sys_template(templateParams) + finish_sys_template(sysTemplate, isCreated, templateParams, plugins) + def add_or_update_pan_bacteria_540_system_templates(): LIBRARY_READ_LENGTH = 150 @@ -4060,6 +4505,7 @@ def add_or_update_all_system_templates(): add_or_update_immune_repertoire_clonality_s5_system_templates() add_or_update_immune_repertoire_SHM_s5_system_templates() add_or_update_trilink_small_rna_system_templates() + add_or_update_hiv_drug_system_templates() except Exception: print(format_exc()) @@ -4153,7 +4599,14 @@ def clean_up_obsolete_templates(): "Ion Carrier Seq DNA - Ion S5 System", "Oncomine BCR IGH FR3-J Assay Reflex 1", "Oncomine BCR IGH FR2-J Assay Reflex 2", - "Oncomine BCR IGHV SHM FR1 - J Assay" + "Oncomine BCR IGHV SHM FR1 - J Assay", + "Oncomine BCR IGH FR1-J RF3 Assay", + "Oncomine BCR IGH FR2-J RF2 Assay", + "Oncomine BCR IGH FR3-J RF1 Assay", + "Oncomine BCR IGH FR3-J Assay", + "Oncomine BCR IGHV SHM Leader-J Assay", + "Oncomine BCR IGHV SHM FR1-J Assay", + "Oncomine BCR IGHKL-SR - DNA" ] templates = models.PlannedExperiment.objects.filter( @@ -4222,6 +4675,7 @@ def add_or_updateSystemTemplate_OffCycleRelease(**sysTemp): return status + def generate_offcycle_params(): """this is used to output template params and plugin config to be used in offcycle json""" @@ -4258,4 +4712,4 @@ def pre_select_plugins(application, pluginsList): add_or_update_all_system_templates() # delete system templates here... - clean_up_obsolete_templates() + clean_up_obsolete_templates() \ No newline at end of file diff --git a/dbReports/iondb/media/resources/scripts/plan/ionreporter_util.js b/dbReports/iondb/media/resources/scripts/plan/ionreporter_util.js index 93270350..63d67746 100644 --- a/dbReports/iondb/media/resources/scripts/plan/ionreporter_util.js +++ b/dbReports/iondb/media/resources/scripts/plan/ionreporter_util.js @@ -87,6 +87,13 @@ function get_workflow_url(start_url, account_id) { return myURL; } + // if ReproSeq, only use ApplicationType filtering + if (planCategories.toLowerCase() == "repro;multi_ir_workflow_support") { + myURL += build_ir_workflow_filters("ApplicationType", "Low-Coverage Whole Genome Sequencing", isFilterSet); + console.log("myURL: " + myURL); + return myURL; + } + // if Application Categories contains 'CarrierSeq' if (planCategories.toLowerCase().indexOf("carrierseq") != -1) { myURL += build_ir_workflow_filters("tag_CARRIERSEQ", "true", isFilterSet); diff --git a/dbReports/iondb/media/resources/scripts/plan/iru_get_user_input.js b/dbReports/iondb/media/resources/scripts/plan/iru_get_user_input.js index c326b49e..a60cc5e7 100644 --- a/dbReports/iondb/media/resources/scripts/plan/iru_get_user_input.js +++ b/dbReports/iondb/media/resources/scripts/plan/iru_get_user_input.js @@ -140,7 +140,7 @@ function getIonReporterColumns(){ var headerText = 'Ion Reporter Workflow ' - if (!($('[name=planCategories]').val() === 'onco_immune;immunology')){ + if (($('[name=planCategories]').val().indexOf("multi_ir_workflow_support") < 0)) { irWorkflowField = { field: "irWorkflow", title: "Ion Reporter Workflow", width: '350px', @@ -148,7 +148,7 @@ function getIonReporterColumns(){ editor: irWorkflowEditor, headerTemplate: headerText, template: dropDnTemplate({'html': $('#irWorkflowColumnTemplate').html()}), - hidden: ($('[name=planCategories]').val() === 'onco_immune;immunology') + hidden: ($('[name=planCategories]').val().indexOf("multi_ir_workflow_support") > 0) }; } else { irWorkflowField = { diff --git a/dbReports/iondb/media/resources/scripts/plan/page_plan_kits.js b/dbReports/iondb/media/resources/scripts/plan/page_plan_kits.js index dc055840..1fc32a57 100644 --- a/dbReports/iondb/media/resources/scripts/plan/page_plan_kits.js +++ b/dbReports/iondb/media/resources/scripts/plan/page_plan_kits.js @@ -11,12 +11,29 @@ $(document).ready(function () { // 8 - categorized applProduct for the application, target technique and categories var categorizedApplProductInUse = null; var isInit = true; + var lockAssayParams = $('input[name = "lockAssayParams"]').val().split(","); $("form").submit(function(){ $("select[name=barcodeId]").prop('disabled', false); $('.advanced').each(function(){ $(this).prop('disabled',false); }); + check_lock_assay_params(); }); + function check_lock_assay_params() { + if(lockAssayParams) { + $.each(lockAssayParams, function (i, val) { + if ($("#" + val).is("select")) { + $("select[id=" + val + "]").prop('disabled', false); + if (val.toLowerCase().indexOf("templatekit") >= 0) { + $("input[id=IonChef__templatekitType]").prop('disabled', false); + $("input[id=IA__templatekitType]").prop('disabled', false); + } + } else if ($("#" + val).is("input")) { + $("input[id=" + val + "]").prop('disabled', false); + } + }); + } + } function init_protocol_n_readLength_visibility() { var templateKit = templateKits[$("#templateKit").val()]; @@ -673,6 +690,9 @@ $(document).ready(function () { updateSummaryPanel("#selectedFlows", flowsSpinner.spinner("value")); }); } + if(lockAssayParams && lockAssayParams.indexOf("flows") !== -1) { + flowsSpinner.spinner("disable").prop('disabled',true); + } var readLengthSpinner = $("#libraryReadLength").spinner({min: 0, max: 1000}); @@ -707,6 +727,7 @@ $(document).ready(function () { update_TemplateKit_select(); update_SequencingKit_select(); } + set_default_flows_from_category_rules(); show_chiptype_warning($(this).val()); updateSummaryPanel("#selectedChipType", chipNameToDisplayName[$(this).val()]); diff --git a/dbReports/iondb/media/resources/scripts/plan/page_plan_sample_table.js b/dbReports/iondb/media/resources/scripts/plan/page_plan_sample_table.js index 3cae42a5..c895d6b7 100644 --- a/dbReports/iondb/media/resources/scripts/plan/page_plan_sample_table.js +++ b/dbReports/iondb/media/resources/scripts/plan/page_plan_sample_table.js @@ -497,6 +497,7 @@ $(document).ready(function () { if (planOpt.isPlanBySample){ toggleDisableElements($('[name=sampleDescription]'), true); toggleDisableElements($('[name=sampleExternalId]'), true); + toggleDisableElements($('[name=barcodeId]'), true); } // display validation errors diff --git a/dbReports/iondb/rundb/PlannedExperimentResource.py b/dbReports/iondb/rundb/PlannedExperimentResource.py index e2f2b058..521df284 100644 --- a/dbReports/iondb/rundb/PlannedExperimentResource.py +++ b/dbReports/iondb/rundb/PlannedExperimentResource.py @@ -1069,7 +1069,6 @@ def _copy_plan_bundle_from_obj(self, planObj): # modify data to create a new plan bundle.obj = None - bundle.data.pop("id") bundle.data.pop("experiment") bundle.data.pop("planGUID") bundle.data.pop("planShortID") @@ -1081,6 +1080,18 @@ def _copy_plan_bundle_from_obj(self, planObj): bundle.data["planExecuted"] = False bundle.data["isSystem"] = False bundle.data["isSystemDefault"] = False + # metaData is required for Dynamic Tech Param + metaData = { + "fromTemplate": bundle.data.get("planName"), + "fromTemplateId": bundle.data.pop("id"), + "fromTemplateCategories": bundle.data.get("categories"), + "fromTemplateChipType": bundle.data.get("chipType"), + "fromTemplateSequenceKitname": bundle.data.get("sequencekitname"), + "fromTemplateSource": "ION" + } + if bundle.data.get("metaData"): + metaData.update(bundle.data.get("metaData")) + bundle.data["metaData"] = metaData return bundle @@ -1271,6 +1282,17 @@ def dehydrate(self, bundle): sampleGrouping.displayedName if sampleGrouping else "" ) + # Chip and Manifold Tec Parameters from experiment + bundle.data["chipTecDfltAmbient"] = experiment.chipTecDfltAmbient + bundle.data["chipTecSlope"] = experiment.chipTecSlope + bundle.data["chipTecMinThreshold"] = experiment.chipTecMinThreshold + bundle.data["manTecDfltAmbient"] = experiment.manTecDfltAmbient + bundle.data["manTecSlope"] = experiment.manTecSlope + bundle.data["manTecMinThreshold"] = experiment.manTecMinThreshold + + bundle.data["metaData"] = experiment.metaData or {} + + # IonChef parameters from Experiment if experiment.chefInstrumentName: @@ -1360,9 +1382,11 @@ def hydrate_barcodedSamples(self, bundle): reference = barcode.get("reference") or bundle.data.get( "reference", "" ) + # this also handles the sse/svb bed files for target_or_hotspot in [ "targetRegionBedFile", "hotSpotRegionBedFile", + "sseBedFile" ]: bedfile = barcode.get(target_or_hotspot) if bedfile: @@ -1551,7 +1575,7 @@ def hydrate_regionfile(self, bundle): return bundle - def hydrate_sseBedfile(self, bundle): + def hydrate_sseBedFile(self, bundle): bedfile = bundle.data.get("sseBedFile") if bedfile: if bedfile.lower() == "none": @@ -2034,6 +2058,13 @@ def _get_barcodedSamples(samplesList, default_nuctype): barcodedSamples = data.get("barcodedSamples") or {} payload_samples_key = "barcodedSamples" default_nuctype = templateObj.get_default_nucleotideType() + isDynamicTecParamsModified, errMsg = plan_validator.get_dynamicTecParams(templateObj, data) + if isDynamicTecParamsModified: + raise SDKValidationError( + { + "Manifold Tec Params": errMsg + } + ) if data.get("samplesList"): if barcodedSamples: raise SDKValidationError( @@ -2158,6 +2189,14 @@ def _get_barcodedSamples(samplesList, default_nuctype): bundle.data["barcodedSamples"] = barcodedSamples + if templateObj.experiment.chipTecDfltAmbient or templateObj.experiment.manTecDfltAmbient: + bundle.data["chipTecDfltAmbient"] = templateObj.experiment.chipTecDfltAmbient + bundle.data["chipTecSlope"] = templateObj.experiment.chipTecSlope + bundle.data["chipTecMinThreshold"] = templateObj.experiment.chipTecMinThreshold + bundle.data["manTecDfltAmbient"] = templateObj.experiment.manTecDfltAmbient + bundle.data["manTecSlope"] = templateObj.experiment.manTecSlope + bundle.data["manTecMinThreshold"] = templateObj.experiment.manTecMinThreshold + # validate all fields and create the plan bundle = self.obj_create(bundle) return self.create_response( diff --git a/dbReports/iondb/rundb/admin.py b/dbReports/iondb/rundb/admin.py index 8e206948..446b97c9 100644 --- a/dbReports/iondb/rundb/admin.py +++ b/dbReports/iondb/rundb/admin.py @@ -1,6 +1,10 @@ # Copyright (C) 2010 Ion Torrent Systems, Inc. All Rights Reserved from __future__ import absolute_import +from django.contrib.auth.forms import UserChangeForm, AdminPasswordChangeForm +from django.contrib.auth.hashers import check_password +from iondb.rundb.login.forms import UserRegistrationForm +from iondb.rundb.login.password_validator import PasswordValidator from iondb.rundb.models import * from iondb.rundb import tasks from iondb.rundb import tsvm @@ -19,6 +23,7 @@ from django.contrib.admin.views.decorators import staff_member_required from django.contrib.sessions.models import Session from django.core.urlresolvers import reverse +from django.contrib.auth.admin import UserAdmin from django import http import httplib2 @@ -719,6 +724,10 @@ def exp_redo_from_scratch(request): ) return HttpResponseRedirect("/admin/rundb/experiment/") +@staff_member_required +def configure_account_admin(request): + return HttpResponseRedirect(reverse("configure_account")) + @staff_member_required def configure_server(request): @@ -1266,3 +1275,53 @@ class PlanSessionAdmin(admin.ModelAdmin): admin.site.register(PlanSession, PlanSessionAdmin) + + +class AdminPasswordChangeForm(AdminPasswordChangeForm): + def clean_password2(self): + password1 = self.cleaned_data.get('password1') + password2 = self.cleaned_data.get('password2') + if password1 and password2: + if password1 != password2: + raise forms.ValidationError( + self.error_messages['password_mismatch'], + code='password_mismatch', + ) + + if password2: + password_validator = PasswordValidator(password2) + exec_validation_methods = PasswordValidator.validation_methods + error_list = {} + for method in exec_validation_methods: + if 'username' in method: + username = str(self.user.username) + message = getattr(password_validator, method)(username) + else: + message = getattr(password_validator, method)() + + if isinstance(message, list): + error_list[method] = str(''.join(message)) + elif message is not None: + error_list[method] = message + if error_list: + raise forms.ValidationError(map(str, error_list.values())) + if check_password(password2, self.user.password): + raise forms.ValidationError('That password has already been used') + + return password2 + + +class CustomUserAdmin(UserAdmin): + form = UserChangeForm + add_form = UserRegistrationForm + change_password_form = AdminPasswordChangeForm + add_fieldsets = ( + (None, { + 'classes': ('wide',), + 'fields': ('username', 'email', 'password1', 'password2')} + ), + ) + + +admin.site.unregister(User) +admin.site.register(User, CustomUserAdmin) diff --git a/dbReports/iondb/rundb/api.py b/dbReports/iondb/rundb/api.py index 6182da11..1534a5b2 100755 --- a/dbReports/iondb/rundb/api.py +++ b/dbReports/iondb/rundb/api.py @@ -289,6 +289,8 @@ def post_activate(self, request, **kwargs): if user.userprofile and user.userprofile.needs_activation: user.userprofile.needs_activation = False user.userprofile.save() + msg = "New pending user registration for '{0}'".format(user.username) + models.Message.objects.filter(body__contains=msg).delete() return HttpAccepted() diff --git a/dbReports/iondb/rundb/barcodedata.py b/dbReports/iondb/rundb/barcodedata.py index c89d33fa..d773e3de 100644 --- a/dbReports/iondb/rundb/barcodedata.py +++ b/dbReports/iondb/rundb/barcodedata.py @@ -271,6 +271,15 @@ def createDnaBarcodeModel(read_group={}): end_sequence=end_sequence, end_adapter=end_adapter, ) + + def getBarcodeName(readGroupName): + # many times it seems that the readGroupId is a join between the results runid and barcodeName + # so they need to break this out and parse the readGroupId + if "." in readGroupName: + runid, barcodeName = readGroupName.split(".", 1) + else: + barcodeName = readGroupName + return barcodeName data = dict() reportFullPath = self.result.get_report_path() @@ -284,31 +293,33 @@ def createDnaBarcodeModel(read_group={}): for dataset in basecallerResults.get("datasets"): barcodeEntry = dict() readGroups = dataset["read_groups"] - # currently multiple read_groups on single barcode not supported - if len(readGroups) != 1: - logger.warn("Multiple read_groups on single barcode not supported") + + # Repeat Sequencing stores more than one read group in one dataset - iterate over read groups + if len(readGroups) == 0: + logger.warn("No read_groups found in dataset " + dataset.get("dataset_name", "")) continue - - readGroupId = readGroups[0] - - # many times it seems that the readGroupId is a join between the results runid and barcodeName - # so they need to break this out and parse the readGroupId - if "." in readGroupId: - runid, barcodeName = readGroupId.split(".", 1) - else: - barcodeName = readGroupId - + + barcodeName = getBarcodeName(readGroups[0]) if NO_MATCH in barcodeName: continue - - # since there should be one and only one read group, we can hard code the first element of the read groups - singleReadGroup = basecallerResults.get("read_groups")[readGroupId] - - barcodeEntry[REFERENCE] = self.eas.reference - barcodeEntry[FILTERED] = singleReadGroup.get(FILTERED, False) - # if this is a "filtered" barcode, then we will skip including it. - if barcodeEntry[FILTERED] and not include_filtered: + + # Infer filtered status & verify all read groups belong to the same barcode + is_filtered = True + same_barcode = True + for readGroupName in readGroups: + is_filtered = is_filtered and basecallerResults.get("read_groups")[readGroupName].get(FILTERED, False) + same_barcode = same_barcode and barcodeName == getBarcodeName(readGroupName) + + if not same_barcode: + logger.warn("Different barcodes in the same dataset are not supported") continue + + if is_filtered and not include_filtered: + continue + + barcodeEntry[FILTERED] = is_filtered + barcodeEntry[READ_COUNT] = dataset.get("read_count", 0) + firstReadGroup = basecallerResults.get("read_groups")[readGroups[0]] try: dnaBarcodeData = dnaBarcode.objects.get( @@ -320,7 +331,7 @@ def createDnaBarcodeModel(read_group={}): barcodeName=barcodeName, barcodeKit=self.eas.barcodeKitName ) ) - dnaBarcodeData = createDnaBarcodeModel(read_group=singleReadGroup) + dnaBarcodeData = createDnaBarcodeModel(read_group=firstReadGroup) if not dnaBarcodeData: logger.error( @@ -330,11 +341,10 @@ def createDnaBarcodeModel(read_group={}): ) continue + barcodeEntry[REFERENCE] = self.eas.reference barcodeEntry[BARCODE_ANNOTATION] = dnaBarcodeData.annotation barcodeEntry[BARCODE_TYPE] = dnaBarcodeData.type - barcodeEntry[READ_COUNT] = singleReadGroup[READ_COUNT] - barcodeEntry[BARCODE_SEQUENCE] = dnaBarcodeData.sequence barcodeEntry[BARCODE_ADAPTER] = dnaBarcodeData.adapter barcodeEntry[BARCODE_NAME] = barcodeName diff --git a/dbReports/iondb/rundb/configure/ampliseq_design_parser.py b/dbReports/iondb/rundb/configure/ampliseq_design_parser.py index 7a77414a..45d9a5e6 100644 --- a/dbReports/iondb/rundb/configure/ampliseq_design_parser.py +++ b/dbReports/iondb/rundb/configure/ampliseq_design_parser.py @@ -96,6 +96,23 @@ def ampliseq_concurrent_api_call(user, password, api_url): return get_ampliseq_designs(user, password, api_url) +def get_status_uploadHistoryLink(downloadObj): + uploadHistoryLink = None + status = None + if downloadObj: + try: + status = downloadObj.status + if "HTTP Error" not in status: + uploadHistoryLink = "/rundb/uploadstatus/{0}/".format( + downloadObj.id + ) + else: + uploadHistoryLink = "#" + except Exception as Err: + logger.error( + "Unknown error %s" % Err + ) # do not crash if any unknown issue + return status, uploadHistoryLink def get_ampliseq_designs(user, password, api_url): ctx = {} @@ -117,21 +134,10 @@ def get_ampliseq_designs(user, password, api_url): solution_id = solution["id"] configurationChoices = solution["configuration_choices"] sourceUrl = solution["resultsUri"] - uploadHistoryLink = None - status = None downloadObj = getASPanelImportStatus( "ordered", design["id"], solution_id, sourceUrl ) - if downloadObj: - try: - uploadHistoryLink = "/rundb/uploadstatus/{0}/".format( - downloadObj.id - ) - status = downloadObj.status - except Exception as Err: - logger.error( - "Unknown error %s" % Err - ) # do not crash if any unknown issue + status, uploadHistoryLink = get_status_uploadHistoryLink(downloadObj) if solution.get("ordered", False): panelType = template.get("panelType") or "on-demand" @@ -213,13 +219,9 @@ def get_fixed_designs_list(fixed_design_data): designID = design["id"] sourceUrl = design["resultsUri"] configurationChoices = design["configuration_choices"] - uploadHistoryLink = None - status = None downloadObj = getASPanelImportStatus("fixed", designID, sourceUrl=sourceUrl) + status, uploadHistoryLink = get_status_uploadHistoryLink(downloadObj) - if downloadObj: - uploadHistoryLink = "/rundb/uploadstatus/{0}/".format(downloadObj.id) - status = downloadObj.status tmpDict = {"id": designID, "configuration_choices": configurationChoices} description = design["description"] rec_app = None diff --git a/dbReports/iondb/rundb/configure/updateProducts.py b/dbReports/iondb/rundb/configure/updateProducts.py index 3825ea8d..3830ac52 100644 --- a/dbReports/iondb/rundb/configure/updateProducts.py +++ b/dbReports/iondb/rundb/configure/updateProducts.py @@ -51,6 +51,7 @@ "E010": "Duplicate product entry found ({0}). Check your product info.", "E011": "Invalid JSON file or response ({0}}", "E012": "Unknown system error: {0}", + "E013": "Invalid Product Update. Template Parameters({0}) for locking are required. Please consult Torrent Suite administrator" } PRODUCT_UPDATE_PATH_LOCAL = os.path.join( @@ -505,6 +506,8 @@ def update_product(name, update_version): if sysTemplatesToUpdate: logger.debug("Going to install system templates via off-cycle release") for sysTemp in sysTemplatesToUpdate: + if sysTemp.get("metaData"): + validate_sysTemp_metaData(monitor_pk, sysTemp) ctx_sys_temp_upd = add_or_updateSystemTemplate_OffCycleRelease(**sysTemp) if not ctx_sys_temp_upd["isValid"]: status = errorCode["E009"] @@ -514,6 +517,29 @@ def update_product(name, update_version): updateFileMonitor(monitor_pk, "Complete") +def validate_sysTemp_metaData(monitor_pk, sysTemplate): + lockAssayParams = sysTemplate.get("metaData").get("lockAssayParams") + err_msg = None + status = errorCode["E009"] + if lockAssayParams and ("runType" in lockAssayParams and "applicationGroupName" not in lockAssayParams) or \ + ("applicationGroupName" in lockAssayParams and "runType" not in lockAssayParams): + if monitor_pk: + updateFileMonitor(monitor_pk, status) + err_msg = errorCode["E013"].format("runType and applicationGroupName") + + if lockAssayParams and "chipType" in lockAssayParams and \ + ("runType" not in lockAssayParams or "applicationGroupName" not in lockAssayParams): + if monitor_pk: + updateFileMonitor(monitor_pk, status) + err_msg = errorCode["E013"].format("chipType, runType and applicationGroupName") + + if err_msg: + logger.debug( + "Error: iondb.rundb.configure.updateProducts.update_product %s", err_msg + ) + raise Exception(err_msg) + + return err_msg def validate_modelObject(modelsToUpdate): """validate incoming models to be updated or created @@ -891,6 +917,11 @@ def validate_productFile(productFile, fileName=None): raise Exception( "Missing product content, please consult Torrent Suite administrator." ) + if ("sys_template_info" in productFileContent + and productFileContent["sys_template_info"] + ): + for sysTemplate in productFileContent["sys_template_info"]: + validate_sysTemp_metaData(None, sysTemplate) if os.path.exists(destinationFilePath): existingProductData = json.loads(open(destinationFilePath).read()) diff --git a/dbReports/iondb/rundb/fixtures/systemtemplateparams/cerebro_mrd_mca_parameters.json b/dbReports/iondb/rundb/fixtures/systemtemplateparams/cerebro_mrd_mca_parameters.json new file mode 100644 index 00000000..05053340 --- /dev/null +++ b/dbReports/iondb/rundb/fixtures/systemtemplateparams/cerebro_mrd_mca_parameters.json @@ -0,0 +1,121 @@ +{ + "tvc_config": { + "freebayes": { + "allow_complex": 0, + "allow_indels": 1, + "allow_mnps": 1, + "allow_snps": 1, + "gen_min_alt_allele_freq": 0.0003, + "gen_min_coverage": 4, + "gen_min_indel_alt_allele_freq": 0.0004, + "min_cov_fraction": 0.9, + "min_mapping_qv": 4, + "read_max_mismatch_fraction": 1, + "read_mismatch_limit": 7, + "read_snp_limit": 10 + }, + "long_indel_assembler": {}, + "meta": { + "based_on": "ampliseq_hd_liquidbiopsy_parameters.json", + "built_in": "true", + "compatibility": { + "panel": "/rundb/api/v1/contentupload/xx", + "chip": [ + "530", + "540", + "550" + ], + "frequency": [ + "rare_somatic" + ], + "library": [ + "ampliseq_hd" + ], + "stringency": [ + "low" + ] + }, + "configuration": "cerebro_ampliseq_hd_cfdna", + "custom": true, + "name": "Cerebro 5.18 Panel -AmpliSeq HD for Oncomine Liquid Biopsy DNA - GeneStudio S5 phase 2", + "replaces": [ + "ampliseq_hd_cfdna" + ], + "repository_id": "", + "tooltip": "Parameters optimized for Cerebro and Microapotype Panel on 550 chips", + "tmapargs": "tmap mapall -g 0 ... --context stage1 map4", + "tvcargs": "tvc", + "unifyargs": "tvcutils unify_vcf --hotspot-positions-only off --filter-by-target on", + "ts_version": "5.18", + "user_selections": { + "chip": "550", + "frequency": "germline", + "library": "ampliseq", + "panel": "/rundb/api/v1/contentupload/xx/" + } + }, + "torrent_variant_caller": { + "data_quality_stringency": 20, + "downsample_to_coverage": 20000, + "error_motifs": "", + "fd_nonsnp_min_var_cov": 1, + "filter_deletion_predictions": 0.2, + "filter_insertion_predictions": 0.2, + "filter_unusual_predictions": 0.2, + "heavy_tailed": 3, + "hotspot_min_allele_freq": 0.0005, + "hotspot_min_cov_each_strand": 0, + "hotspot_min_coverage": 0, + "hotspot_min_var_coverage": 3, + "hotspot_min_variant_score": 3, + "hotspot_strand_bias": 0.65, + "hotspot_strand_bias_pval": 0, + "hp_del_len": [], + "hp_indel_hrun": [], + "hp_ins_len": [], + "hp_max_length": 5, + "indel_as_hpindel": 0, + "indel_func_size_offset": 0, + "indel_min_allele_freq": 0.0005, + "indel_min_cov_each_strand": 0, + "indel_min_coverage": 0, + "indel_min_var_coverage": 3, + "indel_min_variant_score": 10, + "indel_strand_bias": 0.65, + "indel_strand_bias_pval": 0, + "max_flows_to_test": 10, + "min_callable_prob": 0.95, + "min_fam_per_strand_cov": 0, + "min_ratio_for_fd": 0.1, + "min_tag_fam_size": 3, + "mnp_min_allele_freq": 0.0005, + "mnp_min_cov_each_strand": 0, + "mnp_min_coverage": 0, + "mnp_min_var_coverage": 3, + "mnp_min_variant_score": 6, + "mnp_strand_bias": 0.65, + "mnp_strand_bias_pval": 0, + "outlier_probability": 0.001, + "position_bias": 0.75, + "position_bias_pval": 0.05, + "position_bias_ref_fraction": 0.05, + "prediction_precision": 1, + "report_ppa": 0, + "snp_min_allele_freq": 0.0005, + "snp_min_cov_each_strand": 0, + "snp_min_coverage": 0, + "snp_min_var_coverage": 3, + "snp_min_variant_score": 6, + "snp_strand_bias": 0.65, + "snp_strand_bias_pval": 0, + "sse_prob_threshold": 1, + "suppress_called_allele_lod": 1, + "suppress_recalibration": 0, + "tag_sim_max_cov": 10, + "tag_trim_method": "sloppy-trim", + "try_few_restart_freq": 1, + "use_fd_param": 0, + "use_position_bias": 0 + } + } +} \ No newline at end of file diff --git a/dbReports/iondb/rundb/fixtures/systemtemplateparams/cerebro_mrd_parameters.json b/dbReports/iondb/rundb/fixtures/systemtemplateparams/cerebro_mrd_parameters.json new file mode 100644 index 00000000..c7749dbd --- /dev/null +++ b/dbReports/iondb/rundb/fixtures/systemtemplateparams/cerebro_mrd_parameters.json @@ -0,0 +1,119 @@ +{ + "freebayes": { + "allow_complex": 0, + "allow_indels": 1, + "allow_mnps": 1, + "allow_snps": 1, + "gen_min_alt_allele_freq": 0.0003, + "gen_min_coverage": 4, + "gen_min_indel_alt_allele_freq": 0.0004, + "min_cov_fraction": 0.9, + "min_mapping_qv": 4, + "read_max_mismatch_fraction": 1, + "read_mismatch_limit": 7, + "read_snp_limit": 10 + }, + "long_indel_assembler": {}, + "meta": { + "based_on": "ampliseq_hd_liquidbiopsy_parameters.json", + "built_in": "true", + "compatibility": { + "panel": "/rundb/api/v1/contentupload/xx", + "chip": [ + "530", + "540", + "550" + ], + "frequency": [ + "rare_somatic" + ], + "library": [ + "ampliseq_hd" + ], + "stringency": [ + "low" + ] + }, + "configuration": "cerebro_ampliseq_hd_cfdna", + "custom": true, + "name": "Cerebro 5.18 Panel -AmpliSeq HD for Oncomine Liquid Biopsy DNA - GeneStudio S5 phase 2", + "replaces": [ + "ampliseq_hd_cfdna" + ], + "repository_id": "", + "tooltip": "Parameters optimized for Cerebro and Microapotype Panel on 550 chips", + "tmapargs": "tmap mapall -g 0 ... --context stage1 map4", + "tvcargs": "tvc", + "unifyargs": "tvcutils unify_vcf --hotspot-positions-only off --filter-by-target on", + "ts_version": "5.18", + "user_selections": { + "chip": "550", + "frequency": "germline", + "library": "ampliseq", + "panel": "/rundb/api/v1/contentupload/xx/" + } + }, + "torrent_variant_caller": { + "data_quality_stringency": 20, + "downsample_to_coverage": 20000, + "error_motifs": "", + "fd_nonsnp_min_var_cov": 1, + "filter_deletion_predictions": 0.2, + "filter_insertion_predictions": 0.2, + "filter_unusual_predictions": 0.2, + "heavy_tailed": 3, + "hotspot_min_allele_freq": 0.0005, + "hotspot_min_cov_each_strand": 0, + "hotspot_min_coverage": 0, + "hotspot_min_var_coverage": 3, + "hotspot_min_variant_score": 3, + "hotspot_strand_bias": 0.65, + "hotspot_strand_bias_pval": 0, + "hp_del_len": [], + "hp_indel_hrun": [], + "hp_ins_len": [], + "hp_max_length": 5, + "indel_as_hpindel": 0, + "indel_func_size_offset": 0, + "indel_min_allele_freq": 0.0005, + "indel_min_cov_each_strand": 0, + "indel_min_coverage": 0, + "indel_min_var_coverage": 3, + "indel_min_variant_score": 10, + "indel_strand_bias": 0.65, + "indel_strand_bias_pval": 0, + "max_flows_to_test": 10, + "min_callable_prob": 0.95, + "min_fam_per_strand_cov": 0, + "min_ratio_for_fd": 0.1, + "min_tag_fam_size": 3, + "mnp_min_allele_freq": 0.0005, + "mnp_min_cov_each_strand": 0, + "mnp_min_coverage": 0, + "mnp_min_var_coverage": 3, + "mnp_min_variant_score": 6, + "mnp_strand_bias": 0.65, + "mnp_strand_bias_pval": 0, + "outlier_probability": 0.001, + "position_bias": 0.75, + "position_bias_pval": 0.05, + "position_bias_ref_fraction": 0.05, + "prediction_precision": 1, + "report_ppa": 0, + "snp_min_allele_freq": 0.0005, + "snp_min_cov_each_strand": 0, + "snp_min_coverage": 0, + "snp_min_var_coverage": 3, + "snp_min_variant_score": 6, + "snp_strand_bias": 0.65, + "snp_strand_bias_pval": 0, + "sse_prob_threshold": 1, + "suppress_called_allele_lod": 1, + "suppress_recalibration": 0, + "tag_sim_max_cov": 10, + "tag_trim_method": "sloppy-trim", + "try_few_restart_freq": 1, + "use_fd_param": 0, + "use_position_bias": 0 + } +} \ No newline at end of file diff --git a/dbReports/iondb/rundb/fixtures/ts_dbData.json b/dbReports/iondb/rundb/fixtures/ts_dbData.json index 8aeb14a8..745c9128 100644 --- a/dbReports/iondb/rundb/fixtures/ts_dbData.json +++ b/dbReports/iondb/rundb/fixtures/ts_dbData.json @@ -753,6 +753,91 @@ "sequencing_instrumentType": "", "uid": "APPCAT0026" } + }, + { + "pk": 27, + "model": "rundb.common_cv", + "fields": { + "cv_type": "applicationCategory", + "value": "multi_ir_workflow_support", + "displayedValue": "Multi IR Workflow Support", + "description": "Multi IR Workflow launch Support", + "isDefault": false, + "isActive": true, + "isVisible": false, + "categories": "AMPS;AMPS_RNA;AMPS_DNA_RNA;AMPS_HD_DNA;AMPS_HD_RNA;AMPS_HD_DNA_RNA;AMPS_HD_DNA_RNA_1", + "samplePrep_instrumentType": "", + "sequencing_instrumentType": "", + "uid": "APPCAT0027" + } + }, + { + "pk": 28, + "model": "rundb.common_cv", + "fields": { + "cv_type": "samplePrepProtocol", + "value": "cerebro_550", + "displayedValue": "MRD 550 Templating Script", + "description": "Use Ion Chef script protocol optimized for Cerebro 550", + "isDefault": true, + "isActive": true, + "categories": "cerebro_550_cycling", + "samplePrep_instrumentType": "IC", + "sequencing_instrumentType": "S5", + "uid": "CV0007" + } + }, + { + "pk": 29, + "model": "rundb.common_cv", + "fields": { + "cv_type": "libraryPrepProtocol", + "value": "myeloid_dl8_v2_qc", + "displayedValue": "Myeloid V2 QC", + "description": "Myeloid V2 QC Library Prep Protocol", + "isDefault": false, + "isActive": false, + "isVisible": false, + "categories": "myeloid", + "samplePrep_instrumentType": "", + "sequencing_instrumentType": "", + "uid": "CV0022" + } + }, + + { + "pk": 30, + "model": "rundb.common_cv", + "fields": { + "cv_type": "applicationCategory", + "value": "tecParam", + "displayedValue": "Dynamic Manifold Tec parameter support", + "description": "Dynamic Manifold Tec parameter support", + "isDefault": false, + "isActive": true, + "isVisible": false, + "categories": "AMPS;AMPS_RNA;AMPS_DNA_RNA;AMPS_HD_DNA;AMPS_HD_RNA;AMPS_HD_DNA_RNA;AMPS_HD_DNA_RNA_1", + "samplePrep_instrumentType": "", + "sequencing_instrumentType": "", + "uid": "APPCAT0028" + } + }, + { + "pk": 31, + "model": "rundb.common_cv", + "fields": { + "cv_type": "applicationCategory", + "value": "exome", + "displayedValue": "exome", + "description": "Ampliseq Exome Panels", + "isDefault": false, + "isActive": true, + "isVisible": false, + "categories": "AMPS;AMPS_RNA;AMPS_DNA_RNA;AMPS_HD_DNA;AMPS_HD_RNA;AMPS_HD_DNA_RNA;AMPS_HD_DNA_RNA_1;AMPS_EXOME", + "samplePrep_instrumentType": "", + "sequencing_instrumentType": "", + "uid": "APPCAT0029" + } }, { "pk": 1, diff --git a/dbReports/iondb/rundb/fixtures/ts_dbData_analysisargs.json b/dbReports/iondb/rundb/fixtures/ts_dbData_analysisargs.json index cd0db8fb..9e96f264 100644 --- a/dbReports/iondb/rundb/fixtures/ts_dbData_analysisargs.json +++ b/dbReports/iondb/rundb/fixtures/ts_dbData_analysisargs.json @@ -475,6 +475,8 @@ "chipType": "540", "sequenceKitName": "Ion S5 Sequencing Kit", "samplePrepKitName": "Ion AmpliSeq Exome Kit", + "applType": ["AMPS_EXOME"], + "applCategory" : "exome", "beadfindargs" : "justBeadFind --args-json /opt/ion/config/args_540_beadfind.json", "analysisargs" : "Analysis --args-json /opt/ion/config/args_540_analysis.json", "prebasecallerargs" : "BaseCaller --trim-qual-cutoff 15 --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --max-phasing-levels 2 --wells-normalization on", @@ -947,6 +949,7 @@ "applType": ["AMPS_EXOME"], "sequenceKitName": "", "samplePrepKitName": "", + "applCategory" : "exome", "beadfindargs" : "justBeadFind --args-json /opt/ion/config/args_530_beadfind.json", "analysisargs" : "Analysis --args-json /opt/ion/config/args_530_analysis.json", "prebasecallerargs" : "BaseCaller --trim-qual-cutoff 15 --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --wells-normalization on", @@ -1034,6 +1037,7 @@ "applType": ["AMPS_EXOME"], "sequenceKitName": "", "samplePrepKitName": "", + "applCategory" : "exome", "beadfindargs" : "justBeadFind --args-json /opt/ion/config/args_540_beadfind.json", "analysisargs" : "Analysis --args-json /opt/ion/config/args_540_analysis.json", "prebasecallerargs" : "BaseCaller --trim-qual-cutoff 15 --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --max-phasing-levels 2 --wells-normalization on", @@ -2076,6 +2080,8 @@ "chipType": "550", "sequenceKitName": "Ion S5 Sequencing Kit", "samplePrepKitName": "Ion AmpliSeq Exome Kit", + "applType": ["AMPS_EXOME"], + "applCategory" : "exome", "beadfindargs" : "justBeadFind --args-json /opt/ion/config/args_550_beadfind.json", "analysisargs" : "Analysis --args-json /opt/ion/config/args_550_analysis.json", "prebasecallerargs" : "BaseCaller --trim-qual-cutoff 15 --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --max-phasing-levels 2", @@ -2628,14 +2634,14 @@ "prebasecallerargs" : "BaseCaller --trim-qual-cutoff 15 --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --wells-normalization on", "calibrateargs" : "Calibration --num-calibration-regions 1,1", "basecallerargs" : "BaseCaller --trim-qual-cutoff 15 --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --num-unfiltered 1000 --barcode-filter-postpone 1 --qual-filter true --qual-filter-slope 0.040 --qual-filter-offset 1.0 --wells-normalization on --end-barcodes off", - "alignmentargs" : "tmap mapall -q 50000 ... stage1 map4", + "alignmentargs" : "tmap mapall -q 5000 ... stage1 map4", "ionstatsargs" : "ionstats alignment", "thumbnailbeadfindargs" : "justBeadFind --args-json /opt/ion/config/args_530_beadfind.json --thumbnail true", "thumbnailanalysisargs" : "Analysis --args-json /opt/ion/config/args_530_analysis.json --thumbnail true", "prethumbnailbasecallerargs" : "BaseCaller --trim-qual-cutoff 15 --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --wells-normalization on", "thumbnailcalibrateargs" : "Calibration", "thumbnailbasecallerargs" : "BaseCaller --trim-qual-cutoff 15 --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --qual-filter true --qual-filter-slope 0.040 --qual-filter-offset 1.0 --wells-normalization on --end-barcodes off", - "thumbnailalignmentargs" : "tmap mapall -q 50000 ... stage1 map4", + "thumbnailalignmentargs" : "tmap mapall -q 5000 ... stage1 map4", "thumbnailionstatsargs" : "ionstats alignment" } }, @@ -2655,14 +2661,14 @@ "prebasecallerargs" : "BaseCaller --trim-qual-cutoff 15 --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --max-phasing-levels 2 --wells-normalization on", "calibrateargs" : "Calibration", "basecallerargs" : "BaseCaller --trim-qual-cutoff 15 --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --max-phasing-levels 2 --num-unfiltered 1000 --barcode-filter-postpone 1 --wells-normalization on --end-barcodes off", - "alignmentargs" : "tmap mapall -q 50000 ... stage1 map4", + "alignmentargs" : "tmap mapall -q 5000 ... stage1 map4", "ionstatsargs" : "ionstats alignment", "thumbnailbeadfindargs" : "justBeadFind --args-json /opt/ion/config/args_540_beadfind.json --thumbnail true", "thumbnailanalysisargs" : "Analysis --args-json /opt/ion/config/args_540_analysis.json --thumbnail true", "prethumbnailbasecallerargs" : "BaseCaller --trim-qual-cutoff 15 --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --wells-normalization on", "thumbnailcalibrateargs" : "Calibration", "thumbnailbasecallerargs" : "BaseCaller --trim-qual-cutoff 15 --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --wells-normalization on --end-barcodes off", - "thumbnailalignmentargs" : "tmap mapall -q 50000 ... stage1 map4", + "thumbnailalignmentargs" : "tmap mapall -q 5000 ... stage1 map4", "thumbnailionstatsargs" : "ionstats alignment" } }, @@ -2920,14 +2926,14 @@ "analysisargs" : "Analysis --args-json /opt/ion/config/args_520_analysis.json", "prebasecallerargs" : "BaseCaller --trim-qual-cutoff 15 --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --wells-normalization on", "calibrateargs" : "Calibration --num-calibration-regions 1,1", - "basecallerargs" : "BaseCaller --trim-qual-cutoff 15 --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --num-unfiltered 1000 --barcode-filter-postpone 1 --qual-filter true --qual-filter-slope 0.040 --qual-filter-offset 1.0 --wells-normalization on --extra-trim-left 16", + "basecallerargs" : "BaseCaller --trim-qual-cutoff 15 --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --num-unfiltered 1000 --barcode-filter-postpone 1 --qual-filter true --qual-filter-slope 0.040 --qual-filter-offset 1.0 --wells-normalization on --extra-trim-left 16 --min-read-length 8", "alignmentargs" : "tmap mapall ... stage1 map4", "ionstatsargs" : "ionstats alignment", "thumbnailbeadfindargs" : "justBeadFind --args-json /opt/ion/config/args_520_beadfind.json --thumbnail true", "thumbnailanalysisargs" : "Analysis --args-json /opt/ion/config/args_520_analysis.json --thumbnail true", "prethumbnailbasecallerargs" : "BaseCaller --trim-qual-cutoff 15 --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --wells-normalization on", "thumbnailcalibrateargs" : "Calibration", - "thumbnailbasecallerargs" : "BaseCaller --trim-qual-cutoff 15 --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --qual-filter true --qual-filter-slope 0.040 --qual-filter-offset 1.0 --wells-normalization on --extra-trim-left 16", + "thumbnailbasecallerargs" : "BaseCaller --trim-qual-cutoff 15 --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --qual-filter true --qual-filter-slope 0.040 --qual-filter-offset 1.0 --wells-normalization on --extra-trim-left 16 --min-read-length 8", "thumbnailalignmentargs" : "tmap mapall ... stage1 map4", "thumbnailionstatsargs" : "ionstats alignment" } @@ -2950,14 +2956,14 @@ "analysisargs" : "Analysis --args-json /opt/ion/config/args_520_analysis.json", "prebasecallerargs" : "BaseCaller --trim-qual-cutoff 15 --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --wells-normalization on", "calibrateargs" : "Calibration --num-calibration-regions 1,1", - "basecallerargs" : "BaseCaller --trim-qual-cutoff 15 --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --num-unfiltered 1000 --barcode-filter-postpone 1 --qual-filter true --qual-filter-slope 0.040 --qual-filter-offset 1.0 --wells-normalization on --extra-trim-left 16", + "basecallerargs" : "BaseCaller --trim-qual-cutoff 15 --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --num-unfiltered 1000 --barcode-filter-postpone 1 --qual-filter true --qual-filter-slope 0.040 --qual-filter-offset 1.0 --wells-normalization on --extra-trim-left 16 --min-read-length 8", "alignmentargs" : "tmap mapall ... stage1 map4", "ionstatsargs" : "ionstats alignment", "thumbnailbeadfindargs" : "justBeadFind --args-json /opt/ion/config/args_520_beadfind.json --thumbnail true", "thumbnailanalysisargs" : "Analysis --args-json /opt/ion/config/args_520_analysis.json --thumbnail true", "prethumbnailbasecallerargs" : "BaseCaller --trim-qual-cutoff 15 --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --wells-normalization on", "thumbnailcalibrateargs" : "Calibration", - "thumbnailbasecallerargs" : "BaseCaller --trim-qual-cutoff 15 --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --qual-filter true --qual-filter-slope 0.040 --qual-filter-offset 1.0 --wells-normalization on --extra-trim-left 16", + "thumbnailbasecallerargs" : "BaseCaller --trim-qual-cutoff 15 --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --qual-filter true --qual-filter-slope 0.040 --qual-filter-offset 1.0 --wells-normalization on --extra-trim-left 16 --min-read-length 8", "thumbnailalignmentargs" : "tmap mapall ... stage1 map4", "thumbnailionstatsargs" : "ionstats alignment" } @@ -2980,14 +2986,14 @@ "analysisargs" : "Analysis --args-json /opt/ion/config/args_530_analysis.json", "prebasecallerargs" : "BaseCaller --trim-qual-cutoff 15 --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --wells-normalization on", "calibrateargs" : "Calibration --num-calibration-regions 1,1", - "basecallerargs" : "BaseCaller --trim-qual-cutoff 15 --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --num-unfiltered 1000 --barcode-filter-postpone 1 --qual-filter true --qual-filter-slope 0.040 --qual-filter-offset 1.0 --wells-normalization on --extra-trim-left 16", + "basecallerargs" : "BaseCaller --trim-qual-cutoff 15 --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --num-unfiltered 1000 --barcode-filter-postpone 1 --qual-filter true --qual-filter-slope 0.040 --qual-filter-offset 1.0 --wells-normalization on --extra-trim-left 16 --min-read-length 8", "alignmentargs" : "tmap mapall -q 50000 ... stage1 map4", "ionstatsargs" : "ionstats alignment", "thumbnailbeadfindargs" : "justBeadFind --args-json /opt/ion/config/args_530_beadfind.json --thumbnail true", "thumbnailanalysisargs" : "Analysis --args-json /opt/ion/config/args_530_analysis.json --thumbnail true", "prethumbnailbasecallerargs" : "BaseCaller --trim-qual-cutoff 15 --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --wells-normalization on", "thumbnailcalibrateargs" : "Calibration", - "thumbnailbasecallerargs" : "BaseCaller --trim-qual-cutoff 15 --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --qual-filter true --qual-filter-slope 0.040 --qual-filter-offset 1.0 --wells-normalization on --extra-trim-left 16", + "thumbnailbasecallerargs" : "BaseCaller --trim-qual-cutoff 15 --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --qual-filter true --qual-filter-slope 0.040 --qual-filter-offset 1.0 --wells-normalization on --extra-trim-left 16 --min-read-length 8", "thumbnailalignmentargs" : "tmap mapall -q 50000 ... stage1 map4", "thumbnailionstatsargs" : "ionstats alignment" } @@ -3010,14 +3016,14 @@ "analysisargs" : "Analysis --args-json /opt/ion/config/args_540_analysis.json", "prebasecallerargs" : "BaseCaller --trim-qual-cutoff 15 --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --max-phasing-levels 2 --wells-normalization on", "calibrateargs" : "Calibration", - "basecallerargs" : "BaseCaller --trim-qual-cutoff 15 --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --max-phasing-levels 2 --num-unfiltered 1000 --barcode-filter-postpone 1 --wells-normalization on --extra-trim-left 16", + "basecallerargs" : "BaseCaller --trim-qual-cutoff 15 --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --max-phasing-levels 2 --num-unfiltered 1000 --barcode-filter-postpone 1 --wells-normalization on --extra-trim-left 16 --min-read-length 8", "alignmentargs" : "tmap mapall -q 50000 ... stage1 map4", "ionstatsargs" : "ionstats alignment", "thumbnailbeadfindargs" : "justBeadFind --args-json /opt/ion/config/args_540_beadfind.json --thumbnail true", "thumbnailanalysisargs" : "Analysis --args-json /opt/ion/config/args_540_analysis.json --thumbnail true", "prethumbnailbasecallerargs" : "BaseCaller --trim-qual-cutoff 15 --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --wells-normalization on", "thumbnailcalibrateargs" : "Calibration", - "thumbnailbasecallerargs" : "BaseCaller --trim-qual-cutoff 15 --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --wells-normalization on --extra-trim-left 16", + "thumbnailbasecallerargs" : "BaseCaller --trim-qual-cutoff 15 --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --wells-normalization on --extra-trim-left 16 --min-read-length 8", "thumbnailalignmentargs" : "tmap mapall -q 50000 ... stage1 map4", "thumbnailionstatsargs" : "ionstats alignment" } @@ -3038,14 +3044,14 @@ "analysisargs" : "Analysis --args-json /opt/ion/config/args_550_analysis.json", "prebasecallerargs" : "BaseCaller --trim-qual-cutoff 15 --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --max-phasing-levels 2", "calibrateargs" : "Calibration", - "basecallerargs" : "BaseCaller --trim-qual-cutoff 15 --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --max-phasing-levels 2 --num-unfiltered 1000 --barcode-filter-postpone 1 --extra-trim-left 16", + "basecallerargs" : "BaseCaller --trim-qual-cutoff 15 --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --max-phasing-levels 2 --num-unfiltered 1000 --barcode-filter-postpone 1 --extra-trim-left 16 --min-read-length 8", "alignmentargs" : "tmap mapall ... stage1 map4", "ionstatsargs" : "ionstats alignment", "thumbnailbeadfindargs" : "justBeadFind --args-json /opt/ion/config/args_550_beadfind.json --thumbnail true", "thumbnailanalysisargs" : "Analysis --args-json /opt/ion/config/args_550_analysis.json --thumbnail true", "prethumbnailbasecallerargs" : "BaseCaller --trim-qual-cutoff 15 --barcode-filter-minreads 10 --phasing-residual-filter=2.0", "thumbnailcalibrateargs" : "Calibration", - "thumbnailbasecallerargs" : "BaseCaller --trim-qual-cutoff 15 --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --extra-trim-left 16", + "thumbnailbasecallerargs" : "BaseCaller --trim-qual-cutoff 15 --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --extra-trim-left 16 --min-read-length 8", "thumbnailalignmentargs" : "tmap mapall ... stage1 map4", "thumbnailionstatsargs" : "ionstats alignment" } diff --git a/dbReports/iondb/rundb/fixtures/ts_dbData_chips_kits.json b/dbReports/iondb/rundb/fixtures/ts_dbData_chips_kits.json index 778c1f58..dea031fb 100644 --- a/dbReports/iondb/rundb/fixtures/ts_dbData_chips_kits.json +++ b/dbReports/iondb/rundb/fixtures/ts_dbData_chips_kits.json @@ -2197,7 +2197,7 @@ "samplePrep_instrumentType" : "IC", "isActive": true, "description": "Ion 550 Kit-Chef", - "categories" : "s5v1Kit;", + "categories" : "s5v1Kit;samplePrepProtocol;cerebro_550_cycling", "defaultCartridgeUsageCount" : 2, "cartridgeExpirationDayLimit" : 8, "cartridgeBetweenUsageAbsoluteMaxDayLimit" : 30, diff --git a/dbReports/iondb/rundb/forms.py b/dbReports/iondb/rundb/forms.py index 5500621b..e1e2a6bf 100644 --- a/dbReports/iondb/rundb/forms.py +++ b/dbReports/iondb/rundb/forms.py @@ -10,6 +10,8 @@ from django.forms.widgets import PasswordInput from django import shortcuts from iondb.rundb.login.forms import UserRegistrationForm +from iondb.rundb.login.password_validator import PasswordValidator +from django.contrib.auth.hashers import check_password from iondb.rundb import models, labels import datetime @@ -554,7 +556,9 @@ def save(self, *args, **kw): password = self.cleaned_data.get("password", "") if password: self.instance.user.set_password(password) - + self.instance.is_password_valid = True + self.instance.last_password_changed_on = datetime.datetime.utcnow() + self.instance.save() self.instance.user.save() def clean_password_confirm(self): @@ -563,10 +567,29 @@ def clean_password_confirm(self): password2 = str(self.cleaned_data.get("password_confirm")) if password1: + passwordValidator = PasswordValidator(password1) + exec_validation_methods = PasswordValidator.validation_methods + error_list = {} + for method in exec_validation_methods: + if 'username' in method: + username = str(self.instance.user.username) + message = getattr(passwordValidator, method)(username) + else: + message = getattr(passwordValidator, method)() + if isinstance(message, list): + error_list[method] = str(''.join(message)) + elif message is not None: + error_list[method] = message + if error_list: + raise forms.ValidationError(',
          '.join( + map(str, error_list.values()))) if not password2: raise forms.ValidationError("You must confirm your password") if password1 != password2: raise forms.ValidationError("Your passwords do not match") + if check_password(password2, self.instance.user.password): + raise forms.ValidationError('That password has already been used') + return password2 class Meta: @@ -746,10 +769,13 @@ def static_ip(address, subnet, gateway, nameserver=None, search=None): cmd += ["--nameserver", nameserver] if search: cmd += ["--search", search] - proc = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE) - stdout, stderr = proc.communicate() - if stderr: - logger.warning("Network error: %s" % stderr) + try: + proc = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE) + stdout, stderr = proc.communicate() + if stderr: + logger.warning("Network error: %s" % stderr) + except Exception as Err: + logger.error(Err) network_settings = self.get_network_settings() host_config = ["mode", "address", "subnet", "gateway"] diff --git a/dbReports/iondb/rundb/home/views.py b/dbReports/iondb/rundb/home/views.py index c85f3749..2f2689a5 100644 --- a/dbReports/iondb/rundb/home/views.py +++ b/dbReports/iondb/rundb/home/views.py @@ -29,7 +29,7 @@ Cruncher, DMFileStat, NewsPost, - GlobalConfig, + GlobalConfig, UserProfile, ) from iondb.utils import devices from iondb.utils.files import get_disk_attributes_gb, is_mounted @@ -149,6 +149,18 @@ def format_date(date): else: return date +def showPasswordWarningMsg(request): + username = request.user.username + user_profile = UserProfile.objects.filter(user__username__in=[username]) + last_updated = user_profile[0].last_password_changed_on + pwd_max_age = GlobalConfig.objects.get().password_max_age + duration = datetime.datetime.utcnow().date() - last_updated.date() + + if duration.days > pwd_max_age or not user_profile[0].is_password_valid: + return "Strongly recommended to change your password" + + return None + def showDeprecationMsg(): try: majorPlatform = GlobalConfig.get().majorPlatform @@ -256,6 +268,7 @@ def dashboard_fragments(request, skip_runs=False): "ts_version": TS_version, "update_status": update_status, "showDeprecationMsg": showDeprecationMsg(), + "showPasswordWarningMsg": showPasswordWarningMsg(request), "instruments": { "connected": instr_connected, "offline": instr_offline, diff --git a/dbReports/iondb/rundb/login/forms.py b/dbReports/iondb/rundb/login/forms.py index 345fe334..2bd15575 100644 --- a/dbReports/iondb/rundb/login/forms.py +++ b/dbReports/iondb/rundb/login/forms.py @@ -5,6 +5,7 @@ from django.utils.translation import ugettext_lazy as _ from django.contrib.auth.models import User as AuthUser from iondb.rundb import labels +from iondb.rundb.login.password_validator import PasswordValidator class UserRegistrationForm( @@ -17,7 +18,9 @@ class UserRegistrationForm( requires the password to be entered twice to catch typos. """ - + password1 = forms.CharField(label=_("Password"), + widget=forms.PasswordInput, + help_text=_("The password must contain at least a uppercase letter, a digit, special chars(.,@#$%^&*()_-+!;) and minimum 10 characters.")) email = forms.EmailField( widget=forms.TextInput(attrs={"maxlength": 75}), label=labels.User.email.verbose_name, @@ -32,11 +35,32 @@ def __init__(self, *args, **kwargs): def save(self, commit=True): user = super(UserRegistrationForm, self).save(commit=False) - user.set_email(self.cleaned_data["email"]) + user.email = self.cleaned_data["email"] if commit: user.save() return user + def clean_password2(self): + password2 = str(self.cleaned_data.get("password2")) + if password2: + passwordValidator = PasswordValidator(password2) + exec_validation_methods = PasswordValidator.validation_methods + error_list = {} + for method in exec_validation_methods: + if 'username' in method: + username = str(self.cleaned_data.get("username")) + message = getattr(passwordValidator, method)(username) + else: + message = getattr(passwordValidator, method)() + + if isinstance(message, list): + error_list[method] = str(''.join(message)) + elif message is not None: + error_list[method] = message + if error_list: + raise forms.ValidationError(map(str, error_list.values())) + + return password2 class AuthenticationRememberMeForm(AuthenticationForm): @@ -48,4 +72,4 @@ class AuthenticationRememberMeForm(AuthenticationForm): remember_me = forms.BooleanField( label=_("Remember Me"), initial=False, required=False - ) + ) \ No newline at end of file diff --git a/dbReports/iondb/rundb/login/password_validator.py b/dbReports/iondb/rundb/login/password_validator.py new file mode 100644 index 00000000..4771a75e --- /dev/null +++ b/dbReports/iondb/rundb/login/password_validator.py @@ -0,0 +1,91 @@ +import re +from django.forms import ValidationError +from django.utils.translation import ugettext_lazy as _ +from iondb.rundb.models import Rig +from iondb.utils.utils import get_instrument_info + +class PasswordValidator: + validation_methods = ["symbol", "number", "uppercase", "lowercase", "minLength", "blank", + "username", "checkInstrumentName", "sameCharacters", "instrumentSupportedSymbol"] + def __init__(self, password, min_length=10): + self.min_length = min_length + self.password = password + + def minLength(self): + if len(self.password) < self.min_length: + return ValidationError( + _("This password must contain at least %(min_length)d characters."), + code='password_too_short', + params={'min_length': self.min_length}, + ).messages + + def number(self): + if not re.findall('\d', self.password): + return ValidationError( + _("The password must contain at least 1 digit, 0-9."), + code='password_no_number', + ).messages + + def checkInstrumentName(self): + rigs = Rig.objects.exclude(host_address="") + + if len(rigs) > 0: + instruments = [get_instrument_info(rig) for rig in rigs] + for inst in instruments: + if inst['name'].lower() in self.password.lower() or inst['serial'] in self.password.lower(): + return ValidationError( + _("The password must not contain the instrument name or serial no."), + code='password_no_rig_name_serial', + ).messages + + def sameCharacters(self): + regex = "([a-zA-Z0-9.,@#$%^&*()_\-+!;])\\1\\1+" + p = re.compile(regex) + if (re.search(p, self.password)): + return ValidationError( + _("The password should not contain repeated characters, Ex:aaa,###. Choose different password"), + code='password_no_sameChars', + ).messages + + def uppercase(self): + if not re.findall('[A-Z]', self.password): + return ValidationError( + _("The password must contain at least 1 uppercase letter, A-Z."), + code='password_no_upper', + ).messages + + def lowercase(self): + if not re.findall('[a-z]', self.password): + return ValidationError( + _("The password must contain at least 1 lowercase letter, a-z."), + code='password_no_lower', + ).messages + + def symbol(self): + if not re.findall('[.,@#$%^&*()_\-+!;]', self.password): + return ValidationError( + _("The password must contain at least 1 symbol: .,@#$%^&*()_-+!;"), + code='password_no_symbol', + ).messages + + def blank(self): + if re.search('\s', self.password): + return ValidationError( + _("The password must not contain blank space"), + code='password_no_blank', + ).messages + + def username(self, username): + if username.lower() in self.password.lower(): + return ValidationError( + _("The password must not contain the username"), + code='password_no_username', + ).messages + + def instrumentSupportedSymbol(self): + supported_symbols = ".,@#$%^&*()_-+!;" + if [e for e in self.password if not e.isalnum() and e not in supported_symbols]: + return ValidationError( + _("The password must contain only these symbols supported by the Instruments: .,@#$%^&*()_-+!;"), + code='password_invalid_symbol', + ).messages \ No newline at end of file diff --git a/dbReports/iondb/rundb/login/views.py b/dbReports/iondb/rundb/login/views.py index 2d3b569a..083a6ea8 100644 --- a/dbReports/iondb/rundb/login/views.py +++ b/dbReports/iondb/rundb/login/views.py @@ -2,6 +2,7 @@ import json import urlparse +import datetime from django.contrib.auth import REDIRECT_FIELD_NAME, login as auth_login from django.contrib.sites.models import get_current_site from django import shortcuts, template @@ -15,7 +16,6 @@ from iondb.rundb.login.forms import UserRegistrationForm, AuthenticationRememberMeForm from iondb.rundb.models import Message - from iondb.rundb.plan.views import reset_page_plan_session from iondb.rundb.sample.views import clear_samplesetitem_session @@ -164,6 +164,8 @@ def registration(request): # update UserProfile to indicate this account needs activation new_user.userprofile.needs_activation = True + new_user.userprofile.is_password_valid = True + new_user.userprofile.last_password_changed_on = datetime.datetime.utcnow() new_user.userprofile.save() # Send global message notifying of pending registration diff --git a/dbReports/iondb/rundb/migrations/0368_auto__add_field_experiment_chipTecDfltAmbient__add_field_experiment_ch.py b/dbReports/iondb/rundb/migrations/0368_auto__add_field_experiment_chipTecDfltAmbient__add_field_experiment_ch.py new file mode 100644 index 00000000..73f4e9d5 --- /dev/null +++ b/dbReports/iondb/rundb/migrations/0368_auto__add_field_experiment_chipTecDfltAmbient__add_field_experiment_ch.py @@ -0,0 +1,1241 @@ +# -*- coding: utf-8 -*- +from south.utils import datetime_utils as datetime +from south.db import db +from south.v2 import SchemaMigration +from django.db import models + + +class Migration(SchemaMigration): + + def forwards(self, orm): + # Adding field 'Experiment.chipTecDfltAmbient' + db.add_column(u'rundb_experiment', 'chipTecDfltAmbient', + self.gf('django.db.models.fields.FloatField')(default=None, null=True, blank=True), + keep_default=False) + + # Adding field 'Experiment.chipTecSlope' + db.add_column(u'rundb_experiment', 'chipTecSlope', + self.gf('django.db.models.fields.FloatField')(default=None, null=True, blank=True), + keep_default=False) + + # Adding field 'Experiment.chipTecMinThreshold' + db.add_column(u'rundb_experiment', 'chipTecMinThreshold', + self.gf('django.db.models.fields.FloatField')(default=None, null=True, blank=True), + keep_default=False) + + # Adding field 'Experiment.manTecDfltAmbient' + db.add_column(u'rundb_experiment', 'manTecDfltAmbient', + self.gf('django.db.models.fields.FloatField')(default=None, null=True, blank=True), + keep_default=False) + + # Adding field 'Experiment.manTecSlope' + db.add_column(u'rundb_experiment', 'manTecSlope', + self.gf('django.db.models.fields.FloatField')(default=None, null=True, blank=True), + keep_default=False) + + # Adding field 'Experiment.manTecMinThreshold' + db.add_column(u'rundb_experiment', 'manTecMinThreshold', + self.gf('django.db.models.fields.FloatField')(default=None, null=True, blank=True), + keep_default=False) + + + def backwards(self, orm): + # Deleting field 'Experiment.chipTecDfltAmbient' + db.delete_column(u'rundb_experiment', 'chipTecDfltAmbient') + + # Deleting field 'Experiment.chipTecSlope' + db.delete_column(u'rundb_experiment', 'chipTecSlope') + + # Deleting field 'Experiment.chipTecMinThreshold' + db.delete_column(u'rundb_experiment', 'chipTecMinThreshold') + + # Deleting field 'Experiment.manTecDfltAmbient' + db.delete_column(u'rundb_experiment', 'manTecDfltAmbient') + + # Deleting field 'Experiment.manTecSlope' + db.delete_column(u'rundb_experiment', 'manTecSlope') + + # Deleting field 'Experiment.manTecMinThreshold' + db.delete_column(u'rundb_experiment', 'manTecMinThreshold') + + + models = { + u'auth.group': { + 'Meta': {'object_name': 'Group'}, + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '80'}), + 'permissions': ('django.db.models.fields.related.ManyToManyField', [], {'to': u"orm['auth.Permission']", 'symmetrical': 'False', 'blank': 'True'}) + }, + u'auth.permission': { + 'Meta': {'ordering': "(u'content_type__app_label', u'content_type__model', u'codename')", 'unique_together': "((u'content_type', u'codename'),)", 'object_name': 'Permission'}, + 'codename': ('django.db.models.fields.CharField', [], {'max_length': '100'}), + 'content_type': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['contenttypes.ContentType']"}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '50'}) + }, + u'auth.user': { + 'Meta': {'object_name': 'User'}, + 'date_joined': ('django.db.models.fields.DateTimeField', [], {'default': 'datetime.datetime.now'}), + 'email': ('django.db.models.fields.EmailField', [], {'max_length': '75', 'blank': 'True'}), + 'first_name': ('django.db.models.fields.CharField', [], {'max_length': '30', 'blank': 'True'}), + 'groups': ('django.db.models.fields.related.ManyToManyField', [], {'symmetrical': 'False', 'related_name': "u'user_set'", 'blank': 'True', 'to': u"orm['auth.Group']"}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'is_active': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'is_staff': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'is_superuser': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'last_login': ('django.db.models.fields.DateTimeField', [], {'default': 'datetime.datetime.now'}), + 'last_name': ('django.db.models.fields.CharField', [], {'max_length': '30', 'blank': 'True'}), + 'password': ('django.db.models.fields.CharField', [], {'max_length': '128'}), + 'user_permissions': ('django.db.models.fields.related.ManyToManyField', [], {'symmetrical': 'False', 'related_name': "u'user_set'", 'blank': 'True', 'to': u"orm['auth.Permission']"}), + 'username': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '30'}) + }, + u'contenttypes.contenttype': { + 'Meta': {'ordering': "('name',)", 'unique_together': "(('app_label', 'model'),)", 'object_name': 'ContentType', 'db_table': "'django_content_type'"}, + 'app_label': ('django.db.models.fields.CharField', [], {'max_length': '100'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'model': ('django.db.models.fields.CharField', [], {'max_length': '100'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '100'}) + }, + u'rundb.analysisargs': { + 'Meta': {'object_name': 'AnalysisArgs'}, + 'active': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'alignmentargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'analysisargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'applCategory': ('django.db.models.fields.CharField', [], {'max_length': '127', 'null': 'True', 'blank': 'True'}), + 'applGroup': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'applGroup_analysisArgs'", 'null': 'True', 'to': u"orm['rundb.ApplicationGroup']"}), + 'applType': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'applType_analysisArgs'", 'null': 'True', 'to': u"orm['rundb.RunType']"}), + 'basecallerargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'beadfindargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'calibrateargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'chipType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '128'}), + 'chip_default': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'creationDate': ('django.db.models.fields.DateTimeField', [], {'default': 'datetime.datetime.now', 'auto_now_add': 'True', 'null': 'True', 'blank': 'True'}), + 'creator': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'created_analysisArgs'", 'null': 'True', 'on_delete': 'models.SET_NULL', 'to': u"orm['auth.User']"}), + 'description': ('django.db.models.fields.CharField', [], {'max_length': '256', 'unique': 'True', 'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'ionstatsargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'isSystem': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'lastModifiedDate': ('django.db.models.fields.DateTimeField', [], {'default': 'datetime.datetime.now', 'auto_now': 'True', 'null': 'True', 'blank': 'True'}), + 'lastModifiedUser': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'lastModified_analysisArgs'", 'null': 'True', 'on_delete': 'models.SET_NULL', 'to': u"orm['auth.User']"}), + 'libraryKitName': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '512', 'blank': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '256'}), + 'prebasecallerargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'prethumbnailbasecallerargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'samplePrepKitName': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '512', 'blank': 'True'}), + 'sequenceKitName': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '512', 'blank': 'True'}), + 'templateKitName': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '512', 'blank': 'True'}), + 'thumbnailalignmentargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'thumbnailanalysisargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'thumbnailbasecallerargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'thumbnailbeadfindargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'thumbnailcalibrateargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'thumbnailionstatsargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}) + }, + u'rundb.analysismetrics': { + 'Meta': {'object_name': 'AnalysisMetrics'}, + 'adjusted_addressable': ('django.db.models.fields.IntegerField', [], {'default': '0'}), + 'amb': ('django.db.models.fields.IntegerField', [], {}), + 'bead': ('django.db.models.fields.IntegerField', [], {}), + 'dud': ('django.db.models.fields.IntegerField', [], {}), + 'empty': ('django.db.models.fields.IntegerField', [], {}), + 'excluded': ('django.db.models.fields.IntegerField', [], {}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'ignored': ('django.db.models.fields.IntegerField', [], {}), + 'keypass_all_beads': ('django.db.models.fields.IntegerField', [], {}), + 'lib': ('django.db.models.fields.IntegerField', [], {}), + 'libFinal': ('django.db.models.fields.IntegerField', [], {}), + 'libKp': ('django.db.models.fields.IntegerField', [], {}), + 'libLive': ('django.db.models.fields.IntegerField', [], {}), + 'libMix': ('django.db.models.fields.IntegerField', [], {}), + 'lib_pass_basecaller': ('django.db.models.fields.IntegerField', [], {}), + 'lib_pass_cafie': ('django.db.models.fields.IntegerField', [], {}), + 'live': ('django.db.models.fields.IntegerField', [], {}), + 'loading': ('django.db.models.fields.FloatField', [], {'default': '0.0'}), + 'pinned': ('django.db.models.fields.IntegerField', [], {}), + 'report': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'analysismetrics_set'", 'to': u"orm['rundb.Results']"}), + 'sysCF': ('django.db.models.fields.FloatField', [], {}), + 'sysDR': ('django.db.models.fields.FloatField', [], {}), + 'sysIE': ('django.db.models.fields.FloatField', [], {}), + 'tf': ('django.db.models.fields.IntegerField', [], {}), + 'tfFinal': ('django.db.models.fields.IntegerField', [], {}), + 'tfKp': ('django.db.models.fields.IntegerField', [], {}), + 'tfLive': ('django.db.models.fields.IntegerField', [], {}), + 'tfMix': ('django.db.models.fields.IntegerField', [], {}), + 'total': ('django.db.models.fields.IntegerField', [], {'default': '0'}), + 'washout': ('django.db.models.fields.IntegerField', [], {}), + 'washout_ambiguous': ('django.db.models.fields.IntegerField', [], {}), + 'washout_dud': ('django.db.models.fields.IntegerField', [], {}), + 'washout_library': ('django.db.models.fields.IntegerField', [], {}), + 'washout_live': ('django.db.models.fields.IntegerField', [], {}), + 'washout_test_fragment': ('django.db.models.fields.IntegerField', [], {}) + }, + u'rundb.applicationgroup': { + 'Meta': {'object_name': 'ApplicationGroup'}, + 'description': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'isActive': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '127'}), + 'uid': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '32'}) + }, + u'rundb.applproduct': { + 'Meta': {'object_name': 'ApplProduct'}, + 'applType': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.RunType']"}), + 'applicationGroup': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.ApplicationGroup']", 'null': 'True', 'blank': 'True'}), + 'barcodeKitSelectableType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'categories': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '256', 'null': 'True', 'blank': 'True'}), + 'defaultBarcodeKitName': ('django.db.models.fields.CharField', [], {'max_length': '128', 'null': 'True', 'blank': 'True'}), + 'defaultChipType': ('django.db.models.fields.CharField', [], {'max_length': '128', 'null': 'True', 'blank': 'True'}), + 'defaultControlSeqKit': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'controlSeqKit_applProduct_set'", 'null': 'True', 'to': u"orm['rundb.KitInfo']"}), + 'defaultFlowCount': ('django.db.models.fields.PositiveIntegerField', [], {'default': '0'}), + 'defaultFlowOrder': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'flowOrder_applProduct_set'", 'null': 'True', 'to': u"orm['rundb.FlowOrder']"}), + 'defaultGenomeRefName': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}), + 'defaultHotSpotRegionBedFileName': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}), + 'defaultIonChefPrepKit': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'ionChefPrepKit_applProduct_set'", 'null': 'True', 'to': u"orm['rundb.KitInfo']"}), + 'defaultIonChefSequencingKit': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'ionChefSeqKit_applProduct_set'", 'null': 'True', 'to': u"orm['rundb.KitInfo']"}), + 'defaultLibraryKit': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'libKit_applProduct_set'", 'null': 'True', 'to': u"orm['rundb.KitInfo']"}), + 'defaultSamplePrepKit': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'samplePrepKit_applProduct_set'", 'null': 'True', 'to': u"orm['rundb.KitInfo']"}), + 'defaultSamplePrepProtocol': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'common_CV_applProduct_set'", 'null': 'True', 'to': u"orm['rundb.common_CV']"}), + 'defaultSequencingKit': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'seqKit_applProduct_set'", 'null': 'True', 'to': u"orm['rundb.KitInfo']"}), + 'defaultTargetRegionBedFileName': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}), + 'defaultTemplateKit': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'templateKit_applProduct_set'", 'null': 'True', 'to': u"orm['rundb.KitInfo']"}), + 'description': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'blank': 'True'}), + 'dualBarcodingRule': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'instrumentType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'isActive': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'isBarcodeKitSelectionRequired': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isControlSeqTypeBySampleSupported': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isDefault': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isDefaultBarcoded': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isDefaultForInstrumentType': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isDualBarcodingBySampleSupported': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isDualNucleotideTypeBySampleSupported': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isHotSpotBEDFileBySampleSupported': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isHotspotRegionBEDFileSuppported': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'isReferenceBySampleSupported': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isReferenceSelectionSupported': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'isSamplePrepKitSupported': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'isTargetRegionBEDFileBySampleSupported': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isTargetRegionBEDFileSelectionRequiredForRefSelection': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isTargetRegionBEDFileSupported': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'isTargetTechniqueSelectionSupported': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'isVisible': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'productCode': ('django.db.models.fields.CharField', [], {'default': "'any'", 'unique': 'True', 'max_length': '64'}), + 'productName': ('django.db.models.fields.CharField', [], {'max_length': '128'}) + }, + u'rundb.backup': { + 'Meta': {'object_name': 'Backup'}, + 'backupDate': ('django.db.models.fields.DateTimeField', [], {}), + 'backupName': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '256'}), + 'backupPath': ('django.db.models.fields.CharField', [], {'max_length': '512'}), + 'experiment': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.Experiment']"}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'isBackedUp': ('django.db.models.fields.BooleanField', [], {}) + }, + u'rundb.chefpcrplateconfig': { + 'Meta': {'object_name': 'ChefPcrPlateconfig'}, + 'confg': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'kit': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.KitInfo']", 'null': 'True', 'blank': 'True'}) + }, + u'rundb.chip': { + 'Meta': {'object_name': 'Chip'}, + 'description': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '128'}), + 'earlyDatFileDeletion': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '1', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'instrumentType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'isActive': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '128'}), + 'slots': ('django.db.models.fields.IntegerField', [], {}) + }, + u'rundb.common_cv': { + 'Meta': {'unique_together': "(('cv_type', 'value'),)", 'object_name': 'common_CV'}, + 'categories': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '256', 'null': 'True', 'blank': 'True'}), + 'cv_type': ('django.db.models.fields.CharField', [], {'max_length': '127'}), + 'description': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}), + 'displayedValue': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '127'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'isActive': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'isDefault': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'isVisible': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'samplePrep_instrumentType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'sequencing_instrumentType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'uid': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '10'}), + 'value': ('django.db.models.fields.CharField', [], {'max_length': '127'}) + }, + u'rundb.content': { + 'Meta': {'object_name': 'Content'}, + 'application_tags': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + 'contentupload': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'contents'", 'to': u"orm['rundb.ContentUpload']"}), + 'description': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + 'enabled': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'extra': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + 'file': ('django.db.models.fields.CharField', [], {'max_length': '255'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'meta': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'blank': 'True'}), + 'notes': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + 'path': ('django.db.models.fields.CharField', [], {'max_length': '255'}), + 'publisher': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'contents'", 'to': u"orm['rundb.Publisher']"}), + 'type': ('django.db.models.fields.CharField', [], {'max_length': '128', 'blank': 'True'}) + }, + u'rundb.contentupload': { + 'Meta': {'object_name': 'ContentUpload'}, + 'file_path': ('django.db.models.fields.CharField', [], {'max_length': '255'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'meta': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'blank': 'True'}), + 'publisher': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.Publisher']", 'null': 'True'}), + 'source': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + 'status': ('django.db.models.fields.CharField', [], {'max_length': '255', 'blank': 'True'}), + 'upload_date': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'null': 'True', 'blank': 'True'}), + 'upload_type': ('django.db.models.fields.CharField', [], {'max_length': '128', 'blank': 'True'}), + 'username': ('django.db.models.fields.CharField', [], {'max_length': '128', 'blank': 'True'}) + }, + u'rundb.cruncher': { + 'Meta': {'object_name': 'Cruncher'}, + 'comments': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + 'date': ('django.db.models.fields.DateTimeField', [], {'auto_now': 'True', 'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'info': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'null': 'True', 'blank': 'True'}), + 'location': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.Location']"}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '200'}), + 'state': ('django.db.models.fields.CharField', [], {'default': "'U'", 'max_length': '8'}) + }, + u'rundb.dmfileset': { + 'Meta': {'object_name': 'DMFileSet'}, + 'auto_action': ('django.db.models.fields.CharField', [], {'default': "'OFF'", 'max_length': '8'}), + 'auto_trigger_age': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'auto_trigger_usage': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'backup_directory': ('django.db.models.fields.CharField', [], {'max_length': '256', 'null': 'True', 'blank': 'True'}), + 'bandwidth_limit': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'del_empty_dir': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'description': ('django.db.models.fields.CharField', [], {'max_length': '256', 'null': 'True', 'blank': 'True'}), + 'enabled': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'exclude': ('iondb.rundb.separatedValuesField.SeparatedValuesField', [], {'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'include': ('iondb.rundb.separatedValuesField.SeparatedValuesField', [], {'null': 'True', 'blank': 'True'}), + 'keepwith': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'null': 'True', 'blank': 'True'}), + 'type': ('django.db.models.fields.CharField', [], {'max_length': '48'}), + 'version': ('django.db.models.fields.CharField', [], {'max_length': '8'}) + }, + u'rundb.dmfilestat': { + 'Meta': {'object_name': 'DMFileStat'}, + 'action_state': ('django.db.models.fields.CharField', [], {'default': "'L'", 'max_length': '8'}), + 'archivepath': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'created': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + 'diskspace': ('django.db.models.fields.FloatField', [], {'null': 'True', 'blank': 'True'}), + 'dmfileset': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.DMFileSet']", 'null': 'True', 'blank': 'True'}), + 'files_in_use': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '512', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'preserve_data': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'result': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.Results']", 'null': 'True', 'blank': 'True'}), + 'user_comment': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'blank': 'True'}) + }, + u'rundb.dnabarcode': { + 'Meta': {'object_name': 'dnaBarcode'}, + 'active': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'adapter': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '128', 'blank': 'True'}), + 'annotation': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '512', 'blank': 'True'}), + 'end_adapter': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '128', 'blank': 'True'}), + 'end_sequence': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '128', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'id_str': ('django.db.models.fields.CharField', [], {'max_length': '128'}), + 'index': ('django.db.models.fields.IntegerField', [], {}), + 'is_end_barcode': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'length': ('django.db.models.fields.IntegerField', [], {'default': '0', 'blank': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '128'}), + 'score_cutoff': ('django.db.models.fields.FloatField', [], {'default': '0'}), + 'score_mode': ('django.db.models.fields.IntegerField', [], {'default': '0', 'blank': 'True'}), + 'sequence': ('django.db.models.fields.CharField', [], {'max_length': '128'}), + 'system': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'type': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}) + }, + u'rundb.emailaddress': { + 'Meta': {'object_name': 'EmailAddress'}, + 'email': ('django.db.models.fields.EmailField', [], {'max_length': '75', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'selected': ('django.db.models.fields.BooleanField', [], {}) + }, + u'rundb.eventlog': { + 'Meta': {'object_name': 'EventLog'}, + 'content_type': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'content_type_set_for_eventlog'", 'to': u"orm['contenttypes.ContentType']"}), + 'created': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'object_pk': ('django.db.models.fields.PositiveIntegerField', [], {}), + 'text': ('django.db.models.fields.TextField', [], {'max_length': '3000'}), + 'username': ('django.db.models.fields.CharField', [], {'default': "'ION'", 'max_length': '32', 'blank': 'True'}) + }, + u'rundb.experiment': { + 'Meta': {'object_name': 'Experiment'}, + 'autoAnalyze': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'baselineRun': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'chefChipExpiration1': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefChipExpiration2': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefChipType1': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefChipType2': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefEndTime': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + 'chefExtraInfo_1': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '128', 'blank': 'True'}), + 'chefExtraInfo_2': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '128', 'blank': 'True'}), + 'chefFlexibleWorkflow': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefInstrumentName': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '200', 'blank': 'True'}), + 'chefKitType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefLastUpdate': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + 'chefLogPath': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'chefLotNumber': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefManufactureDate': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefMessage': ('django.db.models.fields.TextField', [], {'default': "''", 'blank': 'True'}), + 'chefOperationMode': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefPackageVer': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefProgress': ('django.db.models.fields.FloatField', [], {'default': '0.0', 'blank': 'True'}), + 'chefProtocolDeviationName': ('django.db.models.fields.CharField', [], {'max_length': '127', 'null': 'True', 'blank': 'True'}), + 'chefReagentID': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefReagentsExpiration': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefReagentsLot': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefReagentsPart': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefReagentsSerialNum': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '20', 'blank': 'True'}), + 'chefRemainingSeconds': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'chefSamplePos': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefScriptVersion': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefSolutionsExpiration': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefSolutionsLot': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefSolutionsPart': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefSolutionsSerialNum': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '20', 'blank': 'True'}), + 'chefStartTime': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + 'chefStatus': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '256', 'blank': 'True'}), + 'chefTipRackBarcode': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chipBarcode': ('django.db.models.fields.CharField', [], {'max_length': '64', 'blank': 'True'}), + 'chipTecDfltAmbient': ('django.db.models.fields.FloatField', [], {'default': 'None', 'null': 'True', 'blank': 'True'}), + 'chipTecMinThreshold': ('django.db.models.fields.FloatField', [], {'default': 'None', 'null': 'True', 'blank': 'True'}), + 'chipTecSlope': ('django.db.models.fields.FloatField', [], {'default': 'None', 'null': 'True', 'blank': 'True'}), + 'chipType': ('django.db.models.fields.CharField', [], {'max_length': '32'}), + 'cycles': ('django.db.models.fields.IntegerField', [], {}), + 'date': ('django.db.models.fields.DateTimeField', [], {'db_index': 'True'}), + 'diskusage': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'displayName': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '128'}), + 'expCompInfo': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + 'expDir': ('django.db.models.fields.CharField', [], {'max_length': '512'}), + 'expName': ('django.db.models.fields.CharField', [], {'max_length': '128', 'db_index': 'True'}), + 'flows': ('django.db.models.fields.IntegerField', [], {}), + 'flowsInOrder': ('django.db.models.fields.CharField', [], {'max_length': '1200', 'blank': 'True'}), + 'ftpStatus': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'isReverseRun': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'log': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'blank': 'True'}), + 'manTecDfltAmbient': ('django.db.models.fields.FloatField', [], {'default': 'None', 'null': 'True', 'blank': 'True'}), + 'manTecMinThreshold': ('django.db.models.fields.FloatField', [], {'default': 'None', 'null': 'True', 'blank': 'True'}), + 'manTecSlope': ('django.db.models.fields.FloatField', [], {'default': 'None', 'null': 'True', 'blank': 'True'}), + 'metaData': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'blank': 'True'}), + 'notes': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}), + 'pgmName': ('django.db.models.fields.CharField', [], {'max_length': '64'}), + 'pinnedRepResult': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'plan': ('django.db.models.fields.related.OneToOneField', [], {'blank': 'True', 'related_name': "'experiment'", 'unique': 'True', 'null': 'True', 'to': u"orm['rundb.PlannedExperiment']"}), + 'platform': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '128', 'blank': 'True'}), + 'rawdatastyle': ('django.db.models.fields.CharField', [], {'default': "'single'", 'max_length': '24', 'null': 'True', 'blank': 'True'}), + 'reagentBarcode': ('django.db.models.fields.CharField', [], {'max_length': '64', 'blank': 'True'}), + 'repResult': ('django.db.models.fields.related.OneToOneField', [], {'related_name': "'+'", 'null': 'True', 'on_delete': 'models.SET_NULL', 'to': u"orm['rundb.Results']", 'blank': 'True', 'unique': 'True'}), + 'resultDate': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'null': 'True', 'db_index': 'True', 'blank': 'True'}), + 'reverse_primer': ('django.db.models.fields.CharField', [], {'max_length': '128', 'null': 'True', 'blank': 'True'}), + 'runMode': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'seqKitBarcode': ('django.db.models.fields.CharField', [], {'max_length': '64', 'blank': 'True'}), + 'sequencekitbarcode': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'sequencekitname': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'star': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'status': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '512', 'blank': 'True'}), + 'storageHost': ('django.db.models.fields.CharField', [], {'max_length': '128', 'null': 'True', 'blank': 'True'}), + 'storage_options': ('django.db.models.fields.CharField', [], {'default': "'A'", 'max_length': '200'}), + 'unique': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '512'}), + 'usePreBeadfind': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'user_ack': ('django.db.models.fields.CharField', [], {'default': "'U'", 'max_length': '24'}) + }, + u'rundb.experimentanalysissettings': { + 'Meta': {'object_name': 'ExperimentAnalysisSettings'}, + 'alignmentargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'analysisargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'barcodeKitName': ('django.db.models.fields.CharField', [], {'max_length': '128', 'null': 'True', 'blank': 'True'}), + 'barcodedSamples': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'null': 'True', 'blank': 'True'}), + 'base_recalibration_mode': ('django.db.models.fields.CharField', [], {'default': "'standard_recal'", 'max_length': '64'}), + 'basecallerargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'beadfindargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'calibrateargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'custom_args': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'date': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + 'endBarcodeKitName': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '128', 'null': 'True', 'blank': 'True'}), + 'experiment': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'eas_set'", 'null': 'True', 'to': u"orm['rundb.Experiment']"}), + 'hotSpotRegionBedFile': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'ionstatsargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'isDuplicateReads': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isEditable': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isOneTimeOverride': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'libraryKey': ('django.db.models.fields.CharField', [], {'max_length': '64', 'blank': 'True'}), + 'libraryKitBarcode': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'libraryKitName': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'mixedTypeRNA_hotSpotRegionBedFile': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}), + 'mixedTypeRNA_reference': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'mixedTypeRNA_targetRegionBedFile': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}), + 'prebasecallerargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'prethumbnailbasecallerargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'realign': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'reference': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'selectedPlugins': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'null': 'True', 'blank': 'True'}), + 'sseBedFile': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '1024', 'null': 'True', 'blank': 'True'}), + 'status': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '512', 'blank': 'True'}), + 'targetRegionBedFile': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}), + 'tfKey': ('django.db.models.fields.CharField', [], {'max_length': '64', 'blank': 'True'}), + 'threePrimeAdapter': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'thumbnailalignmentargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'thumbnailanalysisargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'thumbnailbasecallerargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'thumbnailbeadfindargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'thumbnailcalibrateargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'thumbnailionstatsargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}) + }, + u'rundb.filemonitor': { + 'Meta': {'object_name': 'FileMonitor'}, + 'celery_task_id': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '60', 'blank': 'True'}), + 'created': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'local_dir': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '512'}), + 'md5sum': ('django.db.models.fields.CharField', [], {'default': 'None', 'max_length': '32', 'null': 'True', 'blank': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '255'}), + 'progress': ('django.db.models.fields.BigIntegerField', [], {'default': '0'}), + 'size': ('django.db.models.fields.BigIntegerField', [], {'default': 'None', 'null': 'True'}), + 'status': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '60'}), + 'tags': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '1024'}), + 'updated': ('django.db.models.fields.DateTimeField', [], {'auto_now': 'True', 'blank': 'True'}), + 'url': ('django.db.models.fields.CharField', [], {'max_length': '2000'}) + }, + u'rundb.fileserver': { + 'Meta': {'object_name': 'FileServer'}, + 'comments': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + 'filesPrefix': ('django.db.models.fields.CharField', [], {'max_length': '200'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'location': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.Location']"}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '200'}), + 'percentfull': ('django.db.models.fields.FloatField', [], {'default': '0.0', 'null': 'True', 'blank': 'True'}) + }, + u'rundb.floworder': { + 'Meta': {'object_name': 'FlowOrder'}, + 'description': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '128', 'blank': 'True'}), + 'flowOrder': ('django.db.models.fields.CharField', [], {'max_length': '1200', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'isActive': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'isDefault': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isSystem': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '64'}) + }, + u'rundb.globalconfig': { + 'Meta': {'object_name': 'GlobalConfig'}, + 'auto_archive_ack': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'auto_archive_enable': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'base_recalibration_mode': ('django.db.models.fields.CharField', [], {'default': "'standard_recal'", 'max_length': '64'}), + 'check_news_posts': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'cluster_auto_disable': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'default_flow_order': ('django.db.models.fields.CharField', [], {'max_length': '100', 'blank': 'True'}), + 'default_library_key': ('django.db.models.fields.CharField', [], {'max_length': '50', 'blank': 'True'}), + 'default_storage_options': ('django.db.models.fields.CharField', [], {'default': "'D'", 'max_length': '500', 'blank': 'True'}), + 'default_test_fragment_key': ('django.db.models.fields.CharField', [], {'max_length': '50', 'blank': 'True'}), + 'enable_auto_pkg_dl': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'enable_auto_security': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'enable_compendia_OCP': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'enable_nightly_email': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'enable_support_upload': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'enable_version_lock': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'majorPlatform': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '24', 'null': 'True', 'blank': 'True'}), + 'mark_duplicates': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '512'}), + 'plugin_output_folder': ('django.db.models.fields.CharField', [], {'max_length': '500', 'blank': 'True'}), + 'realign': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'records_to_display': ('django.db.models.fields.IntegerField', [], {'default': '20', 'blank': 'True'}), + 'sec_update_status': ('django.db.models.fields.CharField', [], {'max_length': '128', 'blank': 'True'}), + 'selected': ('django.db.models.fields.BooleanField', [], {}), + 'site_name': ('django.db.models.fields.CharField', [], {'max_length': '500', 'blank': 'True'}), + 'telemetry_enabled': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'ts_update_status': ('django.db.models.fields.CharField', [], {'max_length': '256', 'blank': 'True'}), + 'web_root': ('django.db.models.fields.CharField', [], {'max_length': '500', 'blank': 'True'}) + }, + u'rundb.ionmeshnode': { + 'Meta': {'object_name': 'IonMeshNode'}, + 'active': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'apikey_local': ('django.db.models.fields.CharField', [], {'max_length': '256', 'null': 'True', 'blank': 'True'}), + 'apikey_remote': ('django.db.models.fields.CharField', [], {'max_length': '256', 'null': 'True', 'blank': 'True'}), + 'hostname': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '128'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '128', 'unique': 'True', 'null': 'True', 'blank': 'True'}), + 'system_id': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '37'}) + }, + u'rundb.kitinfo': { + 'Meta': {'unique_together': "(('kitType', 'name'),)", 'object_name': 'KitInfo'}, + 'applicationType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'null': 'True', 'blank': 'True'}), + 'cartridgeBetweenUsageAbsoluteMaxDayLimit': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'cartridgeExpirationDayLimit': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'categories': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '256', 'null': 'True', 'blank': 'True'}), + 'chipTypes': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '127', 'blank': 'True'}), + 'defaultCartridgeUsageCount': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'defaultFlowOrder': ('django.db.models.fields.related.ForeignKey', [], {'default': 'None', 'to': u"orm['rundb.FlowOrder']", 'null': 'True', 'blank': 'True'}), + 'defaultThreePrimeAdapter': ('django.db.models.fields.related.ForeignKey', [], {'default': 'None', 'to': u"orm['rundb.ThreePrimeadapter']", 'null': 'True', 'blank': 'True'}), + 'description': ('django.db.models.fields.CharField', [], {'max_length': '3024', 'blank': 'True'}), + 'flowCount': ('django.db.models.fields.PositiveIntegerField', [], {}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'instrumentType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'isActive': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'kitType': ('django.db.models.fields.CharField', [], {'max_length': '64'}), + 'libraryReadLength': ('django.db.models.fields.PositiveIntegerField', [], {'default': '0'}), + 'name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '512'}), + 'nucleotideType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'runMode': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'samplePrep_instrumentType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'uid': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '10'}) + }, + u'rundb.kitpart': { + 'Meta': {'unique_together': "(('barcode',),)", 'object_name': 'KitPart'}, + 'barcode': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '64'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'kit': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.KitInfo']"}) + }, + u'rundb.libmetrics': { + 'Genome_Version': ('django.db.models.fields.CharField', [], {'max_length': '512'}), + 'Index_Version': ('django.db.models.fields.CharField', [], {'max_length': '512'}), + 'Meta': {'object_name': 'LibMetrics'}, + 'align_sample': ('django.db.models.fields.IntegerField', [], {}), + 'aveKeyCounts': ('django.db.models.fields.FloatField', [], {}), + 'cf': ('django.db.models.fields.FloatField', [], {}), + 'dr': ('django.db.models.fields.FloatField', [], {}), + 'duplicate_reads': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'genome': ('django.db.models.fields.CharField', [], {'max_length': '512'}), + 'genomesize': ('django.db.models.fields.BigIntegerField', [], {}), + 'i100Q10_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i100Q17_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i100Q20_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i100Q47_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i100Q7_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i150Q10_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i150Q17_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i150Q20_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i150Q47_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i150Q7_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i200Q10_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i200Q17_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i200Q20_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i200Q47_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i200Q7_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i250Q10_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i250Q17_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i250Q20_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i250Q47_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i250Q7_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i300Q10_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i300Q17_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i300Q20_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i300Q47_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i300Q7_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i350Q10_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i350Q17_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i350Q20_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i350Q47_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i350Q7_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i400Q10_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i400Q17_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i400Q20_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i400Q47_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i400Q7_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i450Q10_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i450Q17_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i450Q20_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i450Q47_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i450Q7_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i500Q10_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i500Q17_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i500Q20_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i500Q47_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i500Q7_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i50Q10_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i50Q17_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i50Q20_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i50Q47_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i50Q7_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i550Q10_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i550Q17_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i550Q20_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i550Q47_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i550Q7_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i600Q10_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i600Q17_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i600Q20_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i600Q47_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i600Q7_reads': ('django.db.models.fields.IntegerField', [], {}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'ie': ('django.db.models.fields.FloatField', [], {}), + 'q10_alignments': ('django.db.models.fields.IntegerField', [], {}), + 'q10_longest_alignment': ('django.db.models.fields.IntegerField', [], {}), + 'q10_mapped_bases': ('django.db.models.fields.BigIntegerField', [], {}), + 'q10_mean_alignment_length': ('django.db.models.fields.IntegerField', [], {}), + 'q17_alignments': ('django.db.models.fields.IntegerField', [], {}), + 'q17_longest_alignment': ('django.db.models.fields.IntegerField', [], {}), + 'q17_mapped_bases': ('django.db.models.fields.BigIntegerField', [], {}), + 'q17_mean_alignment_length': ('django.db.models.fields.IntegerField', [], {}), + 'q20_alignments': ('django.db.models.fields.IntegerField', [], {}), + 'q20_longest_alignment': ('django.db.models.fields.IntegerField', [], {}), + 'q20_mapped_bases': ('django.db.models.fields.BigIntegerField', [], {}), + 'q20_mean_alignment_length': ('django.db.models.fields.IntegerField', [], {}), + 'q47_alignments': ('django.db.models.fields.IntegerField', [], {}), + 'q47_longest_alignment': ('django.db.models.fields.IntegerField', [], {}), + 'q47_mapped_bases': ('django.db.models.fields.BigIntegerField', [], {}), + 'q47_mean_alignment_length': ('django.db.models.fields.IntegerField', [], {}), + 'q7_alignments': ('django.db.models.fields.IntegerField', [], {}), + 'q7_longest_alignment': ('django.db.models.fields.IntegerField', [], {}), + 'q7_mapped_bases': ('django.db.models.fields.BigIntegerField', [], {}), + 'q7_mean_alignment_length': ('django.db.models.fields.IntegerField', [], {}), + 'raw_accuracy': ('django.db.models.fields.FloatField', [], {}), + 'report': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'libmetrics_set'", 'to': u"orm['rundb.Results']"}), + 'sysSNR': ('django.db.models.fields.FloatField', [], {}), + 'totalNumReads': ('django.db.models.fields.IntegerField', [], {}), + 'total_mapped_reads': ('django.db.models.fields.BigIntegerField', [], {}), + 'total_mapped_target_bases': ('django.db.models.fields.BigIntegerField', [], {}) + }, + u'rundb.librarykey': { + 'Meta': {'object_name': 'LibraryKey'}, + 'description': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'blank': 'True'}), + 'direction': ('django.db.models.fields.CharField', [], {'default': "'Forward'", 'max_length': '20'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'isDefault': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '256'}), + 'runMode': ('django.db.models.fields.CharField', [], {'default': "'single'", 'max_length': '64', 'blank': 'True'}), + 'sequence': ('django.db.models.fields.CharField', [], {'max_length': '64'}) + }, + u'rundb.location': { + 'Meta': {'object_name': 'Location'}, + 'comments': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + 'defaultlocation': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '200'}) + }, + u'rundb.message': { + 'Meta': {'object_name': 'Message'}, + 'body': ('django.db.models.fields.TextField', [], {'default': "''", 'blank': 'True'}), + 'expires': ('django.db.models.fields.TextField', [], {'default': "'read'", 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'level': ('django.db.models.fields.IntegerField', [], {'default': '20'}), + 'route': ('django.db.models.fields.TextField', [], {'default': "''", 'blank': 'True'}), + 'status': ('django.db.models.fields.TextField', [], {'default': "'unread'", 'blank': 'True'}), + 'tags': ('django.db.models.fields.TextField', [], {'default': "''", 'blank': 'True'}), + 'time': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}) + }, + u'rundb.monitordata': { + 'Meta': {'object_name': 'MonitorData'}, + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '128'}), + 'treeDat': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'blank': 'True'}) + }, + u'rundb.newspost': { + 'Meta': {'object_name': 'NewsPost'}, + 'guid': ('django.db.models.fields.CharField', [], {'max_length': '2083', 'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'link': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '2083', 'blank': 'True'}), + 'summary': ('django.db.models.fields.TextField', [], {'default': "''", 'blank': 'True'}), + 'title': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '1024', 'blank': 'True'}), + 'updated': ('django.db.models.fields.DateTimeField', [], {'default': 'datetime.datetime.now'}) + }, + u'rundb.plannedexperiment': { + 'Meta': {'ordering': "['-id']", 'object_name': 'PlannedExperiment'}, + 'adapter': ('django.db.models.fields.CharField', [], {'max_length': '256', 'null': 'True', 'blank': 'True'}), + 'applicationGroup': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.ApplicationGroup']", 'null': 'True'}), + 'autoName': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'categories': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'null': 'True', 'db_index': 'True', 'blank': 'True'}), + 'controlSequencekitname': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'cycles': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'date': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + 'expName': ('django.db.models.fields.CharField', [], {'max_length': '128', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'irworkflow': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'blank': 'True'}), + 'isCustom_kitSettings': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isFavorite': ('django.db.models.fields.BooleanField', [], {'default': 'False', 'db_index': 'True'}), + 'isPlanGroup': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isReusable': ('django.db.models.fields.BooleanField', [], {'default': 'False', 'db_index': 'True'}), + 'isReverseRun': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isSystem': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isSystemDefault': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'latestEAS': ('django.db.models.fields.related.OneToOneField', [], {'related_name': "'+'", 'null': 'True', 'on_delete': 'models.SET_NULL', 'to': u"orm['rundb.ExperimentAnalysisSettings']", 'blank': 'True', 'unique': 'True'}), + 'libkit': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'libraryPool': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '12', 'null': 'True', 'blank': 'True'}), + 'libraryReadLength': ('django.db.models.fields.PositiveIntegerField', [], {'default': '0'}), + 'metaData': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'blank': 'True'}), + 'origin': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'null': 'True', 'blank': 'True'}), + 'pairedEndLibraryAdapterName': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'parentPlan': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'childPlan_set'", 'null': 'True', 'to': u"orm['rundb.PlannedExperiment']"}), + 'planDisplayedName': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'planExecuted': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'planExecutedDate': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + 'planGUID': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'planName': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'planPGM': ('django.db.models.fields.CharField', [], {'max_length': '128', 'null': 'True', 'blank': 'True'}), + 'planShortID': ('django.db.models.fields.CharField', [], {'db_index': 'True', 'max_length': '5', 'null': 'True', 'blank': 'True'}), + 'planStatus': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '512', 'db_index': 'True', 'blank': 'True'}), + 'preAnalysis': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'projects': ('django.db.models.fields.related.ManyToManyField', [], {'symmetrical': 'False', 'related_name': "'plans'", 'blank': 'True', 'to': u"orm['rundb.Project']"}), + 'qcValues': ('django.db.models.fields.related.ManyToManyField', [], {'to': u"orm['rundb.QCType']", 'null': 'True', 'through': u"orm['rundb.PlannedExperimentQC']", 'symmetrical': 'False'}), + 'reverse_primer': ('django.db.models.fields.CharField', [], {'max_length': '128', 'null': 'True', 'blank': 'True'}), + 'runMode': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'runType': ('django.db.models.fields.CharField', [], {'default': "'GENS'", 'max_length': '512', 'db_index': 'True'}), + 'runname': ('django.db.models.fields.CharField', [], {'max_length': '255', 'null': 'True', 'blank': 'True'}), + 'sampleGrouping': ('django.db.models.fields.related.ForeignKey', [], {'default': 'None', 'to': u"orm['rundb.SampleGroupType_CV']", 'null': 'True', 'blank': 'True'}), + 'samplePrepKitName': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'samplePrepProtocol': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'null': 'True', 'blank': 'True'}), + 'sampleSets': ('django.db.models.fields.related.ManyToManyField', [], {'blank': 'True', 'related_name': "'plans'", 'null': 'True', 'symmetrical': 'False', 'to': u"orm['rundb.SampleSet']"}), + 'sampleTubeLabel': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'seqKitBarcode': ('django.db.models.fields.CharField', [], {'max_length': '64', 'null': 'True', 'blank': 'True'}), + 'storageHost': ('django.db.models.fields.CharField', [], {'max_length': '128', 'null': 'True', 'blank': 'True'}), + 'storage_options': ('django.db.models.fields.CharField', [], {'default': "'A'", 'max_length': '200'}), + 'templatingKitBarcode': ('django.db.models.fields.CharField', [], {'max_length': '64', 'null': 'True', 'blank': 'True'}), + 'templatingKitName': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'usePostBeadfind': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'usePreBeadfind': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'username': ('django.db.models.fields.CharField', [], {'max_length': '128', 'null': 'True', 'blank': 'True'}) + }, + u'rundb.plannedexperimentqc': { + 'Meta': {'unique_together': "(('plannedExperiment', 'qcType'),)", 'object_name': 'PlannedExperimentQC'}, + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'plannedExperiment': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.PlannedExperiment']"}), + 'qcType': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.QCType']"}), + 'threshold': ('django.db.models.fields.PositiveIntegerField', [], {'default': '0'}) + }, + u'rundb.plansession': { + 'Meta': {'object_name': 'PlanSession'}, + '_session_data': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + 'expire_date': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'plan_key': ('django.db.models.fields.CharField', [], {'max_length': '64'}), + 'session_key': ('django.db.models.fields.CharField', [], {'max_length': '64'}) + }, + u'rundb.plugin': { + 'Meta': {'unique_together': "(('name', 'version'),)", 'object_name': 'Plugin'}, + 'active': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'config': ('django.db.models.fields.TextField', [], {'default': "''", 'null': 'True', 'blank': 'True'}), + 'date': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + 'defaultSelected': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'description': ('django.db.models.fields.TextField', [], {'default': "''", 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'majorBlock': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '512', 'db_index': 'True'}), + 'packageName': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '256', 'db_column': "'packagename'", 'blank': 'True'}), + 'path': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '512', 'blank': 'True'}), + 'pluginsettings': ('django.db.models.fields.TextField', [], {'default': "''", 'null': 'True', 'blank': 'True'}), + 'requires_configuration': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'script': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '256', 'blank': 'True'}), + 'selected': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'status': ('django.db.models.fields.TextField', [], {'default': "''", 'null': 'True', 'blank': 'True'}), + 'url': ('django.db.models.fields.URLField', [], {'default': "''", 'max_length': '256', 'blank': 'True'}), + 'userinputfields': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'null': 'True', 'blank': 'True'}), + 'version': ('django.db.models.fields.CharField', [], {'max_length': '256'}) + }, + u'rundb.pluginresult': { + 'Meta': {'ordering': "['-id']", 'object_name': 'PluginResult'}, + 'apikey': ('django.db.models.fields.CharField', [], {'max_length': '256', 'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'inodes': ('django.db.models.fields.BigIntegerField', [], {'default': '-1'}), + 'owner': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['auth.User']", 'on_delete': 'models.SET_DEFAULT'}), + 'plugin': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.Plugin']"}), + 'result': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'pluginresult_set'", 'to': u"orm['rundb.Results']"}), + 'size': ('django.db.models.fields.BigIntegerField', [], {'default': '-1'}), + 'store': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'blank': 'True'}), + 'validation_errors': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'blank': 'True'}) + }, + u'rundb.pluginresultjob': { + 'Meta': {'object_name': 'PluginResultJob'}, + 'config': ('django.db.models.fields.TextField', [], {'default': "''", 'blank': 'True'}), + 'endtime': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + 'grid_engine_jobid': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'plugin_result': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'plugin_result_jobs'", 'to': u"orm['rundb.PluginResult']"}), + 'run_level': ('django.db.models.fields.CharField', [], {'max_length': '20'}), + 'starttime': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + 'state': ('django.db.models.fields.CharField', [], {'max_length': '20'}) + }, + u'rundb.project': { + 'Meta': {'object_name': 'Project'}, + 'created': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + 'creator': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['auth.User']", 'on_delete': 'models.SET_DEFAULT'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'modified': ('django.db.models.fields.DateTimeField', [], {'auto_now': 'True', 'blank': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '64'}), + 'public': ('django.db.models.fields.BooleanField', [], {'default': 'True'}) + }, + u'rundb.publisher': { + 'Meta': {'object_name': 'Publisher'}, + 'date': ('django.db.models.fields.DateTimeField', [], {}), + 'global_meta': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '200'}), + 'path': ('django.db.models.fields.CharField', [], {'max_length': '512'}), + 'version': ('django.db.models.fields.CharField', [], {'max_length': '256'}) + }, + u'rundb.qctype': { + 'Meta': {'object_name': 'QCType'}, + 'defaultThreshold': ('django.db.models.fields.PositiveIntegerField', [], {'default': '0'}), + 'description': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'maxThreshold': ('django.db.models.fields.PositiveIntegerField', [], {'default': '100'}), + 'minThreshold': ('django.db.models.fields.PositiveIntegerField', [], {'default': '0'}), + 'qcName': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '512'}) + }, + u'rundb.qualitymetrics': { + 'Meta': {'object_name': 'QualityMetrics'}, + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'q0_100bp_reads': ('django.db.models.fields.IntegerField', [], {}), + 'q0_150bp_reads': ('django.db.models.fields.IntegerField', [], {'default': '0'}), + 'q0_50bp_reads': ('django.db.models.fields.IntegerField', [], {}), + 'q0_bases': ('django.db.models.fields.BigIntegerField', [], {}), + 'q0_max_read_length': ('django.db.models.fields.IntegerField', [], {}), + 'q0_mean_read_length': ('django.db.models.fields.FloatField', [], {}), + 'q0_median_read_length': ('django.db.models.fields.IntegerField', [], {'default': '0'}), + 'q0_mode_read_length': ('django.db.models.fields.IntegerField', [], {'default': '0'}), + 'q0_reads': ('django.db.models.fields.IntegerField', [], {}), + 'q17_100bp_reads': ('django.db.models.fields.IntegerField', [], {}), + 'q17_150bp_reads': ('django.db.models.fields.IntegerField', [], {}), + 'q17_50bp_reads': ('django.db.models.fields.IntegerField', [], {}), + 'q17_bases': ('django.db.models.fields.BigIntegerField', [], {}), + 'q17_max_read_length': ('django.db.models.fields.IntegerField', [], {}), + 'q17_mean_read_length': ('django.db.models.fields.FloatField', [], {}), + 'q17_median_read_length': ('django.db.models.fields.IntegerField', [], {'default': '0'}), + 'q17_mode_read_length': ('django.db.models.fields.IntegerField', [], {'default': '0'}), + 'q17_reads': ('django.db.models.fields.IntegerField', [], {}), + 'q20_100bp_reads': ('django.db.models.fields.IntegerField', [], {}), + 'q20_150bp_reads': ('django.db.models.fields.IntegerField', [], {}), + 'q20_50bp_reads': ('django.db.models.fields.IntegerField', [], {}), + 'q20_bases': ('django.db.models.fields.BigIntegerField', [], {}), + 'q20_max_read_length': ('django.db.models.fields.FloatField', [], {}), + 'q20_mean_read_length': ('django.db.models.fields.IntegerField', [], {}), + 'q20_median_read_length': ('django.db.models.fields.IntegerField', [], {'default': '0'}), + 'q20_mode_read_length': ('django.db.models.fields.IntegerField', [], {'default': '0'}), + 'q20_reads': ('django.db.models.fields.IntegerField', [], {}), + 'report': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'qualitymetrics_set'", 'to': u"orm['rundb.Results']"}) + }, + u'rundb.referencegenome': { + 'Meta': {'ordering': "['short_name']", 'object_name': 'ReferenceGenome'}, + 'celery_task_id': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '60', 'blank': 'True'}), + 'date': ('django.db.models.fields.DateTimeField', [], {'default': 'datetime.datetime.now'}), + 'enabled': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'file_monitor': ('django.db.models.fields.related.OneToOneField', [], {'to': u"orm['rundb.FileMonitor']", 'unique': 'True', 'null': 'True', 'on_delete': 'models.SET_NULL', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'identity_hash': ('django.db.models.fields.CharField', [], {'default': 'None', 'max_length': '40', 'null': 'True', 'blank': 'True'}), + 'index_version': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '512'}), + 'notes': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + 'reference_path': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'blank': 'True'}), + 'short_name': ('django.db.models.fields.CharField', [], {'max_length': '512'}), + 'source': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + 'species': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + 'status': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + 'verbose_error': ('django.db.models.fields.CharField', [], {'max_length': '3000', 'blank': 'True'}), + 'version': ('django.db.models.fields.CharField', [], {'max_length': '100', 'blank': 'True'}) + }, + u'rundb.remoteaccount': { + 'Meta': {'object_name': 'RemoteAccount'}, + 'access_token': ('django.db.models.fields.CharField', [], {'max_length': '2048', 'null': 'True', 'blank': 'True'}), + 'account_label': ('django.db.models.fields.CharField', [], {'default': "'Unnamed Account'", 'max_length': '64'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'refresh_token': ('django.db.models.fields.CharField', [], {'max_length': '2048', 'null': 'True', 'blank': 'True'}), + 'remote_resource': ('django.db.models.fields.CharField', [], {'max_length': '2048'}), + 'token_expires': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + 'user_name': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '255', 'blank': 'True'}) + }, + u'rundb.reportstorage': { + 'Meta': {'object_name': 'ReportStorage'}, + 'default': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'dirPath': ('django.db.models.fields.CharField', [], {'max_length': '200'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '200'}), + 'webServerPath': ('django.db.models.fields.CharField', [], {'max_length': '200'}) + }, + u'rundb.results': { + 'Meta': {'object_name': 'Results'}, + 'analysisVersion': ('django.db.models.fields.CharField', [], {'max_length': '256'}), + 'analysismetrics': ('django.db.models.fields.related.OneToOneField', [], {'to': u"orm['rundb.AnalysisMetrics']", 'unique': 'True', 'null': 'True', 'blank': 'True'}), + 'autoExempt': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'diskusage': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'eas': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'results_set'", 'null': 'True', 'to': u"orm['rundb.ExperimentAnalysisSettings']"}), + 'experiment': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'results_set'", 'to': u"orm['rundb.Experiment']"}), + 'framesProcessed': ('django.db.models.fields.IntegerField', [], {}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'libmetrics': ('django.db.models.fields.related.OneToOneField', [], {'to': u"orm['rundb.LibMetrics']", 'unique': 'True', 'null': 'True', 'blank': 'True'}), + 'log': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + 'metaData': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'blank': 'True'}), + 'parentIDs': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + 'parentResult': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'childResults_set'", 'null': 'True', 'on_delete': 'models.SET_NULL', 'to': u"orm['rundb.Results']"}), + 'processedCycles': ('django.db.models.fields.IntegerField', [], {}), + 'processedflows': ('django.db.models.fields.IntegerField', [], {}), + 'projects': ('django.db.models.fields.related.ManyToManyField', [], {'related_name': "'results'", 'symmetrical': 'False', 'to': u"orm['rundb.Project']"}), + 'qualitymetrics': ('django.db.models.fields.related.OneToOneField', [], {'to': u"orm['rundb.QualityMetrics']", 'unique': 'True', 'null': 'True', 'blank': 'True'}), + 'reference': ('django.db.models.fields.CharField', [], {'max_length': '64', 'null': 'True', 'blank': 'True'}), + 'reportLink': ('django.db.models.fields.CharField', [], {'max_length': '512'}), + 'reportStatus': ('django.db.models.fields.CharField', [], {'default': "'Nothing'", 'max_length': '64', 'null': 'True'}), + 'reportstorage': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'storage'", 'null': 'True', 'to': u"orm['rundb.ReportStorage']"}), + 'representative': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'resultsName': ('django.db.models.fields.CharField', [], {'max_length': '512'}), + 'resultsType': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + 'runid': ('django.db.models.fields.CharField', [], {'max_length': '10', 'blank': 'True'}), + 'status': ('django.db.models.fields.CharField', [], {'max_length': '64'}), + 'timeStamp': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'db_index': 'True', 'blank': 'True'}), + 'timeToComplete': ('django.db.models.fields.CharField', [], {'max_length': '64'}) + }, + u'rundb.rig': { + 'Meta': {'object_name': 'Rig'}, + 'alarms': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'blank': 'True'}), + 'comments': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + 'display_state': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + 'ftppassword': ('django.db.models.fields.CharField', [], {'default': "'ionguest'", 'max_length': '64'}), + 'ftprootdir': ('django.db.models.fields.CharField', [], {'default': "'results'", 'max_length': '64'}), + 'ftpserver': ('django.db.models.fields.CharField', [], {'default': "'192.168.201.1'", 'max_length': '128'}), + 'ftpusername': ('django.db.models.fields.CharField', [], {'default': "'ionguest'", 'max_length': '64'}), + 'host_address': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'blank': 'True'}), + 'last_clean_date': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + 'last_experiment': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + 'last_init_date': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + 'location': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.Location']"}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '200', 'primary_key': 'True'}), + 'serial': ('django.db.models.fields.CharField', [], {'max_length': '24', 'null': 'True', 'blank': 'True'}), + 'state': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + 'type': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'blank': 'True'}), + 'updateCommand': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'blank': 'True'}), + 'updateflag': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'updatehome': ('django.db.models.fields.CharField', [], {'default': "'192.168.201.1'", 'max_length': '256'}), + 'version': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'blank': 'True'}) + }, + u'rundb.runtype': { + 'Meta': {'object_name': 'RunType'}, + 'alternate_name': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'applicationGroups': ('django.db.models.fields.related.ManyToManyField', [], {'symmetrical': 'False', 'related_name': "'applications'", 'null': 'True', 'to': u"orm['rundb.ApplicationGroup']"}), + 'barcode': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + 'description': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'isActive': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'meta': ('django.db.models.fields.TextField', [], {'default': "''", 'null': 'True', 'blank': 'True'}), + 'nucleotideType': ('django.db.models.fields.CharField', [], {'default': "'dna'", 'max_length': '64', 'blank': 'True'}), + 'runType': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '512'}) + }, + u'rundb.sample': { + 'Meta': {'unique_together': "(('name', 'externalId'),)", 'object_name': 'Sample'}, + 'date': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'null': 'True', 'blank': 'True'}), + 'description': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}), + 'displayedName': ('django.db.models.fields.CharField', [], {'max_length': '127', 'null': 'True', 'blank': 'True'}), + 'experiments': ('django.db.models.fields.related.ManyToManyField', [], {'symmetrical': 'False', 'related_name': "'samples'", 'null': 'True', 'to': u"orm['rundb.Experiment']"}), + 'externalId': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '127', 'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '127', 'null': 'True', 'blank': 'True'}), + 'status': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '512', 'blank': 'True'}) + }, + u'rundb.sampleannotation_cv': { + 'Meta': {'object_name': 'SampleAnnotation_CV'}, + 'annotationType': ('django.db.models.fields.CharField', [], {'max_length': '127'}), + 'iRAnnotationType': ('django.db.models.fields.CharField', [], {'max_length': '127', 'null': 'True', 'blank': 'True'}), + 'iRValue': ('django.db.models.fields.CharField', [], {'max_length': '127', 'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'isActive': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'isIRCompatible': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'sampleGroupType_CV': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'sampleAnnotation_set'", 'null': 'True', 'to': u"orm['rundb.SampleGroupType_CV']"}), + 'uid': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '32'}), + 'value': ('django.db.models.fields.CharField', [], {'max_length': '127', 'blank': 'True'}) + }, + u'rundb.sampleattribute': { + 'Meta': {'object_name': 'SampleAttribute'}, + 'creationDate': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + 'creator': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'created_sampleAttribute'", 'on_delete': 'models.SET_DEFAULT', 'to': u"orm['auth.User']"}), + 'dataType': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'sampleAttributes'", 'to': u"orm['rundb.SampleAttributeDataType']"}), + 'description': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}), + 'displayedName': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '127'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'isActive': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'isMandatory': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'lastModifiedDate': ('django.db.models.fields.DateTimeField', [], {'auto_now': 'True', 'blank': 'True'}), + 'lastModifiedUser': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'lastModified_sampleAttribute'", 'on_delete': 'models.SET_DEFAULT', 'to': u"orm['auth.User']"}) + }, + u'rundb.sampleattributedatatype': { + 'Meta': {'object_name': 'SampleAttributeDataType'}, + 'dataType': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '64'}), + 'description': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'isActive': ('django.db.models.fields.BooleanField', [], {'default': 'True'}) + }, + u'rundb.sampleattributevalue': { + 'Meta': {'object_name': 'SampleAttributeValue'}, + 'creationDate': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + 'creator': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'created_sampleAttributeValue'", 'on_delete': 'models.SET_DEFAULT', 'to': u"orm['auth.User']"}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'lastModifiedDate': ('django.db.models.fields.DateTimeField', [], {'auto_now': 'True', 'blank': 'True'}), + 'lastModifiedUser': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'lastModified_sampleAttributeValue'", 'on_delete': 'models.SET_DEFAULT', 'to': u"orm['auth.User']"}), + 'sample': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'sampleAttributeValues'", 'to': u"orm['rundb.Sample']"}), + 'sampleAttribute': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'samples'", 'to': u"orm['rundb.SampleAttribute']"}), + 'value': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}) + }, + u'rundb.samplegrouptype_cv': { + 'Meta': {'object_name': 'SampleGroupType_CV'}, + 'description': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}), + 'displayedName': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '127'}), + 'iRAnnotationType': ('django.db.models.fields.CharField', [], {'max_length': '127', 'null': 'True', 'blank': 'True'}), + 'iRValue': ('django.db.models.fields.CharField', [], {'max_length': '127', 'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'isActive': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'isIRCompatible': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'uid': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '32'}) + }, + u'rundb.sampleprepdata': { + 'Meta': {'object_name': 'SamplePrepData'}, + 'endTime': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'instrumentName': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '200', 'blank': 'True'}), + 'instrumentStatus': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '256', 'blank': 'True'}), + 'kitType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'lastUpdate': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + 'logPath': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'message': ('django.db.models.fields.TextField', [], {'default': "''", 'blank': 'True'}), + 'operationMode': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'packageVer': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'progress': ('django.db.models.fields.FloatField', [], {'default': '0.0', 'blank': 'True'}), + 'reagentsExpiration': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'reagentsLot': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'reagentsPart': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'remainingSeconds': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'samplePrepDataType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'scriptVersion': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'solutionsExpiration': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'solutionsLot': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'solutionsPart': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'startTime': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + 'tipRackBarcode': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}) + }, + u'rundb.sampleset': { + 'Meta': {'object_name': 'SampleSet'}, + 'SampleGroupType_CV': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'sampleSets'", 'null': 'True', 'to': u"orm['rundb.SampleGroupType_CV']"}), + 'additionalCycles': ('django.db.models.fields.CharField', [], {'max_length': '64', 'null': 'True', 'blank': 'True'}), + 'categories': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '256', 'blank': 'True'}), + 'combinedLibraryTubeLabel': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'creationDate': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + 'creator': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'created_sampleSet'", 'on_delete': 'models.SET_DEFAULT', 'to': u"orm['auth.User']"}), + 'description': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}), + 'displayedName': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '127'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'lastModifiedDate': ('django.db.models.fields.DateTimeField', [], {'auto_now': 'True', 'blank': 'True'}), + 'lastModifiedUser': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'lastModified_sampleSet'", 'on_delete': 'models.SET_DEFAULT', 'to': u"orm['auth.User']"}), + 'libraryPrepInstrument': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'libraryPrepInstrumentData': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'libraryPrepData_sampleSet'", 'null': 'True', 'on_delete': 'models.SET_NULL', 'to': u"orm['rundb.SamplePrepData']"}), + 'libraryPrepKitName': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'libraryPrepPlateType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'libraryPrepProtocol': ('django.db.models.fields.CharField', [], {'max_length': '64', 'null': 'True', 'blank': 'True'}), + 'libraryPrepType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'pcrPlateSerialNum': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'null': 'True', 'blank': 'True'}), + 'status': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '512', 'blank': 'True'}) + }, + u'rundb.samplesetitem': { + 'Meta': {'object_name': 'SampleSetItem'}, + 'assayGroup': ('django.db.models.fields.CharField', [], {'max_length': '64', 'null': 'True', 'blank': 'True'}), + 'biopsyDays': ('django.db.models.fields.IntegerField', [], {'default': '0', 'null': 'True', 'blank': 'True'}), + 'cancerType': ('django.db.models.fields.CharField', [], {'max_length': '127', 'null': 'True', 'blank': 'True'}), + 'cellNum': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '127', 'null': 'True', 'blank': 'True'}), + 'cellularityPct': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'controlType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '127', 'null': 'True', 'blank': 'True'}), + 'coupleId': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '127', 'null': 'True', 'blank': 'True'}), + 'creationDate': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + 'creator': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'created_sampleSetItem'", 'on_delete': 'models.SET_DEFAULT', 'to': u"orm['auth.User']"}), + 'description': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '1024', 'null': 'True', 'blank': 'True'}), + 'dnabarcode': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'startBarcode'", 'null': 'True', 'to': u"orm['rundb.dnaBarcode']"}), + 'embryoId': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '127', 'null': 'True', 'blank': 'True'}), + 'endDnabarcode': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'endBarcode'", 'null': 'True', 'to': u"orm['rundb.dnaBarcode']"}), + 'gender': ('django.db.models.fields.CharField', [], {'max_length': '127', 'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'lastModifiedDate': ('django.db.models.fields.DateTimeField', [], {'auto_now': 'True', 'blank': 'True'}), + 'lastModifiedUser': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'lastModified_sampleSetItem'", 'on_delete': 'models.SET_DEFAULT', 'to': u"orm['auth.User']"}), + 'mouseStrains': ('django.db.models.fields.CharField', [], {'max_length': '127', 'null': 'True', 'blank': 'True'}), + 'nucleotideType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'panelPoolType': ('django.db.models.fields.CharField', [], {'max_length': '64', 'null': 'True', 'blank': 'True'}), + 'pcrPlateColumn': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '10', 'null': 'True', 'blank': 'True'}), + 'pcrPlateRow': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '10', 'null': 'True', 'blank': 'True'}), + 'population': ('django.db.models.fields.CharField', [], {'max_length': '127', 'null': 'True', 'blank': 'True'}), + 'relationshipGroup': ('django.db.models.fields.IntegerField', [], {}), + 'relationshipRole': ('django.db.models.fields.CharField', [], {'max_length': '127', 'null': 'True', 'blank': 'True'}), + 'sample': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'sampleSets'", 'to': u"orm['rundb.Sample']"}), + 'sampleCollectionDate': ('django.db.models.fields.DateField', [], {'null': 'True', 'blank': 'True'}), + 'sampleReceiptDate': ('django.db.models.fields.DateField', [], {'null': 'True', 'blank': 'True'}), + 'sampleSet': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'samples'", 'to': u"orm['rundb.SampleSet']"}), + 'sampleSource': ('django.db.models.fields.CharField', [], {'max_length': '64', 'null': 'True', 'blank': 'True'}), + 'tubePosition': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '10', 'null': 'True', 'blank': 'True'}) + }, + u'rundb.supportupload': { + 'Meta': {'object_name': 'SupportUpload'}, + 'account': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.RemoteAccount']"}), + 'celery_task_id': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '60', 'blank': 'True'}), + 'contact_email': ('django.db.models.fields.EmailField', [], {'default': "''", 'max_length': '75'}), + 'created': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + 'description': ('django.db.models.fields.TextField', [], {'default': "''"}), + 'file': ('django.db.models.fields.related.OneToOneField', [], {'to': u"orm['rundb.FileMonitor']", 'unique': 'True', 'null': 'True', 'on_delete': 'models.SET_NULL', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'local_message': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '2048', 'blank': 'True'}), + 'local_status': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '255', 'blank': 'True'}), + 'result': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.Results']", 'null': 'True', 'blank': 'True'}), + 'ticket_id': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '255', 'blank': 'True'}), + 'ticket_message': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '2048', 'blank': 'True'}), + 'ticket_status': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '255', 'blank': 'True'}), + 'updated': ('django.db.models.fields.DateTimeField', [], {'auto_now': 'True', 'blank': 'True'}), + 'user': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['auth.User']", 'on_delete': 'models.SET_DEFAULT'}) + }, + u'rundb.template': { + 'Meta': {'object_name': 'Template'}, + 'comments': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'isofficial': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'key': ('django.db.models.fields.CharField', [], {'max_length': '64'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '64'}), + 'sequence': ('django.db.models.fields.TextField', [], {'blank': 'True'}) + }, + u'rundb.tfmetrics': { + 'HPAccuracy': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + 'Meta': {'object_name': 'TFMetrics'}, + 'Q10Histo': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + 'Q10Mean': ('django.db.models.fields.FloatField', [], {}), + 'Q10ReadCount': ('django.db.models.fields.FloatField', [], {}), + 'Q17Histo': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + 'Q17Mean': ('django.db.models.fields.FloatField', [], {}), + 'Q17ReadCount': ('django.db.models.fields.FloatField', [], {}), + 'SysSNR': ('django.db.models.fields.FloatField', [], {}), + 'aveKeyCount': ('django.db.models.fields.FloatField', [], {}), + 'corrHPSNR': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'keypass': ('django.db.models.fields.FloatField', [], {}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '128', 'db_index': 'True'}), + 'number': ('django.db.models.fields.FloatField', [], {}), + 'report': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'tfmetrics_set'", 'to': u"orm['rundb.Results']"}), + 'sequence': ('django.db.models.fields.CharField', [], {'max_length': '512'}) + }, + u'rundb.threeprimeadapter': { + 'Meta': {'object_name': 'ThreePrimeadapter'}, + 'chemistryType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'description': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'blank': 'True'}), + 'direction': ('django.db.models.fields.CharField', [], {'default': "'Forward'", 'max_length': '20'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'isActive': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'isDefault': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '256'}), + 'runMode': ('django.db.models.fields.CharField', [], {'default': "'single'", 'max_length': '64', 'blank': 'True'}), + 'sequence': ('django.db.models.fields.CharField', [], {'max_length': '512'}), + 'uid': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '32'}) + }, + u'rundb.usereventlog': { + 'Meta': {'object_name': 'UserEventLog'}, + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'text': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + 'timeStamp': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + 'upload': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'logs'", 'to': u"orm['rundb.ContentUpload']"}) + }, + u'rundb.userprofile': { + 'Meta': {'object_name': 'UserProfile'}, + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'last_read_news_post': ('django.db.models.fields.DateTimeField', [], {'default': 'datetime.datetime(1984, 11, 5, 0, 0)'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '93'}), + 'needs_activation': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'note': ('django.db.models.fields.TextField', [], {'default': "''", 'blank': 'True'}), + 'phone_number': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '256', 'blank': 'True'}), + 'title': ('django.db.models.fields.CharField', [], {'default': "'user'", 'max_length': '256'}), + 'user': ('django.db.models.fields.related.OneToOneField', [], {'to': u"orm['auth.User']", 'unique': 'True'}) + } + } + + complete_apps = ['rundb'] \ No newline at end of file diff --git a/dbReports/iondb/rundb/migrations/0369_auto__add_field_globalconfig_password_max_age__add_field_userprofile_i.py b/dbReports/iondb/rundb/migrations/0369_auto__add_field_globalconfig_password_max_age__add_field_userprofile_i.py new file mode 100644 index 00000000..9c813749 --- /dev/null +++ b/dbReports/iondb/rundb/migrations/0369_auto__add_field_globalconfig_password_max_age__add_field_userprofile_i.py @@ -0,0 +1,1220 @@ +# -*- coding: utf-8 -*- +from south.utils import datetime_utils as datetime +from south.db import db +from south.v2 import SchemaMigration +from django.db import models + + +class Migration(SchemaMigration): + + def forwards(self, orm): + # Adding field 'GlobalConfig.password_max_age' + db.add_column(u'rundb_globalconfig', 'password_max_age', + self.gf('django.db.models.fields.IntegerField')(default=90, blank=True), + keep_default=False) + + # Adding field 'UserProfile.is_password_valid' + db.add_column(u'rundb_userprofile', 'is_password_valid', + self.gf('django.db.models.fields.BooleanField')(default=False), + keep_default=False) + + # Adding field 'UserProfile.last_password_changed_on' + db.add_column(u'rundb_userprofile', 'last_password_changed_on', + self.gf('django.db.models.fields.DateTimeField')(default=datetime.datetime(1984, 11, 5, 0, 0)), + keep_default=False) + + + def backwards(self, orm): + # Deleting field 'GlobalConfig.password_max_age' + db.delete_column(u'rundb_globalconfig', 'password_max_age') + + # Deleting field 'UserProfile.is_password_valid' + db.delete_column(u'rundb_userprofile', 'is_password_valid') + + # Deleting field 'UserProfile.last_password_changed_on' + db.delete_column(u'rundb_userprofile', 'last_password_changed_on') + + + models = { + u'auth.group': { + 'Meta': {'object_name': 'Group'}, + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '80'}), + 'permissions': ('django.db.models.fields.related.ManyToManyField', [], {'to': u"orm['auth.Permission']", 'symmetrical': 'False', 'blank': 'True'}) + }, + u'auth.permission': { + 'Meta': {'ordering': "(u'content_type__app_label', u'content_type__model', u'codename')", 'unique_together': "((u'content_type', u'codename'),)", 'object_name': 'Permission'}, + 'codename': ('django.db.models.fields.CharField', [], {'max_length': '100'}), + 'content_type': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['contenttypes.ContentType']"}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '50'}) + }, + u'auth.user': { + 'Meta': {'object_name': 'User'}, + 'date_joined': ('django.db.models.fields.DateTimeField', [], {'default': 'datetime.datetime.now'}), + 'email': ('django.db.models.fields.EmailField', [], {'max_length': '75', 'blank': 'True'}), + 'first_name': ('django.db.models.fields.CharField', [], {'max_length': '30', 'blank': 'True'}), + 'groups': ('django.db.models.fields.related.ManyToManyField', [], {'symmetrical': 'False', 'related_name': "u'user_set'", 'blank': 'True', 'to': u"orm['auth.Group']"}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'is_active': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'is_staff': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'is_superuser': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'last_login': ('django.db.models.fields.DateTimeField', [], {'default': 'datetime.datetime.now'}), + 'last_name': ('django.db.models.fields.CharField', [], {'max_length': '30', 'blank': 'True'}), + 'password': ('django.db.models.fields.CharField', [], {'max_length': '128'}), + 'user_permissions': ('django.db.models.fields.related.ManyToManyField', [], {'symmetrical': 'False', 'related_name': "u'user_set'", 'blank': 'True', 'to': u"orm['auth.Permission']"}), + 'username': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '30'}) + }, + u'contenttypes.contenttype': { + 'Meta': {'ordering': "('name',)", 'unique_together': "(('app_label', 'model'),)", 'object_name': 'ContentType', 'db_table': "'django_content_type'"}, + 'app_label': ('django.db.models.fields.CharField', [], {'max_length': '100'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'model': ('django.db.models.fields.CharField', [], {'max_length': '100'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '100'}) + }, + u'rundb.analysisargs': { + 'Meta': {'object_name': 'AnalysisArgs'}, + 'active': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'alignmentargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'analysisargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'applCategory': ('django.db.models.fields.CharField', [], {'max_length': '127', 'null': 'True', 'blank': 'True'}), + 'applGroup': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'applGroup_analysisArgs'", 'null': 'True', 'to': u"orm['rundb.ApplicationGroup']"}), + 'applType': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'applType_analysisArgs'", 'null': 'True', 'to': u"orm['rundb.RunType']"}), + 'basecallerargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'beadfindargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'calibrateargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'chipType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '128'}), + 'chip_default': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'creationDate': ('django.db.models.fields.DateTimeField', [], {'default': 'datetime.datetime.now', 'auto_now_add': 'True', 'null': 'True', 'blank': 'True'}), + 'creator': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'created_analysisArgs'", 'null': 'True', 'on_delete': 'models.SET_NULL', 'to': u"orm['auth.User']"}), + 'description': ('django.db.models.fields.CharField', [], {'max_length': '256', 'unique': 'True', 'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'ionstatsargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'isSystem': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'lastModifiedDate': ('django.db.models.fields.DateTimeField', [], {'default': 'datetime.datetime.now', 'auto_now': 'True', 'null': 'True', 'blank': 'True'}), + 'lastModifiedUser': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'lastModified_analysisArgs'", 'null': 'True', 'on_delete': 'models.SET_NULL', 'to': u"orm['auth.User']"}), + 'libraryKitName': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '512', 'blank': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '256'}), + 'prebasecallerargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'prethumbnailbasecallerargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'samplePrepKitName': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '512', 'blank': 'True'}), + 'sequenceKitName': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '512', 'blank': 'True'}), + 'templateKitName': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '512', 'blank': 'True'}), + 'thumbnailalignmentargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'thumbnailanalysisargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'thumbnailbasecallerargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'thumbnailbeadfindargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'thumbnailcalibrateargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'thumbnailionstatsargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}) + }, + u'rundb.analysismetrics': { + 'Meta': {'object_name': 'AnalysisMetrics'}, + 'adjusted_addressable': ('django.db.models.fields.IntegerField', [], {'default': '0'}), + 'amb': ('django.db.models.fields.IntegerField', [], {}), + 'bead': ('django.db.models.fields.IntegerField', [], {}), + 'dud': ('django.db.models.fields.IntegerField', [], {}), + 'empty': ('django.db.models.fields.IntegerField', [], {}), + 'excluded': ('django.db.models.fields.IntegerField', [], {}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'ignored': ('django.db.models.fields.IntegerField', [], {}), + 'keypass_all_beads': ('django.db.models.fields.IntegerField', [], {}), + 'lib': ('django.db.models.fields.IntegerField', [], {}), + 'libFinal': ('django.db.models.fields.IntegerField', [], {}), + 'libKp': ('django.db.models.fields.IntegerField', [], {}), + 'libLive': ('django.db.models.fields.IntegerField', [], {}), + 'libMix': ('django.db.models.fields.IntegerField', [], {}), + 'lib_pass_basecaller': ('django.db.models.fields.IntegerField', [], {}), + 'lib_pass_cafie': ('django.db.models.fields.IntegerField', [], {}), + 'live': ('django.db.models.fields.IntegerField', [], {}), + 'loading': ('django.db.models.fields.FloatField', [], {'default': '0.0'}), + 'pinned': ('django.db.models.fields.IntegerField', [], {}), + 'report': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'analysismetrics_set'", 'to': u"orm['rundb.Results']"}), + 'sysCF': ('django.db.models.fields.FloatField', [], {}), + 'sysDR': ('django.db.models.fields.FloatField', [], {}), + 'sysIE': ('django.db.models.fields.FloatField', [], {}), + 'tf': ('django.db.models.fields.IntegerField', [], {}), + 'tfFinal': ('django.db.models.fields.IntegerField', [], {}), + 'tfKp': ('django.db.models.fields.IntegerField', [], {}), + 'tfLive': ('django.db.models.fields.IntegerField', [], {}), + 'tfMix': ('django.db.models.fields.IntegerField', [], {}), + 'total': ('django.db.models.fields.IntegerField', [], {'default': '0'}), + 'washout': ('django.db.models.fields.IntegerField', [], {}), + 'washout_ambiguous': ('django.db.models.fields.IntegerField', [], {}), + 'washout_dud': ('django.db.models.fields.IntegerField', [], {}), + 'washout_library': ('django.db.models.fields.IntegerField', [], {}), + 'washout_live': ('django.db.models.fields.IntegerField', [], {}), + 'washout_test_fragment': ('django.db.models.fields.IntegerField', [], {}) + }, + u'rundb.applicationgroup': { + 'Meta': {'object_name': 'ApplicationGroup'}, + 'description': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'isActive': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '127'}), + 'uid': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '32'}) + }, + u'rundb.applproduct': { + 'Meta': {'object_name': 'ApplProduct'}, + 'applType': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.RunType']"}), + 'applicationGroup': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.ApplicationGroup']", 'null': 'True', 'blank': 'True'}), + 'barcodeKitSelectableType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'categories': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '256', 'null': 'True', 'blank': 'True'}), + 'defaultBarcodeKitName': ('django.db.models.fields.CharField', [], {'max_length': '128', 'null': 'True', 'blank': 'True'}), + 'defaultChipType': ('django.db.models.fields.CharField', [], {'max_length': '128', 'null': 'True', 'blank': 'True'}), + 'defaultControlSeqKit': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'controlSeqKit_applProduct_set'", 'null': 'True', 'to': u"orm['rundb.KitInfo']"}), + 'defaultFlowCount': ('django.db.models.fields.PositiveIntegerField', [], {'default': '0'}), + 'defaultFlowOrder': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'flowOrder_applProduct_set'", 'null': 'True', 'to': u"orm['rundb.FlowOrder']"}), + 'defaultGenomeRefName': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}), + 'defaultHotSpotRegionBedFileName': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}), + 'defaultIonChefPrepKit': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'ionChefPrepKit_applProduct_set'", 'null': 'True', 'to': u"orm['rundb.KitInfo']"}), + 'defaultIonChefSequencingKit': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'ionChefSeqKit_applProduct_set'", 'null': 'True', 'to': u"orm['rundb.KitInfo']"}), + 'defaultLibraryKit': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'libKit_applProduct_set'", 'null': 'True', 'to': u"orm['rundb.KitInfo']"}), + 'defaultSamplePrepKit': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'samplePrepKit_applProduct_set'", 'null': 'True', 'to': u"orm['rundb.KitInfo']"}), + 'defaultSamplePrepProtocol': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'common_CV_applProduct_set'", 'null': 'True', 'to': u"orm['rundb.common_CV']"}), + 'defaultSequencingKit': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'seqKit_applProduct_set'", 'null': 'True', 'to': u"orm['rundb.KitInfo']"}), + 'defaultTargetRegionBedFileName': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}), + 'defaultTemplateKit': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'templateKit_applProduct_set'", 'null': 'True', 'to': u"orm['rundb.KitInfo']"}), + 'description': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'blank': 'True'}), + 'dualBarcodingRule': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'instrumentType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'isActive': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'isBarcodeKitSelectionRequired': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isControlSeqTypeBySampleSupported': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isDefault': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isDefaultBarcoded': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isDefaultForInstrumentType': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isDualBarcodingBySampleSupported': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isDualNucleotideTypeBySampleSupported': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isHotSpotBEDFileBySampleSupported': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isHotspotRegionBEDFileSuppported': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'isReferenceBySampleSupported': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isReferenceSelectionSupported': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'isSamplePrepKitSupported': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'isTargetRegionBEDFileBySampleSupported': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isTargetRegionBEDFileSelectionRequiredForRefSelection': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isTargetRegionBEDFileSupported': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'isTargetTechniqueSelectionSupported': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'isVisible': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'productCode': ('django.db.models.fields.CharField', [], {'default': "'any'", 'unique': 'True', 'max_length': '64'}), + 'productName': ('django.db.models.fields.CharField', [], {'max_length': '128'}) + }, + u'rundb.backup': { + 'Meta': {'object_name': 'Backup'}, + 'backupDate': ('django.db.models.fields.DateTimeField', [], {}), + 'backupName': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '256'}), + 'backupPath': ('django.db.models.fields.CharField', [], {'max_length': '512'}), + 'experiment': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.Experiment']"}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'isBackedUp': ('django.db.models.fields.BooleanField', [], {}) + }, + u'rundb.chefpcrplateconfig': { + 'Meta': {'object_name': 'ChefPcrPlateconfig'}, + 'confg': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'kit': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.KitInfo']", 'null': 'True', 'blank': 'True'}) + }, + u'rundb.chip': { + 'Meta': {'object_name': 'Chip'}, + 'description': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '128'}), + 'earlyDatFileDeletion': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '1', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'instrumentType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'isActive': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '128'}), + 'slots': ('django.db.models.fields.IntegerField', [], {}) + }, + u'rundb.common_cv': { + 'Meta': {'unique_together': "(('cv_type', 'value'),)", 'object_name': 'common_CV'}, + 'categories': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '256', 'null': 'True', 'blank': 'True'}), + 'cv_type': ('django.db.models.fields.CharField', [], {'max_length': '127'}), + 'description': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}), + 'displayedValue': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '127'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'isActive': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'isDefault': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'isVisible': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'samplePrep_instrumentType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'sequencing_instrumentType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'uid': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '10'}), + 'value': ('django.db.models.fields.CharField', [], {'max_length': '127'}) + }, + u'rundb.content': { + 'Meta': {'object_name': 'Content'}, + 'application_tags': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + 'contentupload': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'contents'", 'to': u"orm['rundb.ContentUpload']"}), + 'description': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + 'enabled': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'extra': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + 'file': ('django.db.models.fields.CharField', [], {'max_length': '255'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'meta': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'blank': 'True'}), + 'notes': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + 'path': ('django.db.models.fields.CharField', [], {'max_length': '255'}), + 'publisher': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'contents'", 'to': u"orm['rundb.Publisher']"}), + 'type': ('django.db.models.fields.CharField', [], {'max_length': '128', 'blank': 'True'}) + }, + u'rundb.contentupload': { + 'Meta': {'object_name': 'ContentUpload'}, + 'file_path': ('django.db.models.fields.CharField', [], {'max_length': '255'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'meta': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'blank': 'True'}), + 'publisher': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.Publisher']", 'null': 'True'}), + 'source': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + 'status': ('django.db.models.fields.CharField', [], {'max_length': '255', 'blank': 'True'}), + 'upload_date': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'null': 'True', 'blank': 'True'}), + 'upload_type': ('django.db.models.fields.CharField', [], {'max_length': '128', 'blank': 'True'}), + 'username': ('django.db.models.fields.CharField', [], {'max_length': '128', 'blank': 'True'}) + }, + u'rundb.cruncher': { + 'Meta': {'object_name': 'Cruncher'}, + 'comments': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + 'date': ('django.db.models.fields.DateTimeField', [], {'auto_now': 'True', 'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'info': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'null': 'True', 'blank': 'True'}), + 'location': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.Location']"}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '200'}), + 'state': ('django.db.models.fields.CharField', [], {'default': "'U'", 'max_length': '8'}) + }, + u'rundb.dmfileset': { + 'Meta': {'object_name': 'DMFileSet'}, + 'auto_action': ('django.db.models.fields.CharField', [], {'default': "'OFF'", 'max_length': '8'}), + 'auto_trigger_age': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'auto_trigger_usage': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'backup_directory': ('django.db.models.fields.CharField', [], {'max_length': '256', 'null': 'True', 'blank': 'True'}), + 'bandwidth_limit': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'del_empty_dir': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'description': ('django.db.models.fields.CharField', [], {'max_length': '256', 'null': 'True', 'blank': 'True'}), + 'enabled': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'exclude': ('iondb.rundb.separatedValuesField.SeparatedValuesField', [], {'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'include': ('iondb.rundb.separatedValuesField.SeparatedValuesField', [], {'null': 'True', 'blank': 'True'}), + 'keepwith': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'null': 'True', 'blank': 'True'}), + 'type': ('django.db.models.fields.CharField', [], {'max_length': '48'}), + 'version': ('django.db.models.fields.CharField', [], {'max_length': '8'}) + }, + u'rundb.dmfilestat': { + 'Meta': {'object_name': 'DMFileStat'}, + 'action_state': ('django.db.models.fields.CharField', [], {'default': "'L'", 'max_length': '8'}), + 'archivepath': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'created': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + 'diskspace': ('django.db.models.fields.FloatField', [], {'null': 'True', 'blank': 'True'}), + 'dmfileset': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.DMFileSet']", 'null': 'True', 'blank': 'True'}), + 'files_in_use': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '512', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'preserve_data': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'result': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.Results']", 'null': 'True', 'blank': 'True'}), + 'user_comment': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'blank': 'True'}) + }, + u'rundb.dnabarcode': { + 'Meta': {'object_name': 'dnaBarcode'}, + 'active': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'adapter': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '128', 'blank': 'True'}), + 'annotation': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '512', 'blank': 'True'}), + 'end_adapter': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '128', 'blank': 'True'}), + 'end_sequence': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '128', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'id_str': ('django.db.models.fields.CharField', [], {'max_length': '128'}), + 'index': ('django.db.models.fields.IntegerField', [], {}), + 'is_end_barcode': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'length': ('django.db.models.fields.IntegerField', [], {'default': '0', 'blank': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '128'}), + 'score_cutoff': ('django.db.models.fields.FloatField', [], {'default': '0'}), + 'score_mode': ('django.db.models.fields.IntegerField', [], {'default': '0', 'blank': 'True'}), + 'sequence': ('django.db.models.fields.CharField', [], {'max_length': '128'}), + 'system': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'type': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}) + }, + u'rundb.emailaddress': { + 'Meta': {'object_name': 'EmailAddress'}, + 'email': ('django.db.models.fields.EmailField', [], {'max_length': '75', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'selected': ('django.db.models.fields.BooleanField', [], {}) + }, + u'rundb.eventlog': { + 'Meta': {'object_name': 'EventLog'}, + 'content_type': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'content_type_set_for_eventlog'", 'to': u"orm['contenttypes.ContentType']"}), + 'created': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'object_pk': ('django.db.models.fields.PositiveIntegerField', [], {}), + 'text': ('django.db.models.fields.TextField', [], {'max_length': '3000'}), + 'username': ('django.db.models.fields.CharField', [], {'default': "'ION'", 'max_length': '32', 'blank': 'True'}) + }, + u'rundb.experiment': { + 'Meta': {'object_name': 'Experiment'}, + 'autoAnalyze': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'baselineRun': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'chefChipExpiration1': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefChipExpiration2': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefChipType1': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefChipType2': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefEndTime': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + 'chefExtraInfo_1': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '128', 'blank': 'True'}), + 'chefExtraInfo_2': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '128', 'blank': 'True'}), + 'chefFlexibleWorkflow': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefInstrumentName': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '200', 'blank': 'True'}), + 'chefKitType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefLastUpdate': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + 'chefLogPath': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'chefLotNumber': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefManufactureDate': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefMessage': ('django.db.models.fields.TextField', [], {'default': "''", 'blank': 'True'}), + 'chefOperationMode': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefPackageVer': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefProgress': ('django.db.models.fields.FloatField', [], {'default': '0.0', 'blank': 'True'}), + 'chefProtocolDeviationName': ('django.db.models.fields.CharField', [], {'max_length': '127', 'null': 'True', 'blank': 'True'}), + 'chefReagentID': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefReagentsExpiration': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefReagentsLot': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefReagentsPart': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefReagentsSerialNum': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '20', 'blank': 'True'}), + 'chefRemainingSeconds': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'chefSamplePos': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefScriptVersion': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefSolutionsExpiration': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefSolutionsLot': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefSolutionsPart': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefSolutionsSerialNum': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '20', 'blank': 'True'}), + 'chefStartTime': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + 'chefStatus': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '256', 'blank': 'True'}), + 'chefTipRackBarcode': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chipBarcode': ('django.db.models.fields.CharField', [], {'max_length': '64', 'blank': 'True'}), + 'chipTecDfltAmbient': ('django.db.models.fields.FloatField', [], {'default': 'None', 'null': 'True', 'blank': 'True'}), + 'chipTecMinThreshold': ('django.db.models.fields.FloatField', [], {'default': 'None', 'null': 'True', 'blank': 'True'}), + 'chipTecSlope': ('django.db.models.fields.FloatField', [], {'default': 'None', 'null': 'True', 'blank': 'True'}), + 'chipType': ('django.db.models.fields.CharField', [], {'max_length': '32'}), + 'cycles': ('django.db.models.fields.IntegerField', [], {}), + 'date': ('django.db.models.fields.DateTimeField', [], {'db_index': 'True'}), + 'diskusage': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'displayName': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '128'}), + 'expCompInfo': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + 'expDir': ('django.db.models.fields.CharField', [], {'max_length': '512'}), + 'expName': ('django.db.models.fields.CharField', [], {'max_length': '128', 'db_index': 'True'}), + 'flows': ('django.db.models.fields.IntegerField', [], {}), + 'flowsInOrder': ('django.db.models.fields.CharField', [], {'max_length': '1200', 'blank': 'True'}), + 'ftpStatus': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'isReverseRun': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'log': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'blank': 'True'}), + 'manTecDfltAmbient': ('django.db.models.fields.FloatField', [], {'default': 'None', 'null': 'True', 'blank': 'True'}), + 'manTecMinThreshold': ('django.db.models.fields.FloatField', [], {'default': 'None', 'null': 'True', 'blank': 'True'}), + 'manTecSlope': ('django.db.models.fields.FloatField', [], {'default': 'None', 'null': 'True', 'blank': 'True'}), + 'metaData': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'blank': 'True'}), + 'notes': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}), + 'pgmName': ('django.db.models.fields.CharField', [], {'max_length': '64'}), + 'pinnedRepResult': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'plan': ('django.db.models.fields.related.OneToOneField', [], {'blank': 'True', 'related_name': "'experiment'", 'unique': 'True', 'null': 'True', 'to': u"orm['rundb.PlannedExperiment']"}), + 'platform': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '128', 'blank': 'True'}), + 'rawdatastyle': ('django.db.models.fields.CharField', [], {'default': "'single'", 'max_length': '24', 'null': 'True', 'blank': 'True'}), + 'reagentBarcode': ('django.db.models.fields.CharField', [], {'max_length': '64', 'blank': 'True'}), + 'repResult': ('django.db.models.fields.related.OneToOneField', [], {'related_name': "'+'", 'null': 'True', 'on_delete': 'models.SET_NULL', 'to': u"orm['rundb.Results']", 'blank': 'True', 'unique': 'True'}), + 'resultDate': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'null': 'True', 'db_index': 'True', 'blank': 'True'}), + 'reverse_primer': ('django.db.models.fields.CharField', [], {'max_length': '128', 'null': 'True', 'blank': 'True'}), + 'runMode': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'seqKitBarcode': ('django.db.models.fields.CharField', [], {'max_length': '64', 'blank': 'True'}), + 'sequencekitbarcode': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'sequencekitname': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'star': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'status': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '512', 'blank': 'True'}), + 'storageHost': ('django.db.models.fields.CharField', [], {'max_length': '128', 'null': 'True', 'blank': 'True'}), + 'storage_options': ('django.db.models.fields.CharField', [], {'default': "'A'", 'max_length': '200'}), + 'unique': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '512'}), + 'usePreBeadfind': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'user_ack': ('django.db.models.fields.CharField', [], {'default': "'U'", 'max_length': '24'}) + }, + u'rundb.experimentanalysissettings': { + 'Meta': {'object_name': 'ExperimentAnalysisSettings'}, + 'alignmentargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'analysisargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'barcodeKitName': ('django.db.models.fields.CharField', [], {'max_length': '128', 'null': 'True', 'blank': 'True'}), + 'barcodedSamples': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'null': 'True', 'blank': 'True'}), + 'base_recalibration_mode': ('django.db.models.fields.CharField', [], {'default': "'standard_recal'", 'max_length': '64'}), + 'basecallerargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'beadfindargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'calibrateargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'custom_args': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'date': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + 'endBarcodeKitName': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '128', 'null': 'True', 'blank': 'True'}), + 'experiment': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'eas_set'", 'null': 'True', 'to': u"orm['rundb.Experiment']"}), + 'hotSpotRegionBedFile': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'ionstatsargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'isDuplicateReads': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isEditable': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isOneTimeOverride': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'libraryKey': ('django.db.models.fields.CharField', [], {'max_length': '64', 'blank': 'True'}), + 'libraryKitBarcode': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'libraryKitName': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'mixedTypeRNA_hotSpotRegionBedFile': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}), + 'mixedTypeRNA_reference': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'mixedTypeRNA_targetRegionBedFile': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}), + 'prebasecallerargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'prethumbnailbasecallerargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'realign': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'reference': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'selectedPlugins': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'null': 'True', 'blank': 'True'}), + 'sseBedFile': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '1024', 'null': 'True', 'blank': 'True'}), + 'status': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '512', 'blank': 'True'}), + 'targetRegionBedFile': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}), + 'tfKey': ('django.db.models.fields.CharField', [], {'max_length': '64', 'blank': 'True'}), + 'threePrimeAdapter': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'thumbnailalignmentargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'thumbnailanalysisargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'thumbnailbasecallerargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'thumbnailbeadfindargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'thumbnailcalibrateargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'thumbnailionstatsargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}) + }, + u'rundb.filemonitor': { + 'Meta': {'object_name': 'FileMonitor'}, + 'celery_task_id': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '60', 'blank': 'True'}), + 'created': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'local_dir': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '512'}), + 'md5sum': ('django.db.models.fields.CharField', [], {'default': 'None', 'max_length': '32', 'null': 'True', 'blank': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '255'}), + 'progress': ('django.db.models.fields.BigIntegerField', [], {'default': '0'}), + 'size': ('django.db.models.fields.BigIntegerField', [], {'default': 'None', 'null': 'True'}), + 'status': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '60'}), + 'tags': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '1024'}), + 'updated': ('django.db.models.fields.DateTimeField', [], {'auto_now': 'True', 'blank': 'True'}), + 'url': ('django.db.models.fields.CharField', [], {'max_length': '2000'}) + }, + u'rundb.fileserver': { + 'Meta': {'object_name': 'FileServer'}, + 'comments': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + 'filesPrefix': ('django.db.models.fields.CharField', [], {'max_length': '200'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'location': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.Location']"}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '200'}), + 'percentfull': ('django.db.models.fields.FloatField', [], {'default': '0.0', 'null': 'True', 'blank': 'True'}) + }, + u'rundb.floworder': { + 'Meta': {'object_name': 'FlowOrder'}, + 'description': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '128', 'blank': 'True'}), + 'flowOrder': ('django.db.models.fields.CharField', [], {'max_length': '1200', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'isActive': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'isDefault': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isSystem': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '64'}) + }, + u'rundb.globalconfig': { + 'Meta': {'object_name': 'GlobalConfig'}, + 'auto_archive_ack': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'auto_archive_enable': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'base_recalibration_mode': ('django.db.models.fields.CharField', [], {'default': "'standard_recal'", 'max_length': '64'}), + 'check_news_posts': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'cluster_auto_disable': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'default_flow_order': ('django.db.models.fields.CharField', [], {'max_length': '100', 'blank': 'True'}), + 'default_library_key': ('django.db.models.fields.CharField', [], {'max_length': '50', 'blank': 'True'}), + 'default_storage_options': ('django.db.models.fields.CharField', [], {'default': "'D'", 'max_length': '500', 'blank': 'True'}), + 'default_test_fragment_key': ('django.db.models.fields.CharField', [], {'max_length': '50', 'blank': 'True'}), + 'enable_auto_pkg_dl': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'enable_auto_security': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'enable_compendia_OCP': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'enable_nightly_email': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'enable_support_upload': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'enable_version_lock': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'majorPlatform': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '24', 'null': 'True', 'blank': 'True'}), + 'mark_duplicates': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '512'}), + 'password_max_age': ('django.db.models.fields.IntegerField', [], {'default': '90', 'blank': 'True'}), + 'plugin_output_folder': ('django.db.models.fields.CharField', [], {'max_length': '500', 'blank': 'True'}), + 'realign': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'records_to_display': ('django.db.models.fields.IntegerField', [], {'default': '20', 'blank': 'True'}), + 'sec_update_status': ('django.db.models.fields.CharField', [], {'max_length': '128', 'blank': 'True'}), + 'selected': ('django.db.models.fields.BooleanField', [], {}), + 'site_name': ('django.db.models.fields.CharField', [], {'max_length': '500', 'blank': 'True'}), + 'telemetry_enabled': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'ts_update_status': ('django.db.models.fields.CharField', [], {'max_length': '256', 'blank': 'True'}), + 'web_root': ('django.db.models.fields.CharField', [], {'max_length': '500', 'blank': 'True'}) + }, + u'rundb.ionmeshnode': { + 'Meta': {'object_name': 'IonMeshNode'}, + 'active': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'apikey_local': ('django.db.models.fields.CharField', [], {'max_length': '256', 'null': 'True', 'blank': 'True'}), + 'apikey_remote': ('django.db.models.fields.CharField', [], {'max_length': '256', 'null': 'True', 'blank': 'True'}), + 'hostname': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '128'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '128', 'unique': 'True', 'null': 'True', 'blank': 'True'}), + 'system_id': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '37'}) + }, + u'rundb.kitinfo': { + 'Meta': {'unique_together': "(('kitType', 'name'),)", 'object_name': 'KitInfo'}, + 'applicationType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'null': 'True', 'blank': 'True'}), + 'cartridgeBetweenUsageAbsoluteMaxDayLimit': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'cartridgeExpirationDayLimit': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'categories': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '256', 'null': 'True', 'blank': 'True'}), + 'chipTypes': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '127', 'blank': 'True'}), + 'defaultCartridgeUsageCount': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'defaultFlowOrder': ('django.db.models.fields.related.ForeignKey', [], {'default': 'None', 'to': u"orm['rundb.FlowOrder']", 'null': 'True', 'blank': 'True'}), + 'defaultThreePrimeAdapter': ('django.db.models.fields.related.ForeignKey', [], {'default': 'None', 'to': u"orm['rundb.ThreePrimeadapter']", 'null': 'True', 'blank': 'True'}), + 'description': ('django.db.models.fields.CharField', [], {'max_length': '3024', 'blank': 'True'}), + 'flowCount': ('django.db.models.fields.PositiveIntegerField', [], {}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'instrumentType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'isActive': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'kitType': ('django.db.models.fields.CharField', [], {'max_length': '64'}), + 'libraryReadLength': ('django.db.models.fields.PositiveIntegerField', [], {'default': '0'}), + 'name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '512'}), + 'nucleotideType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'runMode': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'samplePrep_instrumentType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'uid': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '10'}) + }, + u'rundb.kitpart': { + 'Meta': {'unique_together': "(('barcode',),)", 'object_name': 'KitPart'}, + 'barcode': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '64'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'kit': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.KitInfo']"}) + }, + u'rundb.libmetrics': { + 'Genome_Version': ('django.db.models.fields.CharField', [], {'max_length': '512'}), + 'Index_Version': ('django.db.models.fields.CharField', [], {'max_length': '512'}), + 'Meta': {'object_name': 'LibMetrics'}, + 'align_sample': ('django.db.models.fields.IntegerField', [], {}), + 'aveKeyCounts': ('django.db.models.fields.FloatField', [], {}), + 'cf': ('django.db.models.fields.FloatField', [], {}), + 'dr': ('django.db.models.fields.FloatField', [], {}), + 'duplicate_reads': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'genome': ('django.db.models.fields.CharField', [], {'max_length': '512'}), + 'genomesize': ('django.db.models.fields.BigIntegerField', [], {}), + 'i100Q10_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i100Q17_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i100Q20_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i100Q47_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i100Q7_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i150Q10_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i150Q17_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i150Q20_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i150Q47_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i150Q7_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i200Q10_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i200Q17_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i200Q20_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i200Q47_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i200Q7_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i250Q10_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i250Q17_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i250Q20_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i250Q47_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i250Q7_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i300Q10_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i300Q17_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i300Q20_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i300Q47_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i300Q7_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i350Q10_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i350Q17_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i350Q20_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i350Q47_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i350Q7_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i400Q10_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i400Q17_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i400Q20_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i400Q47_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i400Q7_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i450Q10_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i450Q17_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i450Q20_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i450Q47_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i450Q7_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i500Q10_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i500Q17_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i500Q20_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i500Q47_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i500Q7_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i50Q10_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i50Q17_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i50Q20_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i50Q47_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i50Q7_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i550Q10_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i550Q17_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i550Q20_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i550Q47_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i550Q7_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i600Q10_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i600Q17_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i600Q20_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i600Q47_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i600Q7_reads': ('django.db.models.fields.IntegerField', [], {}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'ie': ('django.db.models.fields.FloatField', [], {}), + 'q10_alignments': ('django.db.models.fields.IntegerField', [], {}), + 'q10_longest_alignment': ('django.db.models.fields.IntegerField', [], {}), + 'q10_mapped_bases': ('django.db.models.fields.BigIntegerField', [], {}), + 'q10_mean_alignment_length': ('django.db.models.fields.IntegerField', [], {}), + 'q17_alignments': ('django.db.models.fields.IntegerField', [], {}), + 'q17_longest_alignment': ('django.db.models.fields.IntegerField', [], {}), + 'q17_mapped_bases': ('django.db.models.fields.BigIntegerField', [], {}), + 'q17_mean_alignment_length': ('django.db.models.fields.IntegerField', [], {}), + 'q20_alignments': ('django.db.models.fields.IntegerField', [], {}), + 'q20_longest_alignment': ('django.db.models.fields.IntegerField', [], {}), + 'q20_mapped_bases': ('django.db.models.fields.BigIntegerField', [], {}), + 'q20_mean_alignment_length': ('django.db.models.fields.IntegerField', [], {}), + 'q47_alignments': ('django.db.models.fields.IntegerField', [], {}), + 'q47_longest_alignment': ('django.db.models.fields.IntegerField', [], {}), + 'q47_mapped_bases': ('django.db.models.fields.BigIntegerField', [], {}), + 'q47_mean_alignment_length': ('django.db.models.fields.IntegerField', [], {}), + 'q7_alignments': ('django.db.models.fields.IntegerField', [], {}), + 'q7_longest_alignment': ('django.db.models.fields.IntegerField', [], {}), + 'q7_mapped_bases': ('django.db.models.fields.BigIntegerField', [], {}), + 'q7_mean_alignment_length': ('django.db.models.fields.IntegerField', [], {}), + 'raw_accuracy': ('django.db.models.fields.FloatField', [], {}), + 'report': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'libmetrics_set'", 'to': u"orm['rundb.Results']"}), + 'sysSNR': ('django.db.models.fields.FloatField', [], {}), + 'totalNumReads': ('django.db.models.fields.IntegerField', [], {}), + 'total_mapped_reads': ('django.db.models.fields.BigIntegerField', [], {}), + 'total_mapped_target_bases': ('django.db.models.fields.BigIntegerField', [], {}) + }, + u'rundb.librarykey': { + 'Meta': {'object_name': 'LibraryKey'}, + 'description': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'blank': 'True'}), + 'direction': ('django.db.models.fields.CharField', [], {'default': "'Forward'", 'max_length': '20'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'isDefault': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '256'}), + 'runMode': ('django.db.models.fields.CharField', [], {'default': "'single'", 'max_length': '64', 'blank': 'True'}), + 'sequence': ('django.db.models.fields.CharField', [], {'max_length': '64'}) + }, + u'rundb.location': { + 'Meta': {'object_name': 'Location'}, + 'comments': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + 'defaultlocation': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '200'}) + }, + u'rundb.message': { + 'Meta': {'object_name': 'Message'}, + 'body': ('django.db.models.fields.TextField', [], {'default': "''", 'blank': 'True'}), + 'expires': ('django.db.models.fields.TextField', [], {'default': "'read'", 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'level': ('django.db.models.fields.IntegerField', [], {'default': '20'}), + 'route': ('django.db.models.fields.TextField', [], {'default': "''", 'blank': 'True'}), + 'status': ('django.db.models.fields.TextField', [], {'default': "'unread'", 'blank': 'True'}), + 'tags': ('django.db.models.fields.TextField', [], {'default': "''", 'blank': 'True'}), + 'time': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}) + }, + u'rundb.monitordata': { + 'Meta': {'object_name': 'MonitorData'}, + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '128'}), + 'treeDat': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'blank': 'True'}) + }, + u'rundb.newspost': { + 'Meta': {'object_name': 'NewsPost'}, + 'guid': ('django.db.models.fields.CharField', [], {'max_length': '2083', 'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'link': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '2083', 'blank': 'True'}), + 'summary': ('django.db.models.fields.TextField', [], {'default': "''", 'blank': 'True'}), + 'title': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '1024', 'blank': 'True'}), + 'updated': ('django.db.models.fields.DateTimeField', [], {'default': 'datetime.datetime.now'}) + }, + u'rundb.plannedexperiment': { + 'Meta': {'ordering': "['-id']", 'object_name': 'PlannedExperiment'}, + 'adapter': ('django.db.models.fields.CharField', [], {'max_length': '256', 'null': 'True', 'blank': 'True'}), + 'applicationGroup': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.ApplicationGroup']", 'null': 'True'}), + 'autoName': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'categories': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'null': 'True', 'db_index': 'True', 'blank': 'True'}), + 'controlSequencekitname': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'cycles': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'date': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + 'expName': ('django.db.models.fields.CharField', [], {'max_length': '128', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'irworkflow': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'blank': 'True'}), + 'isCustom_kitSettings': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isFavorite': ('django.db.models.fields.BooleanField', [], {'default': 'False', 'db_index': 'True'}), + 'isPlanGroup': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isReusable': ('django.db.models.fields.BooleanField', [], {'default': 'False', 'db_index': 'True'}), + 'isReverseRun': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isSystem': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isSystemDefault': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'latestEAS': ('django.db.models.fields.related.OneToOneField', [], {'related_name': "'+'", 'null': 'True', 'on_delete': 'models.SET_NULL', 'to': u"orm['rundb.ExperimentAnalysisSettings']", 'blank': 'True', 'unique': 'True'}), + 'libkit': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'libraryPool': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '12', 'null': 'True', 'blank': 'True'}), + 'libraryReadLength': ('django.db.models.fields.PositiveIntegerField', [], {'default': '0'}), + 'metaData': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'blank': 'True'}), + 'origin': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'null': 'True', 'blank': 'True'}), + 'pairedEndLibraryAdapterName': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'parentPlan': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'childPlan_set'", 'null': 'True', 'to': u"orm['rundb.PlannedExperiment']"}), + 'planDisplayedName': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'planExecuted': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'planExecutedDate': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + 'planGUID': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'planName': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'planPGM': ('django.db.models.fields.CharField', [], {'max_length': '128', 'null': 'True', 'blank': 'True'}), + 'planShortID': ('django.db.models.fields.CharField', [], {'db_index': 'True', 'max_length': '5', 'null': 'True', 'blank': 'True'}), + 'planStatus': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '512', 'db_index': 'True', 'blank': 'True'}), + 'preAnalysis': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'projects': ('django.db.models.fields.related.ManyToManyField', [], {'symmetrical': 'False', 'related_name': "'plans'", 'blank': 'True', 'to': u"orm['rundb.Project']"}), + 'qcValues': ('django.db.models.fields.related.ManyToManyField', [], {'to': u"orm['rundb.QCType']", 'null': 'True', 'through': u"orm['rundb.PlannedExperimentQC']", 'symmetrical': 'False'}), + 'reverse_primer': ('django.db.models.fields.CharField', [], {'max_length': '128', 'null': 'True', 'blank': 'True'}), + 'runMode': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'runType': ('django.db.models.fields.CharField', [], {'default': "'GENS'", 'max_length': '512', 'db_index': 'True'}), + 'runname': ('django.db.models.fields.CharField', [], {'max_length': '255', 'null': 'True', 'blank': 'True'}), + 'sampleGrouping': ('django.db.models.fields.related.ForeignKey', [], {'default': 'None', 'to': u"orm['rundb.SampleGroupType_CV']", 'null': 'True', 'blank': 'True'}), + 'samplePrepKitName': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'samplePrepProtocol': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'null': 'True', 'blank': 'True'}), + 'sampleSets': ('django.db.models.fields.related.ManyToManyField', [], {'blank': 'True', 'related_name': "'plans'", 'null': 'True', 'symmetrical': 'False', 'to': u"orm['rundb.SampleSet']"}), + 'sampleTubeLabel': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'seqKitBarcode': ('django.db.models.fields.CharField', [], {'max_length': '64', 'null': 'True', 'blank': 'True'}), + 'storageHost': ('django.db.models.fields.CharField', [], {'max_length': '128', 'null': 'True', 'blank': 'True'}), + 'storage_options': ('django.db.models.fields.CharField', [], {'default': "'A'", 'max_length': '200'}), + 'templatingKitBarcode': ('django.db.models.fields.CharField', [], {'max_length': '64', 'null': 'True', 'blank': 'True'}), + 'templatingKitName': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'usePostBeadfind': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'usePreBeadfind': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'username': ('django.db.models.fields.CharField', [], {'max_length': '128', 'null': 'True', 'blank': 'True'}) + }, + u'rundb.plannedexperimentqc': { + 'Meta': {'unique_together': "(('plannedExperiment', 'qcType'),)", 'object_name': 'PlannedExperimentQC'}, + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'plannedExperiment': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.PlannedExperiment']"}), + 'qcType': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.QCType']"}), + 'threshold': ('django.db.models.fields.PositiveIntegerField', [], {'default': '0'}) + }, + u'rundb.plansession': { + 'Meta': {'object_name': 'PlanSession'}, + '_session_data': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + 'expire_date': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'plan_key': ('django.db.models.fields.CharField', [], {'max_length': '64'}), + 'session_key': ('django.db.models.fields.CharField', [], {'max_length': '64'}) + }, + u'rundb.plugin': { + 'Meta': {'unique_together': "(('name', 'version'),)", 'object_name': 'Plugin'}, + 'active': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'config': ('django.db.models.fields.TextField', [], {'default': "''", 'null': 'True', 'blank': 'True'}), + 'date': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + 'defaultSelected': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'description': ('django.db.models.fields.TextField', [], {'default': "''", 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'majorBlock': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '512', 'db_index': 'True'}), + 'packageName': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '256', 'db_column': "'packagename'", 'blank': 'True'}), + 'path': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '512', 'blank': 'True'}), + 'pluginsettings': ('django.db.models.fields.TextField', [], {'default': "''", 'null': 'True', 'blank': 'True'}), + 'requires_configuration': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'script': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '256', 'blank': 'True'}), + 'selected': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'status': ('django.db.models.fields.TextField', [], {'default': "''", 'null': 'True', 'blank': 'True'}), + 'url': ('django.db.models.fields.URLField', [], {'default': "''", 'max_length': '256', 'blank': 'True'}), + 'userinputfields': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'null': 'True', 'blank': 'True'}), + 'version': ('django.db.models.fields.CharField', [], {'max_length': '256'}) + }, + u'rundb.pluginresult': { + 'Meta': {'ordering': "['-id']", 'object_name': 'PluginResult'}, + 'apikey': ('django.db.models.fields.CharField', [], {'max_length': '256', 'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'inodes': ('django.db.models.fields.BigIntegerField', [], {'default': '-1'}), + 'owner': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['auth.User']", 'on_delete': 'models.SET_DEFAULT'}), + 'plugin': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.Plugin']"}), + 'result': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'pluginresult_set'", 'to': u"orm['rundb.Results']"}), + 'size': ('django.db.models.fields.BigIntegerField', [], {'default': '-1'}), + 'store': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'blank': 'True'}), + 'validation_errors': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'blank': 'True'}) + }, + u'rundb.pluginresultjob': { + 'Meta': {'object_name': 'PluginResultJob'}, + 'config': ('django.db.models.fields.TextField', [], {'default': "''", 'blank': 'True'}), + 'endtime': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + 'grid_engine_jobid': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'plugin_result': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'plugin_result_jobs'", 'to': u"orm['rundb.PluginResult']"}), + 'run_level': ('django.db.models.fields.CharField', [], {'max_length': '20'}), + 'starttime': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + 'state': ('django.db.models.fields.CharField', [], {'max_length': '20'}) + }, + u'rundb.project': { + 'Meta': {'object_name': 'Project'}, + 'created': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + 'creator': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['auth.User']", 'on_delete': 'models.SET_DEFAULT'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'modified': ('django.db.models.fields.DateTimeField', [], {'auto_now': 'True', 'blank': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '64'}), + 'public': ('django.db.models.fields.BooleanField', [], {'default': 'True'}) + }, + u'rundb.publisher': { + 'Meta': {'object_name': 'Publisher'}, + 'date': ('django.db.models.fields.DateTimeField', [], {}), + 'global_meta': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '200'}), + 'path': ('django.db.models.fields.CharField', [], {'max_length': '512'}), + 'version': ('django.db.models.fields.CharField', [], {'max_length': '256'}) + }, + u'rundb.qctype': { + 'Meta': {'object_name': 'QCType'}, + 'defaultThreshold': ('django.db.models.fields.PositiveIntegerField', [], {'default': '0'}), + 'description': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'maxThreshold': ('django.db.models.fields.PositiveIntegerField', [], {'default': '100'}), + 'minThreshold': ('django.db.models.fields.PositiveIntegerField', [], {'default': '0'}), + 'qcName': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '512'}) + }, + u'rundb.qualitymetrics': { + 'Meta': {'object_name': 'QualityMetrics'}, + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'q0_100bp_reads': ('django.db.models.fields.IntegerField', [], {}), + 'q0_150bp_reads': ('django.db.models.fields.IntegerField', [], {'default': '0'}), + 'q0_50bp_reads': ('django.db.models.fields.IntegerField', [], {}), + 'q0_bases': ('django.db.models.fields.BigIntegerField', [], {}), + 'q0_max_read_length': ('django.db.models.fields.IntegerField', [], {}), + 'q0_mean_read_length': ('django.db.models.fields.FloatField', [], {}), + 'q0_median_read_length': ('django.db.models.fields.IntegerField', [], {'default': '0'}), + 'q0_mode_read_length': ('django.db.models.fields.IntegerField', [], {'default': '0'}), + 'q0_reads': ('django.db.models.fields.IntegerField', [], {}), + 'q17_100bp_reads': ('django.db.models.fields.IntegerField', [], {}), + 'q17_150bp_reads': ('django.db.models.fields.IntegerField', [], {}), + 'q17_50bp_reads': ('django.db.models.fields.IntegerField', [], {}), + 'q17_bases': ('django.db.models.fields.BigIntegerField', [], {}), + 'q17_max_read_length': ('django.db.models.fields.IntegerField', [], {}), + 'q17_mean_read_length': ('django.db.models.fields.FloatField', [], {}), + 'q17_median_read_length': ('django.db.models.fields.IntegerField', [], {'default': '0'}), + 'q17_mode_read_length': ('django.db.models.fields.IntegerField', [], {'default': '0'}), + 'q17_reads': ('django.db.models.fields.IntegerField', [], {}), + 'q20_100bp_reads': ('django.db.models.fields.IntegerField', [], {}), + 'q20_150bp_reads': ('django.db.models.fields.IntegerField', [], {}), + 'q20_50bp_reads': ('django.db.models.fields.IntegerField', [], {}), + 'q20_bases': ('django.db.models.fields.BigIntegerField', [], {}), + 'q20_max_read_length': ('django.db.models.fields.FloatField', [], {}), + 'q20_mean_read_length': ('django.db.models.fields.IntegerField', [], {}), + 'q20_median_read_length': ('django.db.models.fields.IntegerField', [], {'default': '0'}), + 'q20_mode_read_length': ('django.db.models.fields.IntegerField', [], {'default': '0'}), + 'q20_reads': ('django.db.models.fields.IntegerField', [], {}), + 'report': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'qualitymetrics_set'", 'to': u"orm['rundb.Results']"}) + }, + u'rundb.referencegenome': { + 'Meta': {'ordering': "['short_name']", 'object_name': 'ReferenceGenome'}, + 'celery_task_id': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '60', 'blank': 'True'}), + 'date': ('django.db.models.fields.DateTimeField', [], {'default': 'datetime.datetime.now'}), + 'enabled': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'file_monitor': ('django.db.models.fields.related.OneToOneField', [], {'to': u"orm['rundb.FileMonitor']", 'unique': 'True', 'null': 'True', 'on_delete': 'models.SET_NULL', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'identity_hash': ('django.db.models.fields.CharField', [], {'default': 'None', 'max_length': '40', 'null': 'True', 'blank': 'True'}), + 'index_version': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '512'}), + 'notes': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + 'reference_path': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'blank': 'True'}), + 'short_name': ('django.db.models.fields.CharField', [], {'max_length': '512'}), + 'source': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + 'species': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + 'status': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + 'verbose_error': ('django.db.models.fields.CharField', [], {'max_length': '3000', 'blank': 'True'}), + 'version': ('django.db.models.fields.CharField', [], {'max_length': '100', 'blank': 'True'}) + }, + u'rundb.remoteaccount': { + 'Meta': {'object_name': 'RemoteAccount'}, + 'access_token': ('django.db.models.fields.CharField', [], {'max_length': '2048', 'null': 'True', 'blank': 'True'}), + 'account_label': ('django.db.models.fields.CharField', [], {'default': "'Unnamed Account'", 'max_length': '64'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'refresh_token': ('django.db.models.fields.CharField', [], {'max_length': '2048', 'null': 'True', 'blank': 'True'}), + 'remote_resource': ('django.db.models.fields.CharField', [], {'max_length': '2048'}), + 'token_expires': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + 'user_name': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '255', 'blank': 'True'}) + }, + u'rundb.reportstorage': { + 'Meta': {'object_name': 'ReportStorage'}, + 'default': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'dirPath': ('django.db.models.fields.CharField', [], {'max_length': '200'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '200'}), + 'webServerPath': ('django.db.models.fields.CharField', [], {'max_length': '200'}) + }, + u'rundb.results': { + 'Meta': {'object_name': 'Results'}, + 'analysisVersion': ('django.db.models.fields.CharField', [], {'max_length': '256'}), + 'analysismetrics': ('django.db.models.fields.related.OneToOneField', [], {'to': u"orm['rundb.AnalysisMetrics']", 'unique': 'True', 'null': 'True', 'blank': 'True'}), + 'autoExempt': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'diskusage': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'eas': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'results_set'", 'null': 'True', 'to': u"orm['rundb.ExperimentAnalysisSettings']"}), + 'experiment': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'results_set'", 'to': u"orm['rundb.Experiment']"}), + 'framesProcessed': ('django.db.models.fields.IntegerField', [], {}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'libmetrics': ('django.db.models.fields.related.OneToOneField', [], {'to': u"orm['rundb.LibMetrics']", 'unique': 'True', 'null': 'True', 'blank': 'True'}), + 'log': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + 'metaData': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'blank': 'True'}), + 'parentIDs': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + 'parentResult': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'childResults_set'", 'null': 'True', 'on_delete': 'models.SET_NULL', 'to': u"orm['rundb.Results']"}), + 'processedCycles': ('django.db.models.fields.IntegerField', [], {}), + 'processedflows': ('django.db.models.fields.IntegerField', [], {}), + 'projects': ('django.db.models.fields.related.ManyToManyField', [], {'related_name': "'results'", 'symmetrical': 'False', 'to': u"orm['rundb.Project']"}), + 'qualitymetrics': ('django.db.models.fields.related.OneToOneField', [], {'to': u"orm['rundb.QualityMetrics']", 'unique': 'True', 'null': 'True', 'blank': 'True'}), + 'reference': ('django.db.models.fields.CharField', [], {'max_length': '64', 'null': 'True', 'blank': 'True'}), + 'reportLink': ('django.db.models.fields.CharField', [], {'max_length': '512'}), + 'reportStatus': ('django.db.models.fields.CharField', [], {'default': "'Nothing'", 'max_length': '64', 'null': 'True'}), + 'reportstorage': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'storage'", 'null': 'True', 'to': u"orm['rundb.ReportStorage']"}), + 'representative': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'resultsName': ('django.db.models.fields.CharField', [], {'max_length': '512'}), + 'resultsType': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + 'runid': ('django.db.models.fields.CharField', [], {'max_length': '10', 'blank': 'True'}), + 'status': ('django.db.models.fields.CharField', [], {'max_length': '64'}), + 'timeStamp': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'db_index': 'True', 'blank': 'True'}), + 'timeToComplete': ('django.db.models.fields.CharField', [], {'max_length': '64'}) + }, + u'rundb.rig': { + 'Meta': {'object_name': 'Rig'}, + 'alarms': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'blank': 'True'}), + 'comments': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + 'display_state': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + 'ftppassword': ('django.db.models.fields.CharField', [], {'default': "'ionguest'", 'max_length': '64'}), + 'ftprootdir': ('django.db.models.fields.CharField', [], {'default': "'results'", 'max_length': '64'}), + 'ftpserver': ('django.db.models.fields.CharField', [], {'default': "'192.168.201.1'", 'max_length': '128'}), + 'ftpusername': ('django.db.models.fields.CharField', [], {'default': "'ionguest'", 'max_length': '64'}), + 'host_address': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'blank': 'True'}), + 'last_clean_date': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + 'last_experiment': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + 'last_init_date': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + 'location': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.Location']"}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '200', 'primary_key': 'True'}), + 'serial': ('django.db.models.fields.CharField', [], {'max_length': '24', 'null': 'True', 'blank': 'True'}), + 'state': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + 'type': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'blank': 'True'}), + 'updateCommand': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'blank': 'True'}), + 'updateflag': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'updatehome': ('django.db.models.fields.CharField', [], {'default': "'192.168.201.1'", 'max_length': '256'}), + 'version': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'blank': 'True'}) + }, + u'rundb.runtype': { + 'Meta': {'object_name': 'RunType'}, + 'alternate_name': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'applicationGroups': ('django.db.models.fields.related.ManyToManyField', [], {'symmetrical': 'False', 'related_name': "'applications'", 'null': 'True', 'to': u"orm['rundb.ApplicationGroup']"}), + 'barcode': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + 'description': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'isActive': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'meta': ('django.db.models.fields.TextField', [], {'default': "''", 'null': 'True', 'blank': 'True'}), + 'nucleotideType': ('django.db.models.fields.CharField', [], {'default': "'dna'", 'max_length': '64', 'blank': 'True'}), + 'runType': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '512'}) + }, + u'rundb.sample': { + 'Meta': {'unique_together': "(('name', 'externalId'),)", 'object_name': 'Sample'}, + 'date': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'null': 'True', 'blank': 'True'}), + 'description': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}), + 'displayedName': ('django.db.models.fields.CharField', [], {'max_length': '127', 'null': 'True', 'blank': 'True'}), + 'experiments': ('django.db.models.fields.related.ManyToManyField', [], {'symmetrical': 'False', 'related_name': "'samples'", 'null': 'True', 'to': u"orm['rundb.Experiment']"}), + 'externalId': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '127', 'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '127', 'null': 'True', 'blank': 'True'}), + 'status': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '512', 'blank': 'True'}) + }, + u'rundb.sampleannotation_cv': { + 'Meta': {'object_name': 'SampleAnnotation_CV'}, + 'annotationType': ('django.db.models.fields.CharField', [], {'max_length': '127'}), + 'iRAnnotationType': ('django.db.models.fields.CharField', [], {'max_length': '127', 'null': 'True', 'blank': 'True'}), + 'iRValue': ('django.db.models.fields.CharField', [], {'max_length': '127', 'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'isActive': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'isIRCompatible': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'sampleGroupType_CV': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'sampleAnnotation_set'", 'null': 'True', 'to': u"orm['rundb.SampleGroupType_CV']"}), + 'uid': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '32'}), + 'value': ('django.db.models.fields.CharField', [], {'max_length': '127', 'blank': 'True'}) + }, + u'rundb.sampleattribute': { + 'Meta': {'object_name': 'SampleAttribute'}, + 'creationDate': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + 'creator': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'created_sampleAttribute'", 'on_delete': 'models.SET_DEFAULT', 'to': u"orm['auth.User']"}), + 'dataType': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'sampleAttributes'", 'to': u"orm['rundb.SampleAttributeDataType']"}), + 'description': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}), + 'displayedName': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '127'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'isActive': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'isMandatory': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'lastModifiedDate': ('django.db.models.fields.DateTimeField', [], {'auto_now': 'True', 'blank': 'True'}), + 'lastModifiedUser': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'lastModified_sampleAttribute'", 'on_delete': 'models.SET_DEFAULT', 'to': u"orm['auth.User']"}) + }, + u'rundb.sampleattributedatatype': { + 'Meta': {'object_name': 'SampleAttributeDataType'}, + 'dataType': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '64'}), + 'description': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'isActive': ('django.db.models.fields.BooleanField', [], {'default': 'True'}) + }, + u'rundb.sampleattributevalue': { + 'Meta': {'object_name': 'SampleAttributeValue'}, + 'creationDate': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + 'creator': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'created_sampleAttributeValue'", 'on_delete': 'models.SET_DEFAULT', 'to': u"orm['auth.User']"}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'lastModifiedDate': ('django.db.models.fields.DateTimeField', [], {'auto_now': 'True', 'blank': 'True'}), + 'lastModifiedUser': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'lastModified_sampleAttributeValue'", 'on_delete': 'models.SET_DEFAULT', 'to': u"orm['auth.User']"}), + 'sample': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'sampleAttributeValues'", 'to': u"orm['rundb.Sample']"}), + 'sampleAttribute': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'samples'", 'to': u"orm['rundb.SampleAttribute']"}), + 'value': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}) + }, + u'rundb.samplegrouptype_cv': { + 'Meta': {'object_name': 'SampleGroupType_CV'}, + 'description': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}), + 'displayedName': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '127'}), + 'iRAnnotationType': ('django.db.models.fields.CharField', [], {'max_length': '127', 'null': 'True', 'blank': 'True'}), + 'iRValue': ('django.db.models.fields.CharField', [], {'max_length': '127', 'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'isActive': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'isIRCompatible': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'uid': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '32'}) + }, + u'rundb.sampleprepdata': { + 'Meta': {'object_name': 'SamplePrepData'}, + 'endTime': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'instrumentName': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '200', 'blank': 'True'}), + 'instrumentStatus': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '256', 'blank': 'True'}), + 'kitType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'lastUpdate': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + 'logPath': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'message': ('django.db.models.fields.TextField', [], {'default': "''", 'blank': 'True'}), + 'operationMode': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'packageVer': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'progress': ('django.db.models.fields.FloatField', [], {'default': '0.0', 'blank': 'True'}), + 'reagentsExpiration': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'reagentsLot': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'reagentsPart': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'remainingSeconds': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'samplePrepDataType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'scriptVersion': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'solutionsExpiration': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'solutionsLot': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'solutionsPart': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'startTime': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + 'tipRackBarcode': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}) + }, + u'rundb.sampleset': { + 'Meta': {'object_name': 'SampleSet'}, + 'SampleGroupType_CV': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'sampleSets'", 'null': 'True', 'to': u"orm['rundb.SampleGroupType_CV']"}), + 'additionalCycles': ('django.db.models.fields.CharField', [], {'max_length': '64', 'null': 'True', 'blank': 'True'}), + 'categories': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '256', 'blank': 'True'}), + 'combinedLibraryTubeLabel': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'creationDate': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + 'creator': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'created_sampleSet'", 'on_delete': 'models.SET_DEFAULT', 'to': u"orm['auth.User']"}), + 'description': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}), + 'displayedName': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '127'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'lastModifiedDate': ('django.db.models.fields.DateTimeField', [], {'auto_now': 'True', 'blank': 'True'}), + 'lastModifiedUser': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'lastModified_sampleSet'", 'on_delete': 'models.SET_DEFAULT', 'to': u"orm['auth.User']"}), + 'libraryPrepInstrument': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'libraryPrepInstrumentData': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'libraryPrepData_sampleSet'", 'null': 'True', 'on_delete': 'models.SET_NULL', 'to': u"orm['rundb.SamplePrepData']"}), + 'libraryPrepKitName': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'libraryPrepPlateType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'libraryPrepProtocol': ('django.db.models.fields.CharField', [], {'max_length': '64', 'null': 'True', 'blank': 'True'}), + 'libraryPrepType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'pcrPlateSerialNum': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'null': 'True', 'blank': 'True'}), + 'status': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '512', 'blank': 'True'}) + }, + u'rundb.samplesetitem': { + 'Meta': {'object_name': 'SampleSetItem'}, + 'assayGroup': ('django.db.models.fields.CharField', [], {'max_length': '64', 'null': 'True', 'blank': 'True'}), + 'biopsyDays': ('django.db.models.fields.IntegerField', [], {'default': '0', 'null': 'True', 'blank': 'True'}), + 'cancerType': ('django.db.models.fields.CharField', [], {'max_length': '127', 'null': 'True', 'blank': 'True'}), + 'cellNum': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '127', 'null': 'True', 'blank': 'True'}), + 'cellularityPct': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'controlType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '127', 'null': 'True', 'blank': 'True'}), + 'coupleId': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '127', 'null': 'True', 'blank': 'True'}), + 'creationDate': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + 'creator': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'created_sampleSetItem'", 'on_delete': 'models.SET_DEFAULT', 'to': u"orm['auth.User']"}), + 'description': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '1024', 'null': 'True', 'blank': 'True'}), + 'dnabarcode': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'startBarcode'", 'null': 'True', 'to': u"orm['rundb.dnaBarcode']"}), + 'embryoId': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '127', 'null': 'True', 'blank': 'True'}), + 'endDnabarcode': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'endBarcode'", 'null': 'True', 'to': u"orm['rundb.dnaBarcode']"}), + 'gender': ('django.db.models.fields.CharField', [], {'max_length': '127', 'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'lastModifiedDate': ('django.db.models.fields.DateTimeField', [], {'auto_now': 'True', 'blank': 'True'}), + 'lastModifiedUser': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'lastModified_sampleSetItem'", 'on_delete': 'models.SET_DEFAULT', 'to': u"orm['auth.User']"}), + 'mouseStrains': ('django.db.models.fields.CharField', [], {'max_length': '127', 'null': 'True', 'blank': 'True'}), + 'nucleotideType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'panelPoolType': ('django.db.models.fields.CharField', [], {'max_length': '64', 'null': 'True', 'blank': 'True'}), + 'pcrPlateColumn': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '10', 'null': 'True', 'blank': 'True'}), + 'pcrPlateRow': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '10', 'null': 'True', 'blank': 'True'}), + 'population': ('django.db.models.fields.CharField', [], {'max_length': '127', 'null': 'True', 'blank': 'True'}), + 'relationshipGroup': ('django.db.models.fields.IntegerField', [], {}), + 'relationshipRole': ('django.db.models.fields.CharField', [], {'max_length': '127', 'null': 'True', 'blank': 'True'}), + 'sample': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'sampleSets'", 'to': u"orm['rundb.Sample']"}), + 'sampleCollectionDate': ('django.db.models.fields.DateField', [], {'null': 'True', 'blank': 'True'}), + 'sampleReceiptDate': ('django.db.models.fields.DateField', [], {'null': 'True', 'blank': 'True'}), + 'sampleSet': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'samples'", 'to': u"orm['rundb.SampleSet']"}), + 'sampleSource': ('django.db.models.fields.CharField', [], {'max_length': '64', 'null': 'True', 'blank': 'True'}), + 'tubePosition': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '10', 'null': 'True', 'blank': 'True'}) + }, + u'rundb.supportupload': { + 'Meta': {'object_name': 'SupportUpload'}, + 'account': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.RemoteAccount']"}), + 'celery_task_id': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '60', 'blank': 'True'}), + 'contact_email': ('django.db.models.fields.EmailField', [], {'default': "''", 'max_length': '75'}), + 'created': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + 'description': ('django.db.models.fields.TextField', [], {'default': "''"}), + 'file': ('django.db.models.fields.related.OneToOneField', [], {'to': u"orm['rundb.FileMonitor']", 'unique': 'True', 'null': 'True', 'on_delete': 'models.SET_NULL', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'local_message': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '2048', 'blank': 'True'}), + 'local_status': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '255', 'blank': 'True'}), + 'result': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.Results']", 'null': 'True', 'blank': 'True'}), + 'ticket_id': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '255', 'blank': 'True'}), + 'ticket_message': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '2048', 'blank': 'True'}), + 'ticket_status': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '255', 'blank': 'True'}), + 'updated': ('django.db.models.fields.DateTimeField', [], {'auto_now': 'True', 'blank': 'True'}), + 'user': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['auth.User']", 'on_delete': 'models.SET_DEFAULT'}) + }, + u'rundb.template': { + 'Meta': {'object_name': 'Template'}, + 'comments': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'isofficial': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'key': ('django.db.models.fields.CharField', [], {'max_length': '64'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '64'}), + 'sequence': ('django.db.models.fields.TextField', [], {'blank': 'True'}) + }, + u'rundb.tfmetrics': { + 'HPAccuracy': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + 'Meta': {'object_name': 'TFMetrics'}, + 'Q10Histo': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + 'Q10Mean': ('django.db.models.fields.FloatField', [], {}), + 'Q10ReadCount': ('django.db.models.fields.FloatField', [], {}), + 'Q17Histo': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + 'Q17Mean': ('django.db.models.fields.FloatField', [], {}), + 'Q17ReadCount': ('django.db.models.fields.FloatField', [], {}), + 'SysSNR': ('django.db.models.fields.FloatField', [], {}), + 'aveKeyCount': ('django.db.models.fields.FloatField', [], {}), + 'corrHPSNR': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'keypass': ('django.db.models.fields.FloatField', [], {}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '128', 'db_index': 'True'}), + 'number': ('django.db.models.fields.FloatField', [], {}), + 'report': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'tfmetrics_set'", 'to': u"orm['rundb.Results']"}), + 'sequence': ('django.db.models.fields.CharField', [], {'max_length': '512'}) + }, + u'rundb.threeprimeadapter': { + 'Meta': {'object_name': 'ThreePrimeadapter'}, + 'chemistryType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'description': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'blank': 'True'}), + 'direction': ('django.db.models.fields.CharField', [], {'default': "'Forward'", 'max_length': '20'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'isActive': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'isDefault': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '256'}), + 'runMode': ('django.db.models.fields.CharField', [], {'default': "'single'", 'max_length': '64', 'blank': 'True'}), + 'sequence': ('django.db.models.fields.CharField', [], {'max_length': '512'}), + 'uid': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '32'}) + }, + u'rundb.usereventlog': { + 'Meta': {'object_name': 'UserEventLog'}, + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'text': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + 'timeStamp': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + 'upload': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'logs'", 'to': u"orm['rundb.ContentUpload']"}) + }, + u'rundb.userprofile': { + 'Meta': {'object_name': 'UserProfile'}, + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'is_password_valid': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'last_password_changed_on': ('django.db.models.fields.DateTimeField', [], {'default': 'datetime.datetime(1984, 11, 5, 0, 0)'}), + 'last_read_news_post': ('django.db.models.fields.DateTimeField', [], {'default': 'datetime.datetime(1984, 11, 5, 0, 0)'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '93'}), + 'needs_activation': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'note': ('django.db.models.fields.TextField', [], {'default': "''", 'blank': 'True'}), + 'phone_number': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '256', 'blank': 'True'}), + 'title': ('django.db.models.fields.CharField', [], {'default': "'user'", 'max_length': '256'}), + 'user': ('django.db.models.fields.related.OneToOneField', [], {'to': u"orm['auth.User']", 'unique': 'True'}) + } + } + + complete_apps = ['rundb'] \ No newline at end of file diff --git a/dbReports/iondb/rundb/migrations/0369_auto__chg_field_plannedexperiment_categories.py b/dbReports/iondb/rundb/migrations/0369_auto__chg_field_plannedexperiment_categories.py new file mode 100644 index 00000000..4b5467ff --- /dev/null +++ b/dbReports/iondb/rundb/migrations/0369_auto__chg_field_plannedexperiment_categories.py @@ -0,0 +1,1199 @@ +# -*- coding: utf-8 -*- +from south.utils import datetime_utils as datetime +from south.db import db +from south.v2 import SchemaMigration +from django.db import models + + +class Migration(SchemaMigration): + + def forwards(self, orm): + + # Changing field 'PlannedExperiment.categories' + db.alter_column(u'rundb_plannedexperiment', 'categories', self.gf('django.db.models.fields.CharField')(max_length=256, null=True)) + + def backwards(self, orm): + + # Changing field 'PlannedExperiment.categories' + db.alter_column(u'rundb_plannedexperiment', 'categories', self.gf('django.db.models.fields.CharField')(max_length=64, null=True)) + + models = { + u'auth.group': { + 'Meta': {'object_name': 'Group'}, + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '80'}), + 'permissions': ('django.db.models.fields.related.ManyToManyField', [], {'to': u"orm['auth.Permission']", 'symmetrical': 'False', 'blank': 'True'}) + }, + u'auth.permission': { + 'Meta': {'ordering': "(u'content_type__app_label', u'content_type__model', u'codename')", 'unique_together': "((u'content_type', u'codename'),)", 'object_name': 'Permission'}, + 'codename': ('django.db.models.fields.CharField', [], {'max_length': '100'}), + 'content_type': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['contenttypes.ContentType']"}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '50'}) + }, + u'auth.user': { + 'Meta': {'object_name': 'User'}, + 'date_joined': ('django.db.models.fields.DateTimeField', [], {'default': 'datetime.datetime.now'}), + 'email': ('django.db.models.fields.EmailField', [], {'max_length': '75', 'blank': 'True'}), + 'first_name': ('django.db.models.fields.CharField', [], {'max_length': '30', 'blank': 'True'}), + 'groups': ('django.db.models.fields.related.ManyToManyField', [], {'symmetrical': 'False', 'related_name': "u'user_set'", 'blank': 'True', 'to': u"orm['auth.Group']"}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'is_active': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'is_staff': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'is_superuser': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'last_login': ('django.db.models.fields.DateTimeField', [], {'default': 'datetime.datetime.now'}), + 'last_name': ('django.db.models.fields.CharField', [], {'max_length': '30', 'blank': 'True'}), + 'password': ('django.db.models.fields.CharField', [], {'max_length': '128'}), + 'user_permissions': ('django.db.models.fields.related.ManyToManyField', [], {'symmetrical': 'False', 'related_name': "u'user_set'", 'blank': 'True', 'to': u"orm['auth.Permission']"}), + 'username': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '30'}) + }, + u'contenttypes.contenttype': { + 'Meta': {'ordering': "('name',)", 'unique_together': "(('app_label', 'model'),)", 'object_name': 'ContentType', 'db_table': "'django_content_type'"}, + 'app_label': ('django.db.models.fields.CharField', [], {'max_length': '100'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'model': ('django.db.models.fields.CharField', [], {'max_length': '100'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '100'}) + }, + u'rundb.analysisargs': { + 'Meta': {'object_name': 'AnalysisArgs'}, + 'active': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'alignmentargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'analysisargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'applCategory': ('django.db.models.fields.CharField', [], {'max_length': '127', 'null': 'True', 'blank': 'True'}), + 'applGroup': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'applGroup_analysisArgs'", 'null': 'True', 'to': u"orm['rundb.ApplicationGroup']"}), + 'applType': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'applType_analysisArgs'", 'null': 'True', 'to': u"orm['rundb.RunType']"}), + 'basecallerargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'beadfindargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'calibrateargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'chipType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '128'}), + 'chip_default': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'creationDate': ('django.db.models.fields.DateTimeField', [], {'default': 'datetime.datetime.now', 'auto_now_add': 'True', 'null': 'True', 'blank': 'True'}), + 'creator': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'created_analysisArgs'", 'null': 'True', 'on_delete': 'models.SET_NULL', 'to': u"orm['auth.User']"}), + 'description': ('django.db.models.fields.CharField', [], {'max_length': '256', 'unique': 'True', 'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'ionstatsargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'isSystem': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'lastModifiedDate': ('django.db.models.fields.DateTimeField', [], {'default': 'datetime.datetime.now', 'auto_now': 'True', 'null': 'True', 'blank': 'True'}), + 'lastModifiedUser': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'lastModified_analysisArgs'", 'null': 'True', 'on_delete': 'models.SET_NULL', 'to': u"orm['auth.User']"}), + 'libraryKitName': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '512', 'blank': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '256'}), + 'prebasecallerargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'prethumbnailbasecallerargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'samplePrepKitName': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '512', 'blank': 'True'}), + 'sequenceKitName': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '512', 'blank': 'True'}), + 'templateKitName': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '512', 'blank': 'True'}), + 'thumbnailalignmentargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'thumbnailanalysisargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'thumbnailbasecallerargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'thumbnailbeadfindargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'thumbnailcalibrateargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'thumbnailionstatsargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}) + }, + u'rundb.analysismetrics': { + 'Meta': {'object_name': 'AnalysisMetrics'}, + 'adjusted_addressable': ('django.db.models.fields.IntegerField', [], {'default': '0'}), + 'amb': ('django.db.models.fields.IntegerField', [], {}), + 'bead': ('django.db.models.fields.IntegerField', [], {}), + 'dud': ('django.db.models.fields.IntegerField', [], {}), + 'empty': ('django.db.models.fields.IntegerField', [], {}), + 'excluded': ('django.db.models.fields.IntegerField', [], {}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'ignored': ('django.db.models.fields.IntegerField', [], {}), + 'keypass_all_beads': ('django.db.models.fields.IntegerField', [], {}), + 'lib': ('django.db.models.fields.IntegerField', [], {}), + 'libFinal': ('django.db.models.fields.IntegerField', [], {}), + 'libKp': ('django.db.models.fields.IntegerField', [], {}), + 'libLive': ('django.db.models.fields.IntegerField', [], {}), + 'libMix': ('django.db.models.fields.IntegerField', [], {}), + 'lib_pass_basecaller': ('django.db.models.fields.IntegerField', [], {}), + 'lib_pass_cafie': ('django.db.models.fields.IntegerField', [], {}), + 'live': ('django.db.models.fields.IntegerField', [], {}), + 'loading': ('django.db.models.fields.FloatField', [], {'default': '0.0'}), + 'pinned': ('django.db.models.fields.IntegerField', [], {}), + 'report': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'analysismetrics_set'", 'to': u"orm['rundb.Results']"}), + 'sysCF': ('django.db.models.fields.FloatField', [], {}), + 'sysDR': ('django.db.models.fields.FloatField', [], {}), + 'sysIE': ('django.db.models.fields.FloatField', [], {}), + 'tf': ('django.db.models.fields.IntegerField', [], {}), + 'tfFinal': ('django.db.models.fields.IntegerField', [], {}), + 'tfKp': ('django.db.models.fields.IntegerField', [], {}), + 'tfLive': ('django.db.models.fields.IntegerField', [], {}), + 'tfMix': ('django.db.models.fields.IntegerField', [], {}), + 'total': ('django.db.models.fields.IntegerField', [], {'default': '0'}), + 'washout': ('django.db.models.fields.IntegerField', [], {}), + 'washout_ambiguous': ('django.db.models.fields.IntegerField', [], {}), + 'washout_dud': ('django.db.models.fields.IntegerField', [], {}), + 'washout_library': ('django.db.models.fields.IntegerField', [], {}), + 'washout_live': ('django.db.models.fields.IntegerField', [], {}), + 'washout_test_fragment': ('django.db.models.fields.IntegerField', [], {}) + }, + u'rundb.applicationgroup': { + 'Meta': {'object_name': 'ApplicationGroup'}, + 'description': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'isActive': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '127'}), + 'uid': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '32'}) + }, + u'rundb.applproduct': { + 'Meta': {'object_name': 'ApplProduct'}, + 'applType': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.RunType']"}), + 'applicationGroup': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.ApplicationGroup']", 'null': 'True', 'blank': 'True'}), + 'barcodeKitSelectableType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'categories': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '256', 'null': 'True', 'blank': 'True'}), + 'defaultBarcodeKitName': ('django.db.models.fields.CharField', [], {'max_length': '128', 'null': 'True', 'blank': 'True'}), + 'defaultChipType': ('django.db.models.fields.CharField', [], {'max_length': '128', 'null': 'True', 'blank': 'True'}), + 'defaultControlSeqKit': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'controlSeqKit_applProduct_set'", 'null': 'True', 'to': u"orm['rundb.KitInfo']"}), + 'defaultFlowCount': ('django.db.models.fields.PositiveIntegerField', [], {'default': '0'}), + 'defaultFlowOrder': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'flowOrder_applProduct_set'", 'null': 'True', 'to': u"orm['rundb.FlowOrder']"}), + 'defaultGenomeRefName': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}), + 'defaultHotSpotRegionBedFileName': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}), + 'defaultIonChefPrepKit': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'ionChefPrepKit_applProduct_set'", 'null': 'True', 'to': u"orm['rundb.KitInfo']"}), + 'defaultIonChefSequencingKit': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'ionChefSeqKit_applProduct_set'", 'null': 'True', 'to': u"orm['rundb.KitInfo']"}), + 'defaultLibraryKit': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'libKit_applProduct_set'", 'null': 'True', 'to': u"orm['rundb.KitInfo']"}), + 'defaultSamplePrepKit': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'samplePrepKit_applProduct_set'", 'null': 'True', 'to': u"orm['rundb.KitInfo']"}), + 'defaultSamplePrepProtocol': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'common_CV_applProduct_set'", 'null': 'True', 'to': u"orm['rundb.common_CV']"}), + 'defaultSequencingKit': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'seqKit_applProduct_set'", 'null': 'True', 'to': u"orm['rundb.KitInfo']"}), + 'defaultTargetRegionBedFileName': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}), + 'defaultTemplateKit': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'templateKit_applProduct_set'", 'null': 'True', 'to': u"orm['rundb.KitInfo']"}), + 'description': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'blank': 'True'}), + 'dualBarcodingRule': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'instrumentType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'isActive': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'isBarcodeKitSelectionRequired': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isControlSeqTypeBySampleSupported': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isDefault': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isDefaultBarcoded': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isDefaultForInstrumentType': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isDualBarcodingBySampleSupported': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isDualNucleotideTypeBySampleSupported': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isHotSpotBEDFileBySampleSupported': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isHotspotRegionBEDFileSuppported': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'isReferenceBySampleSupported': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isReferenceSelectionSupported': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'isSamplePrepKitSupported': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'isTargetRegionBEDFileBySampleSupported': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isTargetRegionBEDFileSelectionRequiredForRefSelection': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isTargetRegionBEDFileSupported': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'isTargetTechniqueSelectionSupported': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'isVisible': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'productCode': ('django.db.models.fields.CharField', [], {'default': "'any'", 'unique': 'True', 'max_length': '64'}), + 'productName': ('django.db.models.fields.CharField', [], {'max_length': '128'}) + }, + u'rundb.backup': { + 'Meta': {'object_name': 'Backup'}, + 'backupDate': ('django.db.models.fields.DateTimeField', [], {}), + 'backupName': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '256'}), + 'backupPath': ('django.db.models.fields.CharField', [], {'max_length': '512'}), + 'experiment': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.Experiment']"}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'isBackedUp': ('django.db.models.fields.BooleanField', [], {}) + }, + u'rundb.chefpcrplateconfig': { + 'Meta': {'object_name': 'ChefPcrPlateconfig'}, + 'confg': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'kit': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.KitInfo']", 'null': 'True', 'blank': 'True'}) + }, + u'rundb.chip': { + 'Meta': {'object_name': 'Chip'}, + 'description': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '128'}), + 'earlyDatFileDeletion': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '1', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'instrumentType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'isActive': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '128'}), + 'slots': ('django.db.models.fields.IntegerField', [], {}) + }, + u'rundb.common_cv': { + 'Meta': {'unique_together': "(('cv_type', 'value'),)", 'object_name': 'common_CV'}, + 'categories': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '256', 'null': 'True', 'blank': 'True'}), + 'cv_type': ('django.db.models.fields.CharField', [], {'max_length': '127'}), + 'description': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}), + 'displayedValue': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '127'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'isActive': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'isDefault': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'isVisible': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'samplePrep_instrumentType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'sequencing_instrumentType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'uid': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '10'}), + 'value': ('django.db.models.fields.CharField', [], {'max_length': '127'}) + }, + u'rundb.content': { + 'Meta': {'object_name': 'Content'}, + 'application_tags': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + 'contentupload': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'contents'", 'to': u"orm['rundb.ContentUpload']"}), + 'description': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + 'enabled': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'extra': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + 'file': ('django.db.models.fields.CharField', [], {'max_length': '255'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'meta': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'blank': 'True'}), + 'notes': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + 'path': ('django.db.models.fields.CharField', [], {'max_length': '255'}), + 'publisher': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'contents'", 'to': u"orm['rundb.Publisher']"}), + 'type': ('django.db.models.fields.CharField', [], {'max_length': '128', 'blank': 'True'}) + }, + u'rundb.contentupload': { + 'Meta': {'object_name': 'ContentUpload'}, + 'file_path': ('django.db.models.fields.CharField', [], {'max_length': '255'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'meta': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'blank': 'True'}), + 'publisher': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.Publisher']", 'null': 'True'}), + 'source': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + 'status': ('django.db.models.fields.CharField', [], {'max_length': '255', 'blank': 'True'}), + 'upload_date': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'null': 'True', 'blank': 'True'}), + 'upload_type': ('django.db.models.fields.CharField', [], {'max_length': '128', 'blank': 'True'}), + 'username': ('django.db.models.fields.CharField', [], {'max_length': '128', 'blank': 'True'}) + }, + u'rundb.cruncher': { + 'Meta': {'object_name': 'Cruncher'}, + 'comments': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + 'date': ('django.db.models.fields.DateTimeField', [], {'auto_now': 'True', 'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'info': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'null': 'True', 'blank': 'True'}), + 'location': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.Location']"}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '200'}), + 'state': ('django.db.models.fields.CharField', [], {'default': "'U'", 'max_length': '8'}) + }, + u'rundb.dmfileset': { + 'Meta': {'object_name': 'DMFileSet'}, + 'auto_action': ('django.db.models.fields.CharField', [], {'default': "'OFF'", 'max_length': '8'}), + 'auto_trigger_age': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'auto_trigger_usage': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'backup_directory': ('django.db.models.fields.CharField', [], {'max_length': '256', 'null': 'True', 'blank': 'True'}), + 'bandwidth_limit': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'del_empty_dir': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'description': ('django.db.models.fields.CharField', [], {'max_length': '256', 'null': 'True', 'blank': 'True'}), + 'enabled': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'exclude': ('iondb.rundb.separatedValuesField.SeparatedValuesField', [], {'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'include': ('iondb.rundb.separatedValuesField.SeparatedValuesField', [], {'null': 'True', 'blank': 'True'}), + 'keepwith': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'null': 'True', 'blank': 'True'}), + 'type': ('django.db.models.fields.CharField', [], {'max_length': '48'}), + 'version': ('django.db.models.fields.CharField', [], {'max_length': '8'}) + }, + u'rundb.dmfilestat': { + 'Meta': {'object_name': 'DMFileStat'}, + 'action_state': ('django.db.models.fields.CharField', [], {'default': "'L'", 'max_length': '8'}), + 'archivepath': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'created': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + 'diskspace': ('django.db.models.fields.FloatField', [], {'null': 'True', 'blank': 'True'}), + 'dmfileset': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.DMFileSet']", 'null': 'True', 'blank': 'True'}), + 'files_in_use': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '512', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'preserve_data': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'result': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.Results']", 'null': 'True', 'blank': 'True'}), + 'user_comment': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'blank': 'True'}) + }, + u'rundb.dnabarcode': { + 'Meta': {'object_name': 'dnaBarcode'}, + 'active': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'adapter': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '128', 'blank': 'True'}), + 'annotation': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '512', 'blank': 'True'}), + 'end_adapter': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '128', 'blank': 'True'}), + 'end_sequence': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '128', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'id_str': ('django.db.models.fields.CharField', [], {'max_length': '128'}), + 'index': ('django.db.models.fields.IntegerField', [], {}), + 'is_end_barcode': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'length': ('django.db.models.fields.IntegerField', [], {'default': '0', 'blank': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '128'}), + 'score_cutoff': ('django.db.models.fields.FloatField', [], {'default': '0'}), + 'score_mode': ('django.db.models.fields.IntegerField', [], {'default': '0', 'blank': 'True'}), + 'sequence': ('django.db.models.fields.CharField', [], {'max_length': '128'}), + 'system': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'type': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}) + }, + u'rundb.emailaddress': { + 'Meta': {'object_name': 'EmailAddress'}, + 'email': ('django.db.models.fields.EmailField', [], {'max_length': '75', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'selected': ('django.db.models.fields.BooleanField', [], {}) + }, + u'rundb.eventlog': { + 'Meta': {'object_name': 'EventLog'}, + 'content_type': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'content_type_set_for_eventlog'", 'to': u"orm['contenttypes.ContentType']"}), + 'created': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'object_pk': ('django.db.models.fields.PositiveIntegerField', [], {}), + 'text': ('django.db.models.fields.TextField', [], {'max_length': '3000'}), + 'username': ('django.db.models.fields.CharField', [], {'default': "'ION'", 'max_length': '32', 'blank': 'True'}) + }, + u'rundb.experiment': { + 'Meta': {'object_name': 'Experiment'}, + 'autoAnalyze': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'baselineRun': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'chefChipExpiration1': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefChipExpiration2': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefChipType1': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefChipType2': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefEndTime': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + 'chefExtraInfo_1': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '128', 'blank': 'True'}), + 'chefExtraInfo_2': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '128', 'blank': 'True'}), + 'chefFlexibleWorkflow': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefInstrumentName': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '200', 'blank': 'True'}), + 'chefKitType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefLastUpdate': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + 'chefLogPath': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'chefLotNumber': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefManufactureDate': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefMessage': ('django.db.models.fields.TextField', [], {'default': "''", 'blank': 'True'}), + 'chefOperationMode': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefPackageVer': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefProgress': ('django.db.models.fields.FloatField', [], {'default': '0.0', 'blank': 'True'}), + 'chefProtocolDeviationName': ('django.db.models.fields.CharField', [], {'max_length': '127', 'null': 'True', 'blank': 'True'}), + 'chefReagentID': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefReagentsExpiration': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefReagentsLot': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefReagentsPart': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefReagentsSerialNum': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '20', 'blank': 'True'}), + 'chefRemainingSeconds': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'chefSamplePos': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefScriptVersion': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefSolutionsExpiration': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefSolutionsLot': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefSolutionsPart': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chefSolutionsSerialNum': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '20', 'blank': 'True'}), + 'chefStartTime': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + 'chefStatus': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '256', 'blank': 'True'}), + 'chefTipRackBarcode': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'chipBarcode': ('django.db.models.fields.CharField', [], {'max_length': '64', 'blank': 'True'}), + 'chipTecDfltAmbient': ('django.db.models.fields.FloatField', [], {'default': 'None', 'null': 'True', 'blank': 'True'}), + 'chipTecMinThreshold': ('django.db.models.fields.FloatField', [], {'default': 'None', 'null': 'True', 'blank': 'True'}), + 'chipTecSlope': ('django.db.models.fields.FloatField', [], {'default': 'None', 'null': 'True', 'blank': 'True'}), + 'chipType': ('django.db.models.fields.CharField', [], {'max_length': '32'}), + 'cycles': ('django.db.models.fields.IntegerField', [], {}), + 'date': ('django.db.models.fields.DateTimeField', [], {'db_index': 'True'}), + 'diskusage': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'displayName': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '128'}), + 'expCompInfo': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + 'expDir': ('django.db.models.fields.CharField', [], {'max_length': '512'}), + 'expName': ('django.db.models.fields.CharField', [], {'max_length': '128', 'db_index': 'True'}), + 'flows': ('django.db.models.fields.IntegerField', [], {}), + 'flowsInOrder': ('django.db.models.fields.CharField', [], {'max_length': '1200', 'blank': 'True'}), + 'ftpStatus': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'isReverseRun': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'log': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'blank': 'True'}), + 'manTecDfltAmbient': ('django.db.models.fields.FloatField', [], {'default': 'None', 'null': 'True', 'blank': 'True'}), + 'manTecMinThreshold': ('django.db.models.fields.FloatField', [], {'default': 'None', 'null': 'True', 'blank': 'True'}), + 'manTecSlope': ('django.db.models.fields.FloatField', [], {'default': 'None', 'null': 'True', 'blank': 'True'}), + 'metaData': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'blank': 'True'}), + 'notes': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}), + 'pgmName': ('django.db.models.fields.CharField', [], {'max_length': '64'}), + 'pinnedRepResult': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'plan': ('django.db.models.fields.related.OneToOneField', [], {'blank': 'True', 'related_name': "'experiment'", 'unique': 'True', 'null': 'True', 'to': u"orm['rundb.PlannedExperiment']"}), + 'platform': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '128', 'blank': 'True'}), + 'rawdatastyle': ('django.db.models.fields.CharField', [], {'default': "'single'", 'max_length': '24', 'null': 'True', 'blank': 'True'}), + 'reagentBarcode': ('django.db.models.fields.CharField', [], {'max_length': '64', 'blank': 'True'}), + 'repResult': ('django.db.models.fields.related.OneToOneField', [], {'related_name': "'+'", 'null': 'True', 'on_delete': 'models.SET_NULL', 'to': u"orm['rundb.Results']", 'blank': 'True', 'unique': 'True'}), + 'resultDate': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'null': 'True', 'db_index': 'True', 'blank': 'True'}), + 'reverse_primer': ('django.db.models.fields.CharField', [], {'max_length': '128', 'null': 'True', 'blank': 'True'}), + 'runMode': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'seqKitBarcode': ('django.db.models.fields.CharField', [], {'max_length': '64', 'blank': 'True'}), + 'sequencekitbarcode': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'sequencekitname': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'star': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'status': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '512', 'blank': 'True'}), + 'storageHost': ('django.db.models.fields.CharField', [], {'max_length': '128', 'null': 'True', 'blank': 'True'}), + 'storage_options': ('django.db.models.fields.CharField', [], {'default': "'A'", 'max_length': '200'}), + 'unique': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '512'}), + 'usePreBeadfind': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'user_ack': ('django.db.models.fields.CharField', [], {'default': "'U'", 'max_length': '24'}) + }, + u'rundb.experimentanalysissettings': { + 'Meta': {'object_name': 'ExperimentAnalysisSettings'}, + 'alignmentargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'analysisargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'barcodeKitName': ('django.db.models.fields.CharField', [], {'max_length': '128', 'null': 'True', 'blank': 'True'}), + 'barcodedSamples': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'null': 'True', 'blank': 'True'}), + 'base_recalibration_mode': ('django.db.models.fields.CharField', [], {'default': "'standard_recal'", 'max_length': '64'}), + 'basecallerargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'beadfindargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'calibrateargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'custom_args': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'date': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + 'endBarcodeKitName': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '128', 'null': 'True', 'blank': 'True'}), + 'experiment': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'eas_set'", 'null': 'True', 'to': u"orm['rundb.Experiment']"}), + 'hotSpotRegionBedFile': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'ionstatsargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'isDuplicateReads': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isEditable': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isOneTimeOverride': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'libraryKey': ('django.db.models.fields.CharField', [], {'max_length': '64', 'blank': 'True'}), + 'libraryKitBarcode': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'libraryKitName': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'mixedTypeRNA_hotSpotRegionBedFile': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}), + 'mixedTypeRNA_reference': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'mixedTypeRNA_targetRegionBedFile': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}), + 'prebasecallerargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'prethumbnailbasecallerargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'realign': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'reference': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'selectedPlugins': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'null': 'True', 'blank': 'True'}), + 'sseBedFile': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '1024', 'null': 'True', 'blank': 'True'}), + 'status': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '512', 'blank': 'True'}), + 'targetRegionBedFile': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}), + 'tfKey': ('django.db.models.fields.CharField', [], {'max_length': '64', 'blank': 'True'}), + 'threePrimeAdapter': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'thumbnailalignmentargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'thumbnailanalysisargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'thumbnailbasecallerargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'thumbnailbeadfindargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'thumbnailcalibrateargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}), + 'thumbnailionstatsargs': ('django.db.models.fields.CharField', [], {'max_length': '5000', 'blank': 'True'}) + }, + u'rundb.filemonitor': { + 'Meta': {'object_name': 'FileMonitor'}, + 'celery_task_id': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '60', 'blank': 'True'}), + 'created': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'local_dir': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '512'}), + 'md5sum': ('django.db.models.fields.CharField', [], {'default': 'None', 'max_length': '32', 'null': 'True', 'blank': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '255'}), + 'progress': ('django.db.models.fields.BigIntegerField', [], {'default': '0'}), + 'size': ('django.db.models.fields.BigIntegerField', [], {'default': 'None', 'null': 'True'}), + 'status': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '60'}), + 'tags': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '1024'}), + 'updated': ('django.db.models.fields.DateTimeField', [], {'auto_now': 'True', 'blank': 'True'}), + 'url': ('django.db.models.fields.CharField', [], {'max_length': '2000'}) + }, + u'rundb.fileserver': { + 'Meta': {'object_name': 'FileServer'}, + 'comments': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + 'filesPrefix': ('django.db.models.fields.CharField', [], {'max_length': '200'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'location': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.Location']"}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '200'}), + 'percentfull': ('django.db.models.fields.FloatField', [], {'default': '0.0', 'null': 'True', 'blank': 'True'}) + }, + u'rundb.floworder': { + 'Meta': {'object_name': 'FlowOrder'}, + 'description': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '128', 'blank': 'True'}), + 'flowOrder': ('django.db.models.fields.CharField', [], {'max_length': '1200', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'isActive': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'isDefault': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isSystem': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '64'}) + }, + u'rundb.globalconfig': { + 'Meta': {'object_name': 'GlobalConfig'}, + 'auto_archive_ack': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'auto_archive_enable': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'base_recalibration_mode': ('django.db.models.fields.CharField', [], {'default': "'standard_recal'", 'max_length': '64'}), + 'check_news_posts': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'cluster_auto_disable': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'default_flow_order': ('django.db.models.fields.CharField', [], {'max_length': '100', 'blank': 'True'}), + 'default_library_key': ('django.db.models.fields.CharField', [], {'max_length': '50', 'blank': 'True'}), + 'default_storage_options': ('django.db.models.fields.CharField', [], {'default': "'D'", 'max_length': '500', 'blank': 'True'}), + 'default_test_fragment_key': ('django.db.models.fields.CharField', [], {'max_length': '50', 'blank': 'True'}), + 'enable_auto_pkg_dl': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'enable_auto_security': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'enable_compendia_OCP': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'enable_nightly_email': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'enable_support_upload': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'enable_version_lock': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'majorPlatform': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '24', 'null': 'True', 'blank': 'True'}), + 'mark_duplicates': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '512'}), + 'plugin_output_folder': ('django.db.models.fields.CharField', [], {'max_length': '500', 'blank': 'True'}), + 'realign': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'records_to_display': ('django.db.models.fields.IntegerField', [], {'default': '20', 'blank': 'True'}), + 'sec_update_status': ('django.db.models.fields.CharField', [], {'max_length': '128', 'blank': 'True'}), + 'selected': ('django.db.models.fields.BooleanField', [], {}), + 'site_name': ('django.db.models.fields.CharField', [], {'max_length': '500', 'blank': 'True'}), + 'telemetry_enabled': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'ts_update_status': ('django.db.models.fields.CharField', [], {'max_length': '256', 'blank': 'True'}), + 'web_root': ('django.db.models.fields.CharField', [], {'max_length': '500', 'blank': 'True'}) + }, + u'rundb.ionmeshnode': { + 'Meta': {'object_name': 'IonMeshNode'}, + 'active': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'apikey_local': ('django.db.models.fields.CharField', [], {'max_length': '256', 'null': 'True', 'blank': 'True'}), + 'apikey_remote': ('django.db.models.fields.CharField', [], {'max_length': '256', 'null': 'True', 'blank': 'True'}), + 'hostname': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '128'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '128', 'unique': 'True', 'null': 'True', 'blank': 'True'}), + 'system_id': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '37'}) + }, + u'rundb.kitinfo': { + 'Meta': {'unique_together': "(('kitType', 'name'),)", 'object_name': 'KitInfo'}, + 'applicationType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'null': 'True', 'blank': 'True'}), + 'cartridgeBetweenUsageAbsoluteMaxDayLimit': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'cartridgeExpirationDayLimit': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'categories': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '256', 'null': 'True', 'blank': 'True'}), + 'chipTypes': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '127', 'blank': 'True'}), + 'defaultCartridgeUsageCount': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'defaultFlowOrder': ('django.db.models.fields.related.ForeignKey', [], {'default': 'None', 'to': u"orm['rundb.FlowOrder']", 'null': 'True', 'blank': 'True'}), + 'defaultThreePrimeAdapter': ('django.db.models.fields.related.ForeignKey', [], {'default': 'None', 'to': u"orm['rundb.ThreePrimeadapter']", 'null': 'True', 'blank': 'True'}), + 'description': ('django.db.models.fields.CharField', [], {'max_length': '3024', 'blank': 'True'}), + 'flowCount': ('django.db.models.fields.PositiveIntegerField', [], {}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'instrumentType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'isActive': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'kitType': ('django.db.models.fields.CharField', [], {'max_length': '64'}), + 'libraryReadLength': ('django.db.models.fields.PositiveIntegerField', [], {'default': '0'}), + 'name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '512'}), + 'nucleotideType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'runMode': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'samplePrep_instrumentType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'uid': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '10'}) + }, + u'rundb.kitpart': { + 'Meta': {'unique_together': "(('barcode',),)", 'object_name': 'KitPart'}, + 'barcode': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '64'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'kit': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.KitInfo']"}) + }, + u'rundb.libmetrics': { + 'Genome_Version': ('django.db.models.fields.CharField', [], {'max_length': '512'}), + 'Index_Version': ('django.db.models.fields.CharField', [], {'max_length': '512'}), + 'Meta': {'object_name': 'LibMetrics'}, + 'align_sample': ('django.db.models.fields.IntegerField', [], {}), + 'aveKeyCounts': ('django.db.models.fields.FloatField', [], {}), + 'cf': ('django.db.models.fields.FloatField', [], {}), + 'dr': ('django.db.models.fields.FloatField', [], {}), + 'duplicate_reads': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'genome': ('django.db.models.fields.CharField', [], {'max_length': '512'}), + 'genomesize': ('django.db.models.fields.BigIntegerField', [], {}), + 'i100Q10_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i100Q17_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i100Q20_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i100Q47_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i100Q7_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i150Q10_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i150Q17_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i150Q20_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i150Q47_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i150Q7_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i200Q10_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i200Q17_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i200Q20_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i200Q47_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i200Q7_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i250Q10_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i250Q17_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i250Q20_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i250Q47_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i250Q7_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i300Q10_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i300Q17_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i300Q20_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i300Q47_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i300Q7_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i350Q10_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i350Q17_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i350Q20_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i350Q47_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i350Q7_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i400Q10_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i400Q17_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i400Q20_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i400Q47_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i400Q7_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i450Q10_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i450Q17_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i450Q20_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i450Q47_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i450Q7_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i500Q10_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i500Q17_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i500Q20_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i500Q47_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i500Q7_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i50Q10_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i50Q17_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i50Q20_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i50Q47_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i50Q7_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i550Q10_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i550Q17_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i550Q20_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i550Q47_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i550Q7_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i600Q10_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i600Q17_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i600Q20_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i600Q47_reads': ('django.db.models.fields.IntegerField', [], {}), + 'i600Q7_reads': ('django.db.models.fields.IntegerField', [], {}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'ie': ('django.db.models.fields.FloatField', [], {}), + 'q10_alignments': ('django.db.models.fields.IntegerField', [], {}), + 'q10_longest_alignment': ('django.db.models.fields.IntegerField', [], {}), + 'q10_mapped_bases': ('django.db.models.fields.BigIntegerField', [], {}), + 'q10_mean_alignment_length': ('django.db.models.fields.IntegerField', [], {}), + 'q17_alignments': ('django.db.models.fields.IntegerField', [], {}), + 'q17_longest_alignment': ('django.db.models.fields.IntegerField', [], {}), + 'q17_mapped_bases': ('django.db.models.fields.BigIntegerField', [], {}), + 'q17_mean_alignment_length': ('django.db.models.fields.IntegerField', [], {}), + 'q20_alignments': ('django.db.models.fields.IntegerField', [], {}), + 'q20_longest_alignment': ('django.db.models.fields.IntegerField', [], {}), + 'q20_mapped_bases': ('django.db.models.fields.BigIntegerField', [], {}), + 'q20_mean_alignment_length': ('django.db.models.fields.IntegerField', [], {}), + 'q47_alignments': ('django.db.models.fields.IntegerField', [], {}), + 'q47_longest_alignment': ('django.db.models.fields.IntegerField', [], {}), + 'q47_mapped_bases': ('django.db.models.fields.BigIntegerField', [], {}), + 'q47_mean_alignment_length': ('django.db.models.fields.IntegerField', [], {}), + 'q7_alignments': ('django.db.models.fields.IntegerField', [], {}), + 'q7_longest_alignment': ('django.db.models.fields.IntegerField', [], {}), + 'q7_mapped_bases': ('django.db.models.fields.BigIntegerField', [], {}), + 'q7_mean_alignment_length': ('django.db.models.fields.IntegerField', [], {}), + 'raw_accuracy': ('django.db.models.fields.FloatField', [], {}), + 'report': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'libmetrics_set'", 'to': u"orm['rundb.Results']"}), + 'sysSNR': ('django.db.models.fields.FloatField', [], {}), + 'totalNumReads': ('django.db.models.fields.IntegerField', [], {}), + 'total_mapped_reads': ('django.db.models.fields.BigIntegerField', [], {}), + 'total_mapped_target_bases': ('django.db.models.fields.BigIntegerField', [], {}) + }, + u'rundb.librarykey': { + 'Meta': {'object_name': 'LibraryKey'}, + 'description': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'blank': 'True'}), + 'direction': ('django.db.models.fields.CharField', [], {'default': "'Forward'", 'max_length': '20'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'isDefault': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '256'}), + 'runMode': ('django.db.models.fields.CharField', [], {'default': "'single'", 'max_length': '64', 'blank': 'True'}), + 'sequence': ('django.db.models.fields.CharField', [], {'max_length': '64'}) + }, + u'rundb.location': { + 'Meta': {'object_name': 'Location'}, + 'comments': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + 'defaultlocation': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '200'}) + }, + u'rundb.message': { + 'Meta': {'object_name': 'Message'}, + 'body': ('django.db.models.fields.TextField', [], {'default': "''", 'blank': 'True'}), + 'expires': ('django.db.models.fields.TextField', [], {'default': "'read'", 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'level': ('django.db.models.fields.IntegerField', [], {'default': '20'}), + 'route': ('django.db.models.fields.TextField', [], {'default': "''", 'blank': 'True'}), + 'status': ('django.db.models.fields.TextField', [], {'default': "'unread'", 'blank': 'True'}), + 'tags': ('django.db.models.fields.TextField', [], {'default': "''", 'blank': 'True'}), + 'time': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}) + }, + u'rundb.monitordata': { + 'Meta': {'object_name': 'MonitorData'}, + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '128'}), + 'treeDat': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'blank': 'True'}) + }, + u'rundb.newspost': { + 'Meta': {'object_name': 'NewsPost'}, + 'guid': ('django.db.models.fields.CharField', [], {'max_length': '2083', 'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'link': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '2083', 'blank': 'True'}), + 'summary': ('django.db.models.fields.TextField', [], {'default': "''", 'blank': 'True'}), + 'title': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '1024', 'blank': 'True'}), + 'updated': ('django.db.models.fields.DateTimeField', [], {'default': 'datetime.datetime.now'}) + }, + u'rundb.plannedexperiment': { + 'Meta': {'ordering': "['-id']", 'object_name': 'PlannedExperiment'}, + 'adapter': ('django.db.models.fields.CharField', [], {'max_length': '256', 'null': 'True', 'blank': 'True'}), + 'applicationGroup': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.ApplicationGroup']", 'null': 'True'}), + 'autoName': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'categories': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '256', 'null': 'True', 'db_index': 'True', 'blank': 'True'}), + 'controlSequencekitname': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'cycles': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'date': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + 'expName': ('django.db.models.fields.CharField', [], {'max_length': '128', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'irworkflow': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'blank': 'True'}), + 'isCustom_kitSettings': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isFavorite': ('django.db.models.fields.BooleanField', [], {'default': 'False', 'db_index': 'True'}), + 'isPlanGroup': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isReusable': ('django.db.models.fields.BooleanField', [], {'default': 'False', 'db_index': 'True'}), + 'isReverseRun': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isSystem': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'isSystemDefault': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'latestEAS': ('django.db.models.fields.related.OneToOneField', [], {'related_name': "'+'", 'null': 'True', 'on_delete': 'models.SET_NULL', 'to': u"orm['rundb.ExperimentAnalysisSettings']", 'blank': 'True', 'unique': 'True'}), + 'libkit': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'libraryPool': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '12', 'null': 'True', 'blank': 'True'}), + 'libraryReadLength': ('django.db.models.fields.PositiveIntegerField', [], {'default': '0'}), + 'metaData': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'blank': 'True'}), + 'origin': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'null': 'True', 'blank': 'True'}), + 'pairedEndLibraryAdapterName': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'parentPlan': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'childPlan_set'", 'null': 'True', 'to': u"orm['rundb.PlannedExperiment']"}), + 'planDisplayedName': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'planExecuted': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'planExecutedDate': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + 'planGUID': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'planName': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'planPGM': ('django.db.models.fields.CharField', [], {'max_length': '128', 'null': 'True', 'blank': 'True'}), + 'planShortID': ('django.db.models.fields.CharField', [], {'db_index': 'True', 'max_length': '5', 'null': 'True', 'blank': 'True'}), + 'planStatus': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '512', 'db_index': 'True', 'blank': 'True'}), + 'preAnalysis': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'projects': ('django.db.models.fields.related.ManyToManyField', [], {'symmetrical': 'False', 'related_name': "'plans'", 'blank': 'True', 'to': u"orm['rundb.Project']"}), + 'qcValues': ('django.db.models.fields.related.ManyToManyField', [], {'to': u"orm['rundb.QCType']", 'null': 'True', 'through': u"orm['rundb.PlannedExperimentQC']", 'symmetrical': 'False'}), + 'reverse_primer': ('django.db.models.fields.CharField', [], {'max_length': '128', 'null': 'True', 'blank': 'True'}), + 'runMode': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'runType': ('django.db.models.fields.CharField', [], {'default': "'GENS'", 'max_length': '512', 'db_index': 'True'}), + 'runname': ('django.db.models.fields.CharField', [], {'max_length': '255', 'null': 'True', 'blank': 'True'}), + 'sampleGrouping': ('django.db.models.fields.related.ForeignKey', [], {'default': 'None', 'to': u"orm['rundb.SampleGroupType_CV']", 'null': 'True', 'blank': 'True'}), + 'samplePrepKitName': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'samplePrepProtocol': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'null': 'True', 'blank': 'True'}), + 'sampleSets': ('django.db.models.fields.related.ManyToManyField', [], {'blank': 'True', 'related_name': "'plans'", 'null': 'True', 'symmetrical': 'False', 'to': u"orm['rundb.SampleSet']"}), + 'sampleTubeLabel': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'seqKitBarcode': ('django.db.models.fields.CharField', [], {'max_length': '64', 'null': 'True', 'blank': 'True'}), + 'storageHost': ('django.db.models.fields.CharField', [], {'max_length': '128', 'null': 'True', 'blank': 'True'}), + 'storage_options': ('django.db.models.fields.CharField', [], {'default': "'A'", 'max_length': '200'}), + 'templatingKitBarcode': ('django.db.models.fields.CharField', [], {'max_length': '64', 'null': 'True', 'blank': 'True'}), + 'templatingKitName': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'usePostBeadfind': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'usePreBeadfind': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'username': ('django.db.models.fields.CharField', [], {'max_length': '128', 'null': 'True', 'blank': 'True'}) + }, + u'rundb.plannedexperimentqc': { + 'Meta': {'unique_together': "(('plannedExperiment', 'qcType'),)", 'object_name': 'PlannedExperimentQC'}, + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'plannedExperiment': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.PlannedExperiment']"}), + 'qcType': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.QCType']"}), + 'threshold': ('django.db.models.fields.PositiveIntegerField', [], {'default': '0'}) + }, + u'rundb.plansession': { + 'Meta': {'object_name': 'PlanSession'}, + '_session_data': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + 'expire_date': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'plan_key': ('django.db.models.fields.CharField', [], {'max_length': '64'}), + 'session_key': ('django.db.models.fields.CharField', [], {'max_length': '64'}) + }, + u'rundb.plugin': { + 'Meta': {'unique_together': "(('name', 'version'),)", 'object_name': 'Plugin'}, + 'active': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'config': ('django.db.models.fields.TextField', [], {'default': "''", 'null': 'True', 'blank': 'True'}), + 'date': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + 'defaultSelected': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'description': ('django.db.models.fields.TextField', [], {'default': "''", 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'majorBlock': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '512', 'db_index': 'True'}), + 'packageName': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '256', 'db_column': "'packagename'", 'blank': 'True'}), + 'path': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '512', 'blank': 'True'}), + 'pluginsettings': ('django.db.models.fields.TextField', [], {'default': "''", 'null': 'True', 'blank': 'True'}), + 'requires_configuration': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'script': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '256', 'blank': 'True'}), + 'selected': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'status': ('django.db.models.fields.TextField', [], {'default': "''", 'null': 'True', 'blank': 'True'}), + 'url': ('django.db.models.fields.URLField', [], {'default': "''", 'max_length': '256', 'blank': 'True'}), + 'userinputfields': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'null': 'True', 'blank': 'True'}), + 'version': ('django.db.models.fields.CharField', [], {'max_length': '256'}) + }, + u'rundb.pluginresult': { + 'Meta': {'ordering': "['-id']", 'object_name': 'PluginResult'}, + 'apikey': ('django.db.models.fields.CharField', [], {'max_length': '256', 'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'inodes': ('django.db.models.fields.BigIntegerField', [], {'default': '-1'}), + 'owner': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['auth.User']", 'on_delete': 'models.SET_DEFAULT'}), + 'plugin': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.Plugin']"}), + 'result': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'pluginresult_set'", 'to': u"orm['rundb.Results']"}), + 'size': ('django.db.models.fields.BigIntegerField', [], {'default': '-1'}), + 'store': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'blank': 'True'}), + 'validation_errors': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'blank': 'True'}) + }, + u'rundb.pluginresultjob': { + 'Meta': {'object_name': 'PluginResultJob'}, + 'config': ('django.db.models.fields.TextField', [], {'default': "''", 'blank': 'True'}), + 'endtime': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + 'grid_engine_jobid': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'plugin_result': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'plugin_result_jobs'", 'to': u"orm['rundb.PluginResult']"}), + 'run_level': ('django.db.models.fields.CharField', [], {'max_length': '20'}), + 'starttime': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + 'state': ('django.db.models.fields.CharField', [], {'max_length': '20'}) + }, + u'rundb.project': { + 'Meta': {'object_name': 'Project'}, + 'created': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + 'creator': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['auth.User']", 'on_delete': 'models.SET_DEFAULT'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'modified': ('django.db.models.fields.DateTimeField', [], {'auto_now': 'True', 'blank': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '64'}), + 'public': ('django.db.models.fields.BooleanField', [], {'default': 'True'}) + }, + u'rundb.publisher': { + 'Meta': {'object_name': 'Publisher'}, + 'date': ('django.db.models.fields.DateTimeField', [], {}), + 'global_meta': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '200'}), + 'path': ('django.db.models.fields.CharField', [], {'max_length': '512'}), + 'version': ('django.db.models.fields.CharField', [], {'max_length': '256'}) + }, + u'rundb.qctype': { + 'Meta': {'object_name': 'QCType'}, + 'defaultThreshold': ('django.db.models.fields.PositiveIntegerField', [], {'default': '0'}), + 'description': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'maxThreshold': ('django.db.models.fields.PositiveIntegerField', [], {'default': '100'}), + 'minThreshold': ('django.db.models.fields.PositiveIntegerField', [], {'default': '0'}), + 'qcName': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '512'}) + }, + u'rundb.qualitymetrics': { + 'Meta': {'object_name': 'QualityMetrics'}, + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'q0_100bp_reads': ('django.db.models.fields.IntegerField', [], {}), + 'q0_150bp_reads': ('django.db.models.fields.IntegerField', [], {'default': '0'}), + 'q0_50bp_reads': ('django.db.models.fields.IntegerField', [], {}), + 'q0_bases': ('django.db.models.fields.BigIntegerField', [], {}), + 'q0_max_read_length': ('django.db.models.fields.IntegerField', [], {}), + 'q0_mean_read_length': ('django.db.models.fields.FloatField', [], {}), + 'q0_median_read_length': ('django.db.models.fields.IntegerField', [], {'default': '0'}), + 'q0_mode_read_length': ('django.db.models.fields.IntegerField', [], {'default': '0'}), + 'q0_reads': ('django.db.models.fields.IntegerField', [], {}), + 'q17_100bp_reads': ('django.db.models.fields.IntegerField', [], {}), + 'q17_150bp_reads': ('django.db.models.fields.IntegerField', [], {}), + 'q17_50bp_reads': ('django.db.models.fields.IntegerField', [], {}), + 'q17_bases': ('django.db.models.fields.BigIntegerField', [], {}), + 'q17_max_read_length': ('django.db.models.fields.IntegerField', [], {}), + 'q17_mean_read_length': ('django.db.models.fields.FloatField', [], {}), + 'q17_median_read_length': ('django.db.models.fields.IntegerField', [], {'default': '0'}), + 'q17_mode_read_length': ('django.db.models.fields.IntegerField', [], {'default': '0'}), + 'q17_reads': ('django.db.models.fields.IntegerField', [], {}), + 'q20_100bp_reads': ('django.db.models.fields.IntegerField', [], {}), + 'q20_150bp_reads': ('django.db.models.fields.IntegerField', [], {}), + 'q20_50bp_reads': ('django.db.models.fields.IntegerField', [], {}), + 'q20_bases': ('django.db.models.fields.BigIntegerField', [], {}), + 'q20_max_read_length': ('django.db.models.fields.FloatField', [], {}), + 'q20_mean_read_length': ('django.db.models.fields.IntegerField', [], {}), + 'q20_median_read_length': ('django.db.models.fields.IntegerField', [], {'default': '0'}), + 'q20_mode_read_length': ('django.db.models.fields.IntegerField', [], {'default': '0'}), + 'q20_reads': ('django.db.models.fields.IntegerField', [], {}), + 'report': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'qualitymetrics_set'", 'to': u"orm['rundb.Results']"}) + }, + u'rundb.referencegenome': { + 'Meta': {'ordering': "['short_name']", 'object_name': 'ReferenceGenome'}, + 'celery_task_id': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '60', 'blank': 'True'}), + 'date': ('django.db.models.fields.DateTimeField', [], {'default': 'datetime.datetime.now'}), + 'enabled': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'file_monitor': ('django.db.models.fields.related.OneToOneField', [], {'to': u"orm['rundb.FileMonitor']", 'unique': 'True', 'null': 'True', 'on_delete': 'models.SET_NULL', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'identity_hash': ('django.db.models.fields.CharField', [], {'default': 'None', 'max_length': '40', 'null': 'True', 'blank': 'True'}), + 'index_version': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '512'}), + 'notes': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + 'reference_path': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'blank': 'True'}), + 'short_name': ('django.db.models.fields.CharField', [], {'max_length': '512'}), + 'source': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + 'species': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + 'status': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + 'verbose_error': ('django.db.models.fields.CharField', [], {'max_length': '3000', 'blank': 'True'}), + 'version': ('django.db.models.fields.CharField', [], {'max_length': '100', 'blank': 'True'}) + }, + u'rundb.remoteaccount': { + 'Meta': {'object_name': 'RemoteAccount'}, + 'access_token': ('django.db.models.fields.CharField', [], {'max_length': '2048', 'null': 'True', 'blank': 'True'}), + 'account_label': ('django.db.models.fields.CharField', [], {'default': "'Unnamed Account'", 'max_length': '64'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'refresh_token': ('django.db.models.fields.CharField', [], {'max_length': '2048', 'null': 'True', 'blank': 'True'}), + 'remote_resource': ('django.db.models.fields.CharField', [], {'max_length': '2048'}), + 'token_expires': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + 'user_name': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '255', 'blank': 'True'}) + }, + u'rundb.reportstorage': { + 'Meta': {'object_name': 'ReportStorage'}, + 'default': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'dirPath': ('django.db.models.fields.CharField', [], {'max_length': '200'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '200'}), + 'webServerPath': ('django.db.models.fields.CharField', [], {'max_length': '200'}) + }, + u'rundb.results': { + 'Meta': {'object_name': 'Results'}, + 'analysisVersion': ('django.db.models.fields.CharField', [], {'max_length': '256'}), + 'analysismetrics': ('django.db.models.fields.related.OneToOneField', [], {'to': u"orm['rundb.AnalysisMetrics']", 'unique': 'True', 'null': 'True', 'blank': 'True'}), + 'autoExempt': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'diskusage': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'eas': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'results_set'", 'null': 'True', 'to': u"orm['rundb.ExperimentAnalysisSettings']"}), + 'experiment': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'results_set'", 'to': u"orm['rundb.Experiment']"}), + 'framesProcessed': ('django.db.models.fields.IntegerField', [], {}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'libmetrics': ('django.db.models.fields.related.OneToOneField', [], {'to': u"orm['rundb.LibMetrics']", 'unique': 'True', 'null': 'True', 'blank': 'True'}), + 'log': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + 'metaData': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'blank': 'True'}), + 'parentIDs': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + 'parentResult': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'childResults_set'", 'null': 'True', 'on_delete': 'models.SET_NULL', 'to': u"orm['rundb.Results']"}), + 'processedCycles': ('django.db.models.fields.IntegerField', [], {}), + 'processedflows': ('django.db.models.fields.IntegerField', [], {}), + 'projects': ('django.db.models.fields.related.ManyToManyField', [], {'related_name': "'results'", 'symmetrical': 'False', 'to': u"orm['rundb.Project']"}), + 'qualitymetrics': ('django.db.models.fields.related.OneToOneField', [], {'to': u"orm['rundb.QualityMetrics']", 'unique': 'True', 'null': 'True', 'blank': 'True'}), + 'reference': ('django.db.models.fields.CharField', [], {'max_length': '64', 'null': 'True', 'blank': 'True'}), + 'reportLink': ('django.db.models.fields.CharField', [], {'max_length': '512'}), + 'reportStatus': ('django.db.models.fields.CharField', [], {'default': "'Nothing'", 'max_length': '64', 'null': 'True'}), + 'reportstorage': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'storage'", 'null': 'True', 'to': u"orm['rundb.ReportStorage']"}), + 'representative': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'resultsName': ('django.db.models.fields.CharField', [], {'max_length': '512'}), + 'resultsType': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + 'runid': ('django.db.models.fields.CharField', [], {'max_length': '10', 'blank': 'True'}), + 'status': ('django.db.models.fields.CharField', [], {'max_length': '64'}), + 'timeStamp': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'db_index': 'True', 'blank': 'True'}), + 'timeToComplete': ('django.db.models.fields.CharField', [], {'max_length': '64'}) + }, + u'rundb.rig': { + 'Meta': {'object_name': 'Rig'}, + 'alarms': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'blank': 'True'}), + 'comments': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + 'display_state': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + 'ftppassword': ('django.db.models.fields.CharField', [], {'default': "'ionguest'", 'max_length': '64'}), + 'ftprootdir': ('django.db.models.fields.CharField', [], {'default': "'results'", 'max_length': '64'}), + 'ftpserver': ('django.db.models.fields.CharField', [], {'default': "'192.168.201.1'", 'max_length': '128'}), + 'ftpusername': ('django.db.models.fields.CharField', [], {'default': "'ionguest'", 'max_length': '64'}), + 'host_address': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'blank': 'True'}), + 'last_clean_date': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + 'last_experiment': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + 'last_init_date': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + 'location': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.Location']"}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '200', 'primary_key': 'True'}), + 'serial': ('django.db.models.fields.CharField', [], {'max_length': '24', 'null': 'True', 'blank': 'True'}), + 'state': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + 'type': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'blank': 'True'}), + 'updateCommand': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'blank': 'True'}), + 'updateflag': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'updatehome': ('django.db.models.fields.CharField', [], {'default': "'192.168.201.1'", 'max_length': '256'}), + 'version': ('django.db.models.fields.TextField', [], {'default': "'{}'", 'blank': 'True'}) + }, + u'rundb.runtype': { + 'Meta': {'object_name': 'RunType'}, + 'alternate_name': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'applicationGroups': ('django.db.models.fields.related.ManyToManyField', [], {'symmetrical': 'False', 'related_name': "'applications'", 'null': 'True', 'to': u"orm['rundb.ApplicationGroup']"}), + 'barcode': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), + 'description': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'isActive': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'meta': ('django.db.models.fields.TextField', [], {'default': "''", 'null': 'True', 'blank': 'True'}), + 'nucleotideType': ('django.db.models.fields.CharField', [], {'default': "'dna'", 'max_length': '64', 'blank': 'True'}), + 'runType': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '512'}) + }, + u'rundb.sample': { + 'Meta': {'unique_together': "(('name', 'externalId'),)", 'object_name': 'Sample'}, + 'date': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'null': 'True', 'blank': 'True'}), + 'description': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}), + 'displayedName': ('django.db.models.fields.CharField', [], {'max_length': '127', 'null': 'True', 'blank': 'True'}), + 'experiments': ('django.db.models.fields.related.ManyToManyField', [], {'symmetrical': 'False', 'related_name': "'samples'", 'null': 'True', 'to': u"orm['rundb.Experiment']"}), + 'externalId': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '127', 'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '127', 'null': 'True', 'blank': 'True'}), + 'status': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '512', 'blank': 'True'}) + }, + u'rundb.sampleannotation_cv': { + 'Meta': {'object_name': 'SampleAnnotation_CV'}, + 'annotationType': ('django.db.models.fields.CharField', [], {'max_length': '127'}), + 'iRAnnotationType': ('django.db.models.fields.CharField', [], {'max_length': '127', 'null': 'True', 'blank': 'True'}), + 'iRValue': ('django.db.models.fields.CharField', [], {'max_length': '127', 'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'isActive': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'isIRCompatible': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'sampleGroupType_CV': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'sampleAnnotation_set'", 'null': 'True', 'to': u"orm['rundb.SampleGroupType_CV']"}), + 'uid': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '32'}), + 'value': ('django.db.models.fields.CharField', [], {'max_length': '127', 'blank': 'True'}) + }, + u'rundb.sampleattribute': { + 'Meta': {'object_name': 'SampleAttribute'}, + 'creationDate': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + 'creator': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'created_sampleAttribute'", 'on_delete': 'models.SET_DEFAULT', 'to': u"orm['auth.User']"}), + 'dataType': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'sampleAttributes'", 'to': u"orm['rundb.SampleAttributeDataType']"}), + 'description': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}), + 'displayedName': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '127'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'isActive': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'isMandatory': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'lastModifiedDate': ('django.db.models.fields.DateTimeField', [], {'auto_now': 'True', 'blank': 'True'}), + 'lastModifiedUser': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'lastModified_sampleAttribute'", 'on_delete': 'models.SET_DEFAULT', 'to': u"orm['auth.User']"}) + }, + u'rundb.sampleattributedatatype': { + 'Meta': {'object_name': 'SampleAttributeDataType'}, + 'dataType': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '64'}), + 'description': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'isActive': ('django.db.models.fields.BooleanField', [], {'default': 'True'}) + }, + u'rundb.sampleattributevalue': { + 'Meta': {'object_name': 'SampleAttributeValue'}, + 'creationDate': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + 'creator': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'created_sampleAttributeValue'", 'on_delete': 'models.SET_DEFAULT', 'to': u"orm['auth.User']"}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'lastModifiedDate': ('django.db.models.fields.DateTimeField', [], {'auto_now': 'True', 'blank': 'True'}), + 'lastModifiedUser': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'lastModified_sampleAttributeValue'", 'on_delete': 'models.SET_DEFAULT', 'to': u"orm['auth.User']"}), + 'sample': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'sampleAttributeValues'", 'to': u"orm['rundb.Sample']"}), + 'sampleAttribute': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'samples'", 'to': u"orm['rundb.SampleAttribute']"}), + 'value': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}) + }, + u'rundb.samplegrouptype_cv': { + 'Meta': {'object_name': 'SampleGroupType_CV'}, + 'description': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}), + 'displayedName': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '127'}), + 'iRAnnotationType': ('django.db.models.fields.CharField', [], {'max_length': '127', 'null': 'True', 'blank': 'True'}), + 'iRValue': ('django.db.models.fields.CharField', [], {'max_length': '127', 'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'isActive': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'isIRCompatible': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'uid': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '32'}) + }, + u'rundb.sampleprepdata': { + 'Meta': {'object_name': 'SamplePrepData'}, + 'endTime': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'instrumentName': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '200', 'blank': 'True'}), + 'instrumentStatus': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '256', 'blank': 'True'}), + 'kitType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'lastUpdate': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + 'logPath': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'message': ('django.db.models.fields.TextField', [], {'default': "''", 'blank': 'True'}), + 'operationMode': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'packageVer': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'progress': ('django.db.models.fields.FloatField', [], {'default': '0.0', 'blank': 'True'}), + 'reagentsExpiration': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'reagentsLot': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'reagentsPart': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'remainingSeconds': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'samplePrepDataType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'scriptVersion': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'solutionsExpiration': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'solutionsLot': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'solutionsPart': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'startTime': ('django.db.models.fields.DateTimeField', [], {'null': 'True', 'blank': 'True'}), + 'tipRackBarcode': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}) + }, + u'rundb.sampleset': { + 'Meta': {'object_name': 'SampleSet'}, + 'SampleGroupType_CV': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'sampleSets'", 'null': 'True', 'to': u"orm['rundb.SampleGroupType_CV']"}), + 'additionalCycles': ('django.db.models.fields.CharField', [], {'max_length': '64', 'null': 'True', 'blank': 'True'}), + 'categories': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '256', 'blank': 'True'}), + 'combinedLibraryTubeLabel': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'creationDate': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + 'creator': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'created_sampleSet'", 'on_delete': 'models.SET_DEFAULT', 'to': u"orm['auth.User']"}), + 'description': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'null': 'True', 'blank': 'True'}), + 'displayedName': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '127'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'lastModifiedDate': ('django.db.models.fields.DateTimeField', [], {'auto_now': 'True', 'blank': 'True'}), + 'lastModifiedUser': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'lastModified_sampleSet'", 'on_delete': 'models.SET_DEFAULT', 'to': u"orm['auth.User']"}), + 'libraryPrepInstrument': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'libraryPrepInstrumentData': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'libraryPrepData_sampleSet'", 'null': 'True', 'on_delete': 'models.SET_NULL', 'to': u"orm['rundb.SamplePrepData']"}), + 'libraryPrepKitName': ('django.db.models.fields.CharField', [], {'max_length': '512', 'null': 'True', 'blank': 'True'}), + 'libraryPrepPlateType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'libraryPrepProtocol': ('django.db.models.fields.CharField', [], {'max_length': '64', 'null': 'True', 'blank': 'True'}), + 'libraryPrepType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'pcrPlateSerialNum': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'null': 'True', 'blank': 'True'}), + 'status': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '512', 'blank': 'True'}) + }, + u'rundb.samplesetitem': { + 'Meta': {'object_name': 'SampleSetItem'}, + 'assayGroup': ('django.db.models.fields.CharField', [], {'max_length': '64', 'null': 'True', 'blank': 'True'}), + 'biopsyDays': ('django.db.models.fields.IntegerField', [], {'default': '0', 'null': 'True', 'blank': 'True'}), + 'cancerType': ('django.db.models.fields.CharField', [], {'max_length': '127', 'null': 'True', 'blank': 'True'}), + 'cellNum': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '127', 'null': 'True', 'blank': 'True'}), + 'cellularityPct': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'controlType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '127', 'null': 'True', 'blank': 'True'}), + 'coupleId': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '127', 'null': 'True', 'blank': 'True'}), + 'creationDate': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + 'creator': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'created_sampleSetItem'", 'on_delete': 'models.SET_DEFAULT', 'to': u"orm['auth.User']"}), + 'description': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '1024', 'null': 'True', 'blank': 'True'}), + 'dnabarcode': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'startBarcode'", 'null': 'True', 'to': u"orm['rundb.dnaBarcode']"}), + 'embryoId': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '127', 'null': 'True', 'blank': 'True'}), + 'endDnabarcode': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'endBarcode'", 'null': 'True', 'to': u"orm['rundb.dnaBarcode']"}), + 'gender': ('django.db.models.fields.CharField', [], {'max_length': '127', 'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'lastModifiedDate': ('django.db.models.fields.DateTimeField', [], {'auto_now': 'True', 'blank': 'True'}), + 'lastModifiedUser': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'lastModified_sampleSetItem'", 'on_delete': 'models.SET_DEFAULT', 'to': u"orm['auth.User']"}), + 'mouseStrains': ('django.db.models.fields.CharField', [], {'max_length': '127', 'null': 'True', 'blank': 'True'}), + 'nucleotideType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'panelPoolType': ('django.db.models.fields.CharField', [], {'max_length': '64', 'null': 'True', 'blank': 'True'}), + 'pcrPlateColumn': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '10', 'null': 'True', 'blank': 'True'}), + 'pcrPlateRow': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '10', 'null': 'True', 'blank': 'True'}), + 'population': ('django.db.models.fields.CharField', [], {'max_length': '127', 'null': 'True', 'blank': 'True'}), + 'relationshipGroup': ('django.db.models.fields.IntegerField', [], {}), + 'relationshipRole': ('django.db.models.fields.CharField', [], {'max_length': '127', 'null': 'True', 'blank': 'True'}), + 'sample': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'sampleSets'", 'to': u"orm['rundb.Sample']"}), + 'sampleCollectionDate': ('django.db.models.fields.DateField', [], {'null': 'True', 'blank': 'True'}), + 'sampleReceiptDate': ('django.db.models.fields.DateField', [], {'null': 'True', 'blank': 'True'}), + 'sampleSet': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'samples'", 'to': u"orm['rundb.SampleSet']"}), + 'sampleSource': ('django.db.models.fields.CharField', [], {'max_length': '64', 'null': 'True', 'blank': 'True'}), + 'tubePosition': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '10', 'null': 'True', 'blank': 'True'}) + }, + u'rundb.supportupload': { + 'Meta': {'object_name': 'SupportUpload'}, + 'account': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.RemoteAccount']"}), + 'celery_task_id': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '60', 'blank': 'True'}), + 'contact_email': ('django.db.models.fields.EmailField', [], {'default': "''", 'max_length': '75'}), + 'created': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + 'description': ('django.db.models.fields.TextField', [], {'default': "''"}), + 'file': ('django.db.models.fields.related.OneToOneField', [], {'to': u"orm['rundb.FileMonitor']", 'unique': 'True', 'null': 'True', 'on_delete': 'models.SET_NULL', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'local_message': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '2048', 'blank': 'True'}), + 'local_status': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '255', 'blank': 'True'}), + 'result': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['rundb.Results']", 'null': 'True', 'blank': 'True'}), + 'ticket_id': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '255', 'blank': 'True'}), + 'ticket_message': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '2048', 'blank': 'True'}), + 'ticket_status': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '255', 'blank': 'True'}), + 'updated': ('django.db.models.fields.DateTimeField', [], {'auto_now': 'True', 'blank': 'True'}), + 'user': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['auth.User']", 'on_delete': 'models.SET_DEFAULT'}) + }, + u'rundb.template': { + 'Meta': {'object_name': 'Template'}, + 'comments': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'isofficial': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'key': ('django.db.models.fields.CharField', [], {'max_length': '64'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '64'}), + 'sequence': ('django.db.models.fields.TextField', [], {'blank': 'True'}) + }, + u'rundb.tfmetrics': { + 'HPAccuracy': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + 'Meta': {'object_name': 'TFMetrics'}, + 'Q10Histo': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + 'Q10Mean': ('django.db.models.fields.FloatField', [], {}), + 'Q10ReadCount': ('django.db.models.fields.FloatField', [], {}), + 'Q17Histo': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + 'Q17Mean': ('django.db.models.fields.FloatField', [], {}), + 'Q17ReadCount': ('django.db.models.fields.FloatField', [], {}), + 'SysSNR': ('django.db.models.fields.FloatField', [], {}), + 'aveKeyCount': ('django.db.models.fields.FloatField', [], {}), + 'corrHPSNR': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'keypass': ('django.db.models.fields.FloatField', [], {}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '128', 'db_index': 'True'}), + 'number': ('django.db.models.fields.FloatField', [], {}), + 'report': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'tfmetrics_set'", 'to': u"orm['rundb.Results']"}), + 'sequence': ('django.db.models.fields.CharField', [], {'max_length': '512'}) + }, + u'rundb.threeprimeadapter': { + 'Meta': {'object_name': 'ThreePrimeadapter'}, + 'chemistryType': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '64', 'blank': 'True'}), + 'description': ('django.db.models.fields.CharField', [], {'max_length': '1024', 'blank': 'True'}), + 'direction': ('django.db.models.fields.CharField', [], {'default': "'Forward'", 'max_length': '20'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'isActive': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'isDefault': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '256'}), + 'runMode': ('django.db.models.fields.CharField', [], {'default': "'single'", 'max_length': '64', 'blank': 'True'}), + 'sequence': ('django.db.models.fields.CharField', [], {'max_length': '512'}), + 'uid': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '32'}) + }, + u'rundb.usereventlog': { + 'Meta': {'object_name': 'UserEventLog'}, + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'text': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + 'timeStamp': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), + 'upload': ('django.db.models.fields.related.ForeignKey', [], {'related_name': "'logs'", 'to': u"orm['rundb.ContentUpload']"}) + }, + u'rundb.userprofile': { + 'Meta': {'object_name': 'UserProfile'}, + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'last_read_news_post': ('django.db.models.fields.DateTimeField', [], {'default': 'datetime.datetime(1984, 11, 5, 0, 0)'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '93'}), + 'needs_activation': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'note': ('django.db.models.fields.TextField', [], {'default': "''", 'blank': 'True'}), + 'phone_number': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '256', 'blank': 'True'}), + 'title': ('django.db.models.fields.CharField', [], {'default': "'user'", 'max_length': '256'}), + 'user': ('django.db.models.fields.related.OneToOneField', [], {'to': u"orm['auth.User']", 'unique': 'True'}) + } + } + + complete_apps = ['rundb'] \ No newline at end of file diff --git a/dbReports/iondb/rundb/models.py b/dbReports/iondb/rundb/models.py index 3c022f94..96a4c777 100755 --- a/dbReports/iondb/rundb/models.py +++ b/dbReports/iondb/rundb/models.py @@ -348,6 +348,7 @@ class KitInfo(models.Model): # ("readLengthDerivableFromFlows;flowsDerivableFromReadLength;", "Non-Hi-Q sequencing kit categories"), ("readLengthDerivableFromFlows;", "Non-Hi-Q sequencing kit categories"), ("s5v1Kit", "S5 v1 kit categories"), + ("s5v1Kit;samplePrepProtocol;cerebro_550_cycling", "S5 v1 and Cerebro kit categories"), ( "s5v1Kit;flowOverridable;", "S5 v1 kit categories with special flow count handling", @@ -626,6 +627,7 @@ class common_CV(models.Model): ("AMPS_RNA", "AmpliSeq RNA products"), ("WGNM", "Whole genome products"), ("TARS_16S", "16S products"), + ("EXOME", "Ampliseq Exome products"), ) categories = models.CharField( max_length=256, choices=ALLOWED_CATEGORIES, default="", blank=True, null=True @@ -916,6 +918,12 @@ def _extract_extra_kwargs(self, **kwargs): extra_kwargs["platform"] = kwargs.pop("x_platform", "") extra_kwargs["x_isSaveBySample"] = kwargs.pop("x_isSaveBySample", False) extra_kwargs["flowsInOrder"] = kwargs.pop("x_flowsInOrder", "") + extra_kwargs["chipTecDfltAmbient"] = kwargs.pop("x_chipTecDfltAmbient", None) + extra_kwargs["chipTecSlope"] = kwargs.pop("x_chipTecSlope", None) + extra_kwargs["chipTecMinThreshold"] = kwargs.pop("x_chipTecMinThreshold", None) + extra_kwargs["manTecDfltAmbient"] = kwargs.pop("x_manTecDfltAmbient", None) + extra_kwargs["manTecSlope"] = kwargs.pop("x_manTecSlope", None) + extra_kwargs["manTecMinThreshold"] = kwargs.pop("x_manTecMinThreshold", None) # EAS extra_kwargs["barcodedSamples"] = kwargs.pop("x_barcodedSamples", {}) @@ -946,6 +954,9 @@ def _extract_extra_kwargs(self, **kwargs): extra_kwargs["mixedTypeRNA_hotSpotRegionBedFile"] = kwargs.pop( "x_mixedTypeRNA_regionfile", "" ) + extra_kwargs["metaData"] = kwargs.pop( + "x_metaData", {} + ) # EAS - analysis args extra_kwargs["beadfindargs"] = kwargs.pop("x_beadfindargs", "") @@ -1282,10 +1293,11 @@ class PlannedExperiment(models.Model): ("onco_liquidBiopsy", "Liquid Biopsy"), ("onco_solidTumor;onco_heme", "AmpliSeq HD for Tumor"), ("carrierSeq", "Carrier Seq"), + ("exome", "Ampliseq Exome"), ) categories = models.CharField( - max_length=64, + max_length=256, choices=ALLOWED_CATEGORIES, default="", blank=True, @@ -1598,6 +1610,48 @@ def get_sequencekitname(self): else: return "" + def get_chipTecDfltAmbient(self): + experiment = self.experiment + if experiment and experiment.chipTecDfltAmbient: + return round(experiment.chipTecDfltAmbient, 4) + else: + return None + + def get_chipTecSlope(self): + experiment = self.experiment + if experiment and experiment.chipTecSlope: + return round(experiment.chipTecSlope, 4) + else: + return None + + def get_chipTecMinThreshold(self): + experiment = self.experiment + if experiment and experiment.chipTecMinThreshold: + return round(experiment.chipTecMinThreshold, 4) + else: + return None + + def get_manTecDfltAmbient(self): + experiment = self.experiment + if experiment and experiment.manTecDfltAmbient: + return round(experiment.manTecDfltAmbient, 4) + else: + return None + + def get_manTecSlope(self): + experiment = self.experiment + if experiment and experiment.manTecSlope: + return round(experiment.manTecSlope, 4) + else: + return None + + def get_manTecMinThreshold(self): + experiment = self.experiment + if experiment and experiment.manTecMinThreshold: + return round(experiment.manTecMinThreshold, 4) + else: + return None + def get_variantfrequency(self): return "" @@ -1897,6 +1951,13 @@ def save_plannedExperiment_association(self, isPlanCreated, **kwargs): "platform", "chipBarcode", "flowsInOrder", + "chipTecDfltAmbient", + "chipTecSlope", + "chipTecMinThreshold", + "manTecDfltAmbient", + "manTecSlope", + "manTecMinThreshold", + "metaData" ] for key in exp_keys: if key in kwargs: @@ -2521,6 +2582,13 @@ class Experiment(models.Model): chefProtocolDeviationName = models.CharField(max_length=127, blank=True, null=True) chefEndTime = models.DateTimeField(null=True, blank=True) + chipTecDfltAmbient = models.FloatField(default=None, blank=True, null=True) + chipTecSlope = models.FloatField(default=None, blank=True, null=True) + chipTecMinThreshold = models.FloatField(default=None, blank=True, null=True) + manTecDfltAmbient = models.FloatField(default=None, blank=True, null=True) + manTecSlope = models.FloatField(default=None, blank=True, null=True) + manTecMinThreshold = models.FloatField(default=None, blank=True, null=True) + def __unicode__(self): return self.expName @@ -5295,6 +5363,7 @@ class GlobalConfig(models.Model): ) majorPlatform = models.CharField(max_length=24, blank=True, null=True, default="") + password_max_age = models.IntegerField(default=90, blank=True) def set_TS_update_status(self, inputstr): self.ts_update_status = inputstr @@ -7143,6 +7212,8 @@ class UserProfile(models.Model): ) # needs_activation will be used to request user activation by admin needs_activation = models.BooleanField(default=False) + is_password_valid = models.BooleanField(default=False) + last_password_changed_on = models.DateTimeField(default=datetime.datetime(1984, 11, 6, tzinfo=timezone.utc)) def save(self, *args, **kwargs): if self.user and not self.name: diff --git a/dbReports/iondb/rundb/plan/ampliseq_to_TS_plan_convertor.py b/dbReports/iondb/rundb/plan/ampliseq_to_TS_plan_convertor.py index 422fbd59..70fb1bec 100644 --- a/dbReports/iondb/rundb/plan/ampliseq_to_TS_plan_convertor.py +++ b/dbReports/iondb/rundb/plan/ampliseq_to_TS_plan_convertor.py @@ -49,6 +49,13 @@ def __init__(self): self.libkit = None self.library = "" self.libraryKey = "TCAG" + self.chipTecDfltAmbient = None + self.chipTecSlope = None + self.chipTecMinThreshold = None + self.manTecDfltAmbient = None + self.manTecSlope = None + self.manTecMinThreshold = None + self.categories = None # Kit self.librarykitname = "" self.metaData = {} @@ -246,22 +253,33 @@ def get_applicationGroupDisplayedName(self): def update_chip_inst_type(self, app=None): # Parse the meta data and set the default chip type and instrument type for the Panel which is being imported metaData = self.ampliSeq_plan_metaData - run_type = metaData["run_type"] - plan_name = metaData["plan_name"] + # The plan.json has PGM, Proton (legacy), and S5 chip type as choice instrument_type = metaData["choice"] + chip_type = "540" # "choice": "None" will be in the JSON from 3.6 schema imports decoratedInstType = None if instrument_type == "None": instrument_type = "s5" if instrument_type in self.get_s5_chips(): - decoratedInstType = self.decorate_S5_instruments(instrument_type) chip_type = instrument_type - instrument_type = "s5" - else: - chip_type = "540" + elif app and app.applicationGroup: # TS-18344 + if app.defaultChipType in self.get_s5_chips(): + chip_type = app.defaultChipType + self.chipType = chip_type + + return chip_type + def set_decorated_inst_type(self): + # Parse the meta data and set the default chip type and instrument type for the Panel which is being imported + metaData = self.ampliSeq_plan_metaData + instrument_type = metaData["choice"] + decoratedInstType = None + if instrument_type == "None": + instrument_type = "s5" + if instrument_type in self.get_s5_chips(): + decoratedInstType = self.decorate_S5_instruments(instrument_type) + instrument_type = "s5" self.platform = instrument_type - self.chipType = chip_type self.decoratedInstType = decoratedInstType def get_applProductObj(self): @@ -273,9 +291,8 @@ def get_applProductObj(self): app_group, app_group_name = self.get_applicationGroupDisplayedName() - self.update_chip_inst_type() + self.set_decorated_inst_type() instrument_type = self.platform - chip_type = self.chipType decoratedInstType = self.decoratedInstType print( @@ -335,7 +352,7 @@ def get_applProductObj(self): print(self.errMessage["E002"].format(available_choice)) sys.exit(1) - return app, app_group_name, instrument_type, chip_type + return app, app_group_name, instrument_type def get_defaultTemplateKit(self, app): defaultTemplateKit = app.defaultTemplateKit and app.defaultTemplateKit.name @@ -376,17 +393,30 @@ def plan_json( "choice", "None" ), # "None" this is default choice for legacy 3.6 "design_name": meta["design"].get("design_name", None), + "categories": meta["design"]["plan"].get("categories", None), "plugin_details": meta["design"]["plan"].get("selectedPlugins", {}), "upload_id": upload_id, + "templatingKitName": meta["design"]["plan"].get("templatingKitName", None), + "samplePrepKitName": meta["design"]["plan"].get("samplePrepKitName", None), + "sequencekitname": meta["design"]["plan"].get("sequencekitname", None), + "barcodeId": meta["design"]["plan"].get("barcodeId", None), + "flows": meta["design"]["plan"].get("flows", None), + "chipTecDfltAmbient": meta["design"]["plan"].get("chipTecDfltAmbient", None), + "chipTecSlope": meta["design"]["plan"].get("chipTecSlope", None), + "chipTecMinThreshold": meta["design"]["plan"].get("chipTecMinThreshold", None), + "manTecDfltAmbient": meta["design"]["plan"].get("manTecDfltAmbient", None), + "manTecSlope": meta["design"]["plan"].get("manTecSlope", None), + "manTecMinThreshold": meta["design"]["plan"].get("manTecMinThreshold", None), + "metaData": meta["design"]["plan"].get("metaData", {}) } ampliSeqTemplate = processAmpliSeqPanel() ampliSeqTemplate.ampliSeq_plan_metaData = ampliSeq_plan_metaData - app, app_group_name, instrument_type, chip_type = ( + app, app_group_name, instrument_type = ( ampliSeqTemplate.get_applProductObj() ) - ampliSeqTemplate.update_chip_inst_type(app=app) + chip_type = ampliSeqTemplate.update_chip_inst_type(app=app) plugin_details, alignmentargs_override = ampliSeqTemplate.get_pluginDetails() @@ -401,20 +431,38 @@ def plan_json( "runType": ampliSeq_plan_metaData["run_type"], "chipType": chip_type, "applicationGroupDisplayedName": app_group_name, - "barcodeId": app.defaultBarcodeKitName, + "categories": ampliSeq_plan_metaData.get("categories", None), + "barcodeId": ampliSeq_plan_metaData.get("barcodeId") or app.defaultBarcodeKitName, "bedfile": target_regions_bed_path, "regionfile": hotspots_bed_path, "sseBedFile": sse_bed_path, - "flows": app.defaultFlowCount, + "flows": ampliSeq_plan_metaData.get("flows") or app.defaultFlowCount, "flowsInOrder": ampliSeqTemplate.get_flowOrder(app), "platform": instrument_type, "library": meta["reference"], - "librarykitname": app.defaultLibraryKit and app.defaultLibraryKit.name, - "samplePrepKitName": app.defaultSamplePrepKit and app.defaultSamplePrepKit.name, + "librarykitname": ampliSeq_plan_metaData.get("librarykitname") or app.defaultLibraryKit and app.defaultLibraryKit.name, + "samplePrepKitName": ampliSeq_plan_metaData.get("samplePrepKitName") or app.defaultSamplePrepKit and app.defaultSamplePrepKit.name, "selectedPlugins": plugin_details, - "sequencekitname": app.defaultSequencingKit and app.defaultSequencingKit.name, - "templatingKitName": ampliSeqTemplate.get_defaultTemplateKit(app), + "sequencekitname": ampliSeq_plan_metaData.get("sequencekitname") or app.defaultSequencingKit and app.defaultSequencingKit.name, + "templatingKitName": ampliSeq_plan_metaData.get("templatingKitName") or ampliSeqTemplate.get_defaultTemplateKit(app), + "chipTecDfltAmbient": ampliSeq_plan_metaData.get("chipTecDfltAmbient", None), + "chipTecSlope": ampliSeq_plan_metaData.get("chipTecSlope", None), + "chipTecMinThreshold": ampliSeq_plan_metaData.get("chipTecMinThreshold", None), + "manTecDfltAmbient": ampliSeq_plan_metaData.get("manTecDfltAmbient", None), + "manTecSlope": ampliSeq_plan_metaData.get("manTecSlope", None), + "manTecMinThreshold": ampliSeq_plan_metaData.get("manTecMinThreshold", None), + "metaData": ampliSeq_plan_metaData.get("metaData", {}) } + # Update source template meta for Dynamic Tec Params + templateMetadata = { + "fromTemplate": plan_stub.get("planName"), + "isAmpliseqTecParamEnabled": True if plan_stub.get("manTecDfltAmbient") or plan_stub.get("chipTecDfltAmbient") else False, + "fromTemplateChipType": plan_stub.get("chipType"), + "fromTemplateSequenceKitname": plan_stub.get("sequencekitname"), + "fromAmpliseqTemplateSource": True + } + plan_stub.get("metaData").update(templateMetadata) + ampliSeqTemplate.update(plan_stub) plan_stub = ampliSeqTemplate.get_plan_stub() diff --git a/dbReports/iondb/rundb/plan/ampliseq_validator.py b/dbReports/iondb/rundb/plan/ampliseq_validator.py index 72c54ccf..88d0dacc 100644 --- a/dbReports/iondb/rundb/plan/ampliseq_validator.py +++ b/dbReports/iondb/rundb/plan/ampliseq_validator.py @@ -42,8 +42,9 @@ def validate_reference(meta, args, reference): # The identity_hash matching the files_md5sum.fasta hash determines whether # or not the genome is installed - print("Checking reference " + ref_hash) - if not models.ReferenceGenome.objects.filter(identity_hash=ref_hash).exists(): + print("Checking reference with Identity Hash %s and Short Name %s " % (ref_hash, short_name)) + if not models.ReferenceGenome.objects.filter(identity_hash=ref_hash).exists() \ + and not models.ReferenceGenome.objects.filter(short_name=short_name).exists(): reference_args = { "identity_hash": ref_hash, "name": name, diff --git a/dbReports/iondb/rundb/plan/page_plan/kits_step_data.py b/dbReports/iondb/rundb/plan/page_plan/kits_step_data.py index 13735752..9074cb45 100644 --- a/dbReports/iondb/rundb/plan/page_plan/kits_step_data.py +++ b/dbReports/iondb/rundb/plan/page_plan/kits_step_data.py @@ -81,6 +81,7 @@ class KitsFieldNames: PLAN_CATEGORIES = "planCategories" ADVANCED_SETTINGS_CHOICE = "advancedSettingsChoice" ADVANCED_SETTINGS = "advancedSettings" + META_DATA = "metaData" class KitsStepData(AbstractStepData): @@ -256,6 +257,7 @@ def __init__(self, sh_type): self.savedFields[KitsFieldNames.FLOWS] = 0 self.savedFields[KitsFieldNames.LIBRARY_READ_LENGTH] = 0 self.savedFields[KitsFieldNames.READ_LENGTH] = 0 + self.savedFields[KitsFieldNames.META_DATA] = {} self.prepopulatedFields[ KitsFieldNames.IS_BARCODE_KIT_SELECTION_REQUIRED diff --git a/dbReports/iondb/rundb/plan/page_plan/step_helper_db_loader.py b/dbReports/iondb/rundb/plan/page_plan/step_helper_db_loader.py index 1f7f87ef..e62c7dca 100644 --- a/dbReports/iondb/rundb/plan/page_plan/step_helper_db_loader.py +++ b/dbReports/iondb/rundb/plan/page_plan/step_helper_db_loader.py @@ -183,12 +183,16 @@ def _updateSaveStepData(self, runTypeObj, step_helper, save_plan_step_data): ] = num_samples def _metaDataFromPlan(self, step_helper, planned_experiment): - metaData = planned_experiment.metaData or {} + metaData = planned_experiment.metaData or planned_experiment.experiment.metaData or {} if ( step_helper.isCreate() or step_helper.sh_type == StepHelperType.COPY_TEMPLATE ): metaData["fromTemplate"] = planned_experiment.planName + metaData["fromTemplateId"] = planned_experiment.id + metaData["fromTemplateChipType"] = planned_experiment.get_chipType() + metaData["fromTemplateSequenceKitname"] = planned_experiment.get_sequencekitname() + metaData["fromTemplateCategories"] = planned_experiment.get_categories_display() metaData["fromTemplateSource"] = ( "ION" if planned_experiment.isSystem else planned_experiment.username ) @@ -294,6 +298,8 @@ def updateTemplateSpecificStepHelper(self, step_helper, planned_experiment): else: save_template_step_data = step_helper.steps[StepNames.SAVE_TEMPLATE] + kits_plan_step_data = step_helper.steps[StepNames.KITS] + planDisplayedName = getPlanDisplayedName(planned_experiment) if step_helper.sh_type == StepHelperType.COPY_TEMPLATE: @@ -331,6 +337,10 @@ def updateTemplateSpecificStepHelper(self, step_helper, planned_experiment): SaveTemplateStepDataFieldNames.META ] = self._metaDataFromPlan(step_helper, planned_experiment) + kits_plan_step_data.savedObjects[ + SavePlanFieldNames.META + ] = self._metaDataFromPlan(step_helper, planned_experiment) + def updatePlanSpecificStepHelper( self, step_helper, planned_experiment, set_template_name=False ): @@ -355,6 +365,7 @@ def updatePlanSpecificStepHelper( ] = planDisplayedName save_plan_step_data = step_helper.steps[StepNames.SAVE_PLAN] + kits_plan_step_data = step_helper.steps[StepNames.KITS] # Add a "copy of" if we're copying. if step_helper.isCopy(): @@ -386,6 +397,10 @@ def updatePlanSpecificStepHelper( SavePlanFieldNames.META ] = self._metaDataFromPlan(step_helper, planned_experiment) + kits_plan_step_data.savedObjects[ + SavePlanFieldNames.META + ] = self._metaDataFromPlan(step_helper, planned_experiment) + barcodeSet = planned_experiment.get_barcodeId() endBarcodeSet = planned_experiment.get_endBarcodeKitName() self._update_barcode_sets_for_edit( @@ -853,6 +868,10 @@ def _updateUniversalStep_kitData( KitsFieldNames.SAMPLE_PREP_PROTOCOL ] = planned_experiment.samplePrepProtocol + kits_step_data.savedFields[ + KitsFieldNames.META_DATA + ] = planned_experiment.experiment.metaData or {} + kits_step_data.prepopulatedFields[KitsFieldNames.PLAN_CATEGORIES] = ( planned_experiment.categories or "" ) @@ -867,6 +886,7 @@ def _updateUniversalStep_kitData( KitsFieldNames.ADVANCED_SETTINGS ] = json.dumps(self.get_kit_advanced_settings(step_helper, planned_experiment)) + def _updateUniversalStep_kitData_for_edit( self, step_helper, @@ -2434,7 +2454,7 @@ def get_kit_advanced_settings(self, step_helper, planned_experiment=None): KitsFieldNames.FORWARD_3_PRIME_ADAPTER: system_template.get_forward3primeadapter(), KitsFieldNames.LIBRARY_KEY: system_template.get_libraryKey(), KitsFieldNames.SAMPLE_PREP_PROTOCOL: system_template.samplePrepProtocol, - KitsFieldNames.TF_KEY: system_template.get_tfKey(), + KitsFieldNames.TF_KEY: system_template.get_tfKey() } else: kits_step_data = step_helper.steps[StepNames.KITS] diff --git a/dbReports/iondb/rundb/plan/page_plan/step_helper_db_saver.py b/dbReports/iondb/rundb/plan/page_plan/step_helper_db_saver.py index 9be6e22f..45ac8ca5 100644 --- a/dbReports/iondb/rundb/plan/page_plan/step_helper_db_saver.py +++ b/dbReports/iondb/rundb/plan/page_plan/step_helper_db_saver.py @@ -91,6 +91,7 @@ def __get_universal_params(self, step_helper, username): save_plan_step_data = step_helper.steps.get(StepNames.SAVE_PLAN, "") isFavorite = False + enableTecParam = False categories = application_step_data.prepopulatedFields.get( ApplicationFieldNames.CATEGORIES, "" @@ -222,6 +223,35 @@ def __get_universal_params(self, step_helper, username): x_mixedTypeRNA_regionfile = reference_step_data.savedFields[ ReferenceFieldNames.MIXED_TYPE_RNA_HOT_SPOT_BED_FILE ] + try: + # Dynamic Manifold Params + fromTemplteMeta = {} + + # Handle dynamic tec params for plan, template and plan by sample + if save_plan_step_data: + fromTemplteMeta.update(save_plan_step_data.savedObjects.get('meta')) + elif step_helper.steps.get("Save_plan_by_sample"): + fromTemplteMeta.update(step_helper.steps["Save_plan_by_sample"].getCurrentSavedObjectDict().get('meta')) + elif save_template_step_data: + fromTemplteMeta.update(save_template_step_data.savedObjects.get('meta')) + + if "tecParam" in fromTemplteMeta.get("fromTemplateCategories", None) or fromTemplteMeta.get("isAmpliseqTecParamEnabled"): + if x_chipType == fromTemplteMeta.get("fromTemplateChipType") \ + and x_sequencekitname == fromTemplteMeta.get("fromTemplateSequenceKitname"): + enableTecParam = True + templateObj = PlannedExperiment.objects.get(pk=fromTemplteMeta["fromTemplateId"]) + x_chipTecDfltAmbient = templateObj.get_chipTecDfltAmbient() + x_chipTecSlope = templateObj.get_chipTecSlope() + x_chipTecMinThreshold = templateObj.get_chipTecMinThreshold() + x_manTecDfltAmbient = templateObj.get_manTecDfltAmbient() + x_manTecSlope = templateObj.get_manTecSlope() + x_manTecMinThreshold = templateObj.get_manTecMinThreshold() + else: + logger.debug( + "step_helper_db_saver.__get_universal_params() save_step_data dynamic manifold tec param mismatch. Setting the default chip based tec param" + ) + except Exception as err: + logger.debug("step_helper_db_saver.__get_universal_params() save_step_data dynamic manifold tec param unknown errors %s" % str(err)) x_beadfindargs = analysisParams_step_data.savedFields[ AnalysisParamsFieldNames.AP_BEADFIND_SELECTED @@ -382,8 +412,19 @@ def __get_universal_params(self, step_helper, username): "x_thumbnailbasecallerargs": x_thumbnailbasecallerargs, "x_thumbnailalignmentargs": x_thumbnailalignmentargs, "x_thumbnailionstatsargs": x_thumbnailionstatsargs, - "x_custom_args": x_custom_args, + "x_custom_args": x_custom_args } + if fromTemplteMeta: + retval["x_metaData"] = fromTemplteMeta + if enableTecParam: + retval.update({ + "x_chipTecDfltAmbient": x_chipTecDfltAmbient, + "x_chipTecSlope": x_chipTecSlope, + "x_chipTecMinThreshold": x_chipTecMinThreshold, + "x_manTecDfltAmbient": x_manTecDfltAmbient, + "x_manTecSlope": x_manTecSlope, + "x_manTecMinThreshold": x_manTecMinThreshold + }) return retval def __get_specific_params_by_sample( @@ -550,7 +591,7 @@ def __get_specific_params( # 'sampleTubeLabel' : sampleTubeLabel.strip().lstrip("0") if sampleTubeLabel else "", "sampleTubeLabel": sampleTubeLabel.strip() if sampleTubeLabel else "", "chipBarcode": chipBarcode.strip() if chipBarcode else "", - "metaData": self.__update_metaData_for_LIMS(existing_meta, LIMS_meta), + "x_metaData": self.__update_metaData_for_LIMS(existing_meta, LIMS_meta), "isReusable": isReusable, "x_notes": note, "x_sample": sample, diff --git a/dbReports/iondb/rundb/plan/plan_csv_writer.py b/dbReports/iondb/rundb/plan/plan_csv_writer.py index 44ef31af..83dcc02e 100644 --- a/dbReports/iondb/rundb/plan/plan_csv_writer.py +++ b/dbReports/iondb/rundb/plan/plan_csv_writer.py @@ -114,6 +114,14 @@ class PlanCSVcolumns: REALIGN = "Enable Realignment" CATEGORIES = "Categories" CUSTOM_ARGS = "Custom Args" + # Dynamic tec manifold : TS-18354 + # Show only when exported template has these settings + CHIPTEC_DFLT_AMBIENT = "Chip Heater (Do not change)" + CHIPTEC_SLOPE = "Chip Slope (Do not change)" + CHIPTEC_MIN_THRESHOLD = "Chip Min Threshold (Do not change)" + MANTEC_DFLT_AMBIENT = "Manifold Heater (Do not change)" + MANTEC_SLOPE = "Manifold Slope (Do not change)" + MANTEC_MIN_THRESHOLD = "Manifold Min Threshold (Do not change)" FUSIONS_REF = "Fusions Reference library" FUSIONS_TARGET_BED = "Fusions Target regions BED file" @@ -259,6 +267,41 @@ def _get_fusions_target_regions_bed_file(template): filePath = _get_bed_file_path(template.get_mixedType_rna_bedfile()) return filePath +def _get_chipTecDfltAmbient(template): + ct = None + if template: + ct = template.get_chipTecDfltAmbient() + return ct + +def _get_chipTecSlope(template): + cts = None + if template: + cts = template.get_chipTecSlope() + return cts + +def _get_chipTecMinThreshold(template): + ctmt = None + if template: + ctmt = template.get_chipTecMinThreshold() + return ctmt + +def _get_manTecDfltAmbient(template): + mt = None + if template: + mt = template.get_manTecDfltAmbient() + return mt + +def _get_manTecSlope(template): + mts = None + if template: + mts = template.get_manTecSlope() + return mts + +def _get_manTecMinThreshold(template): + mtmt = None + if template: + mtmt = template.get_manTecMinThreshold() + return mtmt def _get_plugins(template, delimiter): plugins = "" @@ -605,6 +648,26 @@ def get_template_data_for_batch_planning(templateId, single_samples_file): logger.exception(format_exc()) return [], [], [] +def get_dynamicTecParams(template): + dynamicTecParams = [] + chipTecDfltAmbient = _get_chipTecDfltAmbient(template) + chipTecSlope = _get_chipTecSlope(template) + chipTecMinThreshold = _get_chipTecMinThreshold(template) + manTecDfltAmbient = _get_manTecDfltAmbient(template) + manTecSlope = _get_manTecSlope(template) + manTecMinThreshold = _get_manTecMinThreshold(template) + + + if chipTecDfltAmbient or manTecDfltAmbient: + dynamicTecParams = [ + (PlanCSVcolumns.CHIPTEC_DFLT_AMBIENT, chipTecDfltAmbient), + (PlanCSVcolumns.CHIPTEC_SLOPE, chipTecSlope), + (PlanCSVcolumns.CHIPTEC_MIN_THRESHOLD, chipTecMinThreshold), + (PlanCSVcolumns.MANTEC_DFLT_AMBIENT, manTecDfltAmbient), + (PlanCSVcolumns.MANTEC_SLOPE, manTecSlope), + (PlanCSVcolumns.MANTEC_MIN_THRESHOLD, manTecMinThreshold), + ] + return dynamicTecParams def get_sampleAnnotations(template): annotations = [] @@ -745,6 +808,12 @@ def export_template_keys(custom_args): "custom_args": PlanCSVcolumns.CUSTOM_ARGS, "mixedTypeRNA_reference": PlanCSVcolumns.FUSIONS_REF, "mixedTypeRNA_targetRegionBedFile": PlanCSVcolumns.FUSIONS_TARGET_BED, + "chipTecDfltAmbient": PlanCSVcolumns.CHIPTEC_DFLT_AMBIENT, + "chipTecSlope": PlanCSVcolumns.CHIPTEC_SLOPE, + "chipTecMinThreshold": PlanCSVcolumns.CHIPTEC_MIN_THRESHOLD, + "manTecDfltAmbient": PlanCSVcolumns.MANTEC_DFLT_AMBIENT, + "manTecSlope": PlanCSVcolumns.MANTEC_SLOPE, + "manTecMinThreshold": PlanCSVcolumns.MANTEC_MIN_THRESHOLD, } # QC values keys.update( @@ -809,6 +878,11 @@ def get_template_data_for_export(templateId): (PlanCSVcolumns.COLUMN_HOTSPOT_BED, _get_hotspot_regions_bed_file(template)), ] + # Add dynamic Tec params only if exists in the template + dynamicTecParams = get_dynamicTecParams(template) + if dynamicTecParams: + data.extend(dynamicTecParams) + # add fusions reference for DNA/Fusions application if RunType.is_dna_rna(runType): data.extend( diff --git a/dbReports/iondb/rundb/plan/plan_validator.py b/dbReports/iondb/rundb/plan/plan_validator.py index 416eb6a2..ec33a524 100644 --- a/dbReports/iondb/rundb/plan/plan_validator.py +++ b/dbReports/iondb/rundb/plan/plan_validator.py @@ -616,6 +616,21 @@ def validate_plan_templating_kit_name(value, field_label, isNewPlan=None): return errors, warnings +def get_dynamicTecParams(templateObj, data): + chipTecDfltAmbient = templateObj.experiment.chipTecDfltAmbient + chipTecSlope = templateObj.experiment.chipTecSlope + chipTecMinThreshold = templateObj.experiment.chipTecMinThreshold + manTecDfltAmbient = templateObj.experiment.manTecDfltAmbient + manTecSlope = templateObj.experiment.manTecSlope + manTecMinThreshold = templateObj.experiment.manTecMinThreshold + changed = False + errMsg = None + if {'chipTecDfltAmbient', 'chipTecSlope', 'chipTecMinThreshold', 'manTecDfltAmbient', 'manTecSlope', 'manTecMinThreshold'} <= set(data): + errMsg = "Use System default for Manifold temperatures. Do not provide any inputs.Default template configuration:" \ + "(chipTecDfltAmbient: %.4f, chipTecSlope: %.4f, chipTecMinThreshold: %.4f, manTecDfltAmbient: %.4f, manTecSlope: %.4f, manTecMinThreshold: %.4f)" % \ + (chipTecDfltAmbient, chipTecSlope, chipTecMinThreshold, manTecDfltAmbient, manTecSlope, manTecMinThreshold) + changed = True + return changed, errMsg def validate_runType(runType, field_label): errors = [] diff --git a/dbReports/iondb/rundb/plan/views.py b/dbReports/iondb/rundb/plan/views.py index cceae282..ee83d720 100644 --- a/dbReports/iondb/rundb/plan/views.py +++ b/dbReports/iondb/rundb/plan/views.py @@ -2204,6 +2204,44 @@ def plan_template_export(request, templateId): return response +def parse_tec_params(dtp): + try: + return float(dtp) + except ValueError: + return None + +def get_template_meta(row): + return { + "fromTemplate": row.get("Template name (required)"), + "fromTemplateCategories": row.get("Categories"), + "fromTemplateChipType": row.get("Chip type (required)"), + "fromTemplateSequenceKitname": row.get("Sequence kit name"), + "fromTemplateSource": "ION" + } + +def convert_tec_params_to_float(row): + ct = 'Chip Heater (Do not change)' + cts = 'Chip Slope (Do not change)' + ctmt = 'Chip Min Threshold (Do not change)' + + mt = 'Manifold Heater (Do not change)' + mts = 'Manifold Slope (Do not change)' + mtmt = 'Manifold Min Threshold (Do not change)' + if ct in row or mt in row: + if ct in row: + row[ct] = parse_tec_params(row[ct]) + if cts in row: + row[cts] = parse_tec_params(row[cts]) + if ctmt in row: + row[ctmt] = parse_tec_params(row[ctmt]) + if mt in row: + row[mt] = parse_tec_params(row[mt]) + if mts in row: + row[mts] = parse_tec_params(row[mts]) + if mtmt in row: + row[mtmt] = parse_tec_params(row[mtmt]) + + return row def plan_template_import(request): def _get_kit_name(value, kitTypes): @@ -2265,7 +2303,7 @@ def _get_kit_name(value, kitTypes): # skip blank rows if not any(v.strip() for v in list(row.values())): continue - + row = convert_tec_params_to_float(row) planDict = {} planDict["isNewPlan"] = True # this will trigger validation planDict["isReusable"] = True @@ -2276,7 +2314,10 @@ def _get_kit_name(value, kitTypes): planCsvKeys = export_template_keys(custom_args) for field, csvKey in list(planCsvKeys.items()): if csvKey in row: - value = row[csvKey].strip() if row[csvKey] else "" + if isinstance(row[csvKey], str): + value = row[csvKey].strip() if row[csvKey] else "" + else: + value = row[csvKey] if csvKey == PlanCSVcolumns.TEMPLATE_NAME: planDict["planName"] = value.replace(" ", "_") elif csvKey == PlanCSVcolumns.RUNTYPE: @@ -2353,6 +2394,7 @@ def _get_kit_name(value, kitTypes): value = value.split(";") elif csvKey == PlanCSVcolumns.COLUMN_LIMS_DATA: value = {"LIMS": [value]} + value.update(get_template_meta(row)) elif csvKey == PlanCSVcolumns.CUSTOM_ARGS: value = custom_args diff --git a/dbReports/iondb/rundb/report/views.py b/dbReports/iondb/rundb/report/views.py index b8c55128..cf40c335 100644 --- a/dbReports/iondb/rundb/report/views.py +++ b/dbReports/iondb/rundb/report/views.py @@ -27,6 +27,7 @@ HttpResponseRedirect, HttpResponse, HttpResponseServerError, + StreamingHttpResponse, ) from django.shortcuts import get_object_or_404, render_to_response from django.template import RequestContext @@ -2347,6 +2348,15 @@ def plain_text(request, full_path): return HttpResponse(FileWrapper(open(full_path, "rb")), mimetype="text/plain") +def download_file(request, full_path): + response = StreamingHttpResponse(open(full_path, "rb")) + response["Content-Type"] = "application/octet-stream" + response["Content-Disposition"] = 'attachment; filename="%s"' % os.path.basename( + full_path + ) + return response + + # These handlers are in strict priority order, i.e. as soon as one matches # the search for a match halts. More specific patterns must preceed more # general patterns that might incorrectly match them. @@ -2361,12 +2371,12 @@ def plain_text(request, full_path): (r"basecaller_results/.*\.txt$", show_whitespace_csv), (r"sigproc_results/.*\.txt$", show_whitespace_csv), (r"\.dat$", show_whitespace_csv), - (r"\.bin$", show_binary), - (r"\.bam$", show_binary), - (r"\.bai$", show_binary), - (r"\.h5$", show_binary), + (r"\.bin$", download_file), + (r"\.bam$", download_file), + (r"\.bai$", download_file), + (r"\.h5$", download_file), (r"\.sff$", show_binary), - (r"\.wells$", show_binary), + (r"\.wells$", download_file), (r"\.stats$", show_config), (r"\.summary$", show_config), (r"\.png$", show_png_image), diff --git a/dbReports/iondb/settings.py b/dbReports/iondb/settings.py index 9fca1b90..67012c4d 100644 --- a/dbReports/iondb/settings.py +++ b/dbReports/iondb/settings.py @@ -370,8 +370,8 @@ EULA_TEXT_URL = "products/" -PLAN_CSV_VERSION = "2.2" -SUPPORTED_PLAN_CSV_VERSION = ["1.0", "2.0", "2.1", "2.2"] +PLAN_CSV_VERSION = "2.3" +SUPPORTED_PLAN_CSV_VERSION = ["1.0", "2.0", "2.1", "2.2", "2.3"] SAMPLE_CSV_VERSION = "2.0" SUPPORTED_SAMPLE_CSV_VERSION = ["1.0", "2.0"] diff --git a/dbReports/iondb/templates/admin/updateOneTouch.html b/dbReports/iondb/templates/admin/updateOneTouch.html index eb59d3c3..91ca0f23 100644 --- a/dbReports/iondb/templates/admin/updateOneTouch.html +++ b/dbReports/iondb/templates/admin/updateOneTouch.html @@ -58,7 +58,6 @@

The OneTouch devices are being updated , the log messages will be Optional: Download the OneTouch update file manually, to place on a USB Drive diff --git a/dbReports/iondb/templates/rundb/configure/account.html b/dbReports/iondb/templates/rundb/configure/account.html index c76b8560..69059b56 100644 --- a/dbReports/iondb/templates/rundb/configure/account.html +++ b/dbReports/iondb/templates/rundb/configure/account.html @@ -32,6 +32,7 @@ console.log("Approved/Activated user " + userId); btn.parents(".pending-user").remove(); $('#modal_confirm_approve').modal('hide'); + window.location.reload(true); }).fail(function (data) { $('#modal_confirm_approve .modal-body #modal-error-messages').empty().append('

{% trans "global.messages.error.label" %}:

' + data.responseText + '

').show(); }); @@ -60,6 +61,7 @@ console.log("Rejected user " + userId); btn.parents(".pending-user").remove(); $('#modal_confirm_reject').modal('hide'); + window.location.reload(true); }).fail(function (data) { $('#modal_confirm_reject .modal-body #modal-error-messages').empty().append('

{% trans "global.messages.error.label" %}:

' + data.responseText + '

').show(); }); @@ -91,11 +93,8 @@ {% endblock extra_head_js %} - - {% block content %} - -
+

{% trans "configure_account.title" %} {% trans "configure_account.subtitle" %}

{% csrf_token %} @@ -103,7 +102,7 @@

{% trans "configure_account.title" %} {% trans "configure_account. {% for field in form %} {% for error in field.errors %}
- {{ field.label }} - {{ error|escape }} + {{ field.label }} - {{ error|escape|safe }}
{% endfor %} {% endfor %} @@ -113,6 +112,11 @@

{% trans "configure_account.title" %} {% trans "configure_account.

{% endfor %} {% endif %} + {% if updated or form.is_valid %} +
+ User Information updated successfully +
+ {% endif %}
@@ -174,6 +178,7 @@

{% trans "configure_account.title" %} {% trans "configure_account.
{{form.password}} +

diff --git a/dbReports/iondb/templates/rundb/home/fragments/summary.html b/dbReports/iondb/templates/rundb/home/fragments/summary.html index 8b61cff5..cbfb127e 100644 --- a/dbReports/iondb/templates/rundb/home/fragments/summary.html +++ b/dbReports/iondb/templates/rundb/home/fragments/summary.html @@ -8,6 +8,10 @@ {% if summary.showDeprecationMsg %}
  • {{ summary.showDeprecationMsg }}
    • {% endif %} + {% if summary.showPasswordWarningMsg %} +
  • {{ summary.showPasswordWarningMsg|safe }} + here
    • + {% endif %} {% if summary.update_status.lower == "available" or "ready" in summary.update_status.lower %}
  • Update available
    • {% elif "fail" in summary.update_status.lower %} diff --git a/dbReports/iondb/templates/rundb/plan/modal_plannedexperiment_detail.html b/dbReports/iondb/templates/rundb/plan/modal_plannedexperiment_detail.html index 16c52fd6..b6ad55fa 100644 --- a/dbReports/iondb/templates/rundb/plan/modal_plannedexperiment_detail.html +++ b/dbReports/iondb/templates/rundb/plan/modal_plannedexperiment_detail.html @@ -152,6 +152,18 @@

    {% trans "reviewplan.fields.eas.realign.label" %}: {{ eas.realign }} + {% if plan.experiment.chipTecDfltAmbient %} + + Chip Heater: + Dynamic + + {% endif %} + + Manifold Heater: + + {% if plan.experiment.manTecDfltAmbient %} Dynamic {% else %} Default {% endif %} + +

    diff --git a/dbReports/iondb/templates/rundb/plan/page_plan/base.html b/dbReports/iondb/templates/rundb/plan/page_plan/base.html index c21b24c0..0088648f 100644 --- a/dbReports/iondb/templates/rundb/plan/page_plan/base.html +++ b/dbReports/iondb/templates/rundb/plan/page_plan/base.html @@ -56,6 +56,7 @@ {% endblock sub-nav %} {%block extra-main-class%}clearbg{%endblock extra-main-class%} {% block content %} +
    @@ -339,6 +340,19 @@

    {% trans "workflow.step.saveplan.bysample.fields.sampleSets.label" %}: {{hel $("#showSummary").hide(); }); + function check_lock_assay_params() { + var lockAssayParams = $('input[name = "lockAssayParams"]').val().split(","); + if(lockAssayParams) { + $.each(lockAssayParams, function (i, val) { + if ($("#" + val).is("select")) { + $("select[id=" + val + "]").prop('disabled', false); + } else if ($("#" + val).is("input")) { + $("input[id=" + val + "]").prop('disabled', false); + } + }); + } + } + $(".submitStepForm").click(function(){ var url = $(this).attr('href'); var $form = $('#step_form').attr('action', url); @@ -346,7 +360,7 @@

    {% trans "workflow.step.saveplan.bysample.fields.sampleSets.label" %}: {{hel .attr("name","plan_session_key") .val("{{plan_session_key}}") .appendTo($form); - + check_lock_assay_params(); $form.submit(); return false; }); diff --git a/dbReports/iondb/templates/rundb/plan/page_plan/page_plan_application.html b/dbReports/iondb/templates/rundb/plan/page_plan/page_plan_application.html index f784042b..2f0c5b2a 100644 --- a/dbReports/iondb/templates/rundb/plan/page_plan/page_plan_application.html +++ b/dbReports/iondb/templates/rundb/plan/page_plan/page_plan_application.html @@ -4,6 +4,8 @@ {% block main-title %}{% trans "workflow.step.application.subtitle" %}{% endblock main-title %} {% block page-plan-content %} +{% with lockAssayParams=helper.getStepDict.Kits.savedObjects.meta.lockAssayParams %} +

    {% trans "workflow.step.application.fields.applicationGroup.label" %}

    @@ -12,12 +14,12 @@

    {% trans "workflow.step.application.fields.applicationGroup.label" %}

    {% for application in step.prepopulatedFields.applicationGroups %} {% if application.name == step.savedFields.applicationGroupName %} {% else %} {% endif %} @@ -73,7 +75,8 @@

    Template Preparation Instrument

    {% for key, value in step.validationErrors.items %}

    {{value}}

    {% endfor %} -
    +
    +{% endwith %} {% endblock page-plan-content %} {% block summary-table %} @@ -87,6 +90,11 @@

    {{value}}

    updateRuntypeFromApplication = function(applicationId, selectedRuntypeId) { var runTypeIds = applicationToRuntype[applicationId]; $('.runTypeOptionsContent').empty(); + var lockAssayParams = $('input[name = "lockAssayParams"]').val(); + if (lockAssayParams){ + lockAssayParams = $('input[name = "lockAssayParams"]').val().split(","); + } + $.each(runTypeIds, function(indexInArray, valueOfElement){ var inputHolder = $('