From a83f99f27075a2e7368634e7e13d84ab8b9e3e8a Mon Sep 17 00:00:00 2001 From: daniel Date: Wed, 27 Jan 2021 11:25:56 +0200 Subject: [PATCH] updates --- bin/add_ambiguous_counts.py | 2 +- bin/add_custom_gene.py | 2 +- bin/add_gap_gene.py | 2 +- bin/analyze_exon-exon_mappings.py | 2 +- bin/analyze_splits_sam.py | 2 +- bin/analyze_star_chimeric.py | 2 +- bin/biopython_version.py | 2 +- bin/blat-filter-fusion.py | 2 +- bin/blat_parallel.py | 2 +- bin/bootstrap.py | 2 +- bin/build_ig.py | 2 +- bin/build_report_fusions_map.py | 2 +- bin/build_report_fusions_psl.py | 2 +- bin/build_report_fusions_psl2.py | 2 +- bin/build_summary.py | 2 +- bin/clean_bed.py | 2 +- bin/clip_quality.py | 2 +- bin/compress-reads-ids.py | 2 +- bin/concatenate.py | 2 +- bin/configuration.py | 2 +- bin/convert_pairs_symbols.py | 2 +- bin/droppe.py | 4 ++-- bin/enlarge_genes.py | 2 +- bin/extract_fusion_genes.py | 2 +- bin/extract_reads_ids.py | 2 +- bin/extract_short_reads.py | 2 +- bin/extract_transcripts.py | 2 +- bin/fasta2reads.py | 2 +- bin/fastq2fasta.py | 2 +- bin/fastq_b2n.py | 2 +- bin/fc2vcf.py | 2 +- bin/filter-wiggle.py | 4 ++-- bin/filter_fusion_sequences.py | 4 ++-- bin/filter_map_pre-splitting.py | 4 ++-- bin/filter_pairs.py | 4 ++-- bin/filter_splits.py | 4 ++-- bin/find_fusion_genes_map.py | 2 +- bin/find_fusion_genes_psl.py | 2 +- bin/find_fusion_genes_psl2.py | 2 +- bin/find_homolog_genes.py | 2 +- bin/fix.py | 4 ++-- bin/fragment_fastq.py | 4 ++-- bin/fragments_fusion_genes.py | 2 +- bin/fusioncatcher-batch.py | 4 ++-- bin/fusioncatcher-build.py | 4 ++-- bin/fusioncatcher.py | 4 ++-- bin/generate_1000genomes.py | 2 +- bin/generate_18cancers.py | 2 +- bin/generate_adjacent_genes.py | 2 +- bin/generate_banned.py | 2 +- bin/generate_banned_seq.py | 2 +- bin/generate_bodymap2.py | 2 +- bin/generate_ccle3.py | 2 +- bin/generate_chrom_lens.py | 2 +- bin/generate_cortex.py | 2 +- bin/generate_enlarge.py | 2 +- bin/generate_exon-exon_junctions.py | 2 +- bin/generate_exons.py | 2 +- bin/generate_gene-gene_junctions.py | 2 +- bin/generate_genes.py | 2 +- bin/generate_genes_symbols.py | 2 +- bin/generate_genes_with_no_proteins.py | 2 +- bin/generate_gliomas.py | 2 +- bin/generate_healthy.py | 2 +- bin/generate_hpa.py | 2 +- bin/generate_known.py | 2 +- bin/generate_labels_descriptions.py | 2 +- bin/generate_metastasis.py | 2 +- bin/generate_nontumor.py | 2 +- bin/generate_oesophagus.py | 2 +- bin/generate_overlapping_genes.py | 2 +- bin/generate_pairs_pseudogenes.py | 2 +- bin/generate_rrna_unit.py | 2 +- bin/generate_tcga.py | 2 +- bin/generate_tcga3.py | 2 +- bin/generate_transcripts.py | 2 +- bin/generate_tumor-genes.py | 2 +- bin/get_biotypes.py | 2 +- bin/get_cacg.py | 2 +- bin/get_cancer-genes.py | 2 +- bin/get_ccle.py | 2 +- bin/get_ccle2.py | 2 +- bin/get_cgp.py | 2 +- bin/get_chimerdb2.py | 2 +- bin/get_chimerdb3.py | 2 +- bin/get_chimerdb4.py | 2 +- bin/get_civic.py | 2 +- bin/get_conjoing.py | 2 +- bin/get_cosmic.py | 2 +- bin/get_dgd.py | 2 +- bin/get_exons_positions.py | 2 +- bin/get_gencode.py | 2 +- bin/get_genes_descriptions.py | 2 +- bin/get_genome.py | 2 +- bin/get_gtex.py | 2 +- bin/get_gtf.py | 2 +- bin/get_hla.py | 2 +- bin/get_hla2.py | 2 +- bin/get_mitelman.py | 2 +- bin/get_mtrna.py | 2 +- bin/get_noncancer.py | 2 +- bin/get_oncogenes.py | 2 +- bin/get_oncokb.py | 2 +- bin/get_pancreases.py | 2 +- bin/get_paralogs.py | 2 +- bin/get_pcawg.py | 2 +- bin/get_phix174.py | 2 +- bin/get_prostate_cancer.py | 2 +- bin/get_refseq.py | 2 +- bin/get_refseq_ensembl.py | 2 +- bin/get_rrna.py | 2 +- bin/get_rtcircrna.py | 2 +- bin/get_synonyms.py | 2 +- bin/get_tcga.py | 2 +- bin/get_tcga2.py | 2 +- bin/get_ticdb.py | 2 +- bin/get_trna.py | 2 +- bin/get_ucsc.py | 2 +- bin/get_viruses.py | 2 +- bin/inspect_fusion_sequences.py | 4 ++-- bin/join_homolog_genes.py | 2 +- bin/label_ambiguous_fusion_genes.py | 2 +- bin/label_exonexon.py | 4 ++-- bin/label_found_fusions.py | 2 +- bin/label_fusion_genes.py | 2 +- bin/label_fusion_genes_trim2.py | 2 +- bin/label_multi.py | 2 +- bin/label_rtcircrna.py | 4 ++-- bin/lengths_reads.py | 2 +- bin/liftover.py | 2 +- bin/merge-reads.py | 2 +- bin/merge-sam.py | 2 +- bin/merge_reports.py | 2 +- bin/overlap.py | 2 +- bin/padding-fastq.py | 2 +- bin/pair8removal.py | 4 ++-- bin/phred.py | 2 +- bin/predict_frame.py | 4 ++-- bin/prep-1by1.py | 2 +- bin/psl_best_unique_contigs.py | 2 +- bin/python_version.py | 2 +- bin/reads_from_map.py | 2 +- bin/remove-adapter.py | 4 ++-- bin/remove-bad-illumina.py | 2 +- bin/remove_custom_feature.py | 2 +- bin/remove_reads_exon_exon_fastq.py | 2 +- bin/remove_reads_exon_exon_map.py | 2 +- bin/remove_reads_exon_exon_psl.py | 2 +- bin/remove_reads_genome_transcriptome.py | 2 +- bin/remove_shorter_reads.py | 2 +- bin/remove_str.py | 2 +- bin/sam2psl.py | 2 +- bin/shebang.py | 4 ++-- bin/shield_genes.py | 2 +- bin/shuffle.py | 2 +- bin/sliding-read.py | 2 +- bin/smoothing_fusions_psl.py | 2 +- bin/solexa18to15.py | 2 +- bin/sort_ttdb.py | 2 +- bin/split-fasta.py | 2 +- bin/split-reads.py | 2 +- bin/sra2illumina.py | 2 +- bin/symbols.py | 2 +- bin/trim_poly_tails.py | 2 +- bin/trim_reads.py | 2 +- bin/unshuffle.py | 2 +- bin/update-config.py | 2 +- bin/workflow.py | 4 ++-- 168 files changed, 187 insertions(+), 187 deletions(-) diff --git a/bin/add_ambiguous_counts.py b/bin/add_ambiguous_counts.py index 9f66208..e599218 100755 --- a/bin/add_ambiguous_counts.py +++ b/bin/add_ambiguous_counts.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/add_custom_gene.py b/bin/add_custom_gene.py index 6f09642..e89171b 100755 --- a/bin/add_custom_gene.py +++ b/bin/add_custom_gene.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/add_gap_gene.py b/bin/add_gap_gene.py index c07c1bb..f3aeb0d 100755 --- a/bin/add_gap_gene.py +++ b/bin/add_gap_gene.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/analyze_exon-exon_mappings.py b/bin/analyze_exon-exon_mappings.py index 8403ac3..4860702 100755 --- a/bin/analyze_exon-exon_mappings.py +++ b/bin/analyze_exon-exon_mappings.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/analyze_splits_sam.py b/bin/analyze_splits_sam.py index 24d8d99..e478178 100755 --- a/bin/analyze_splits_sam.py +++ b/bin/analyze_splits_sam.py @@ -10,7 +10,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/analyze_star_chimeric.py b/bin/analyze_star_chimeric.py index c08c45c..0318b2c 100755 --- a/bin/analyze_star_chimeric.py +++ b/bin/analyze_star_chimeric.py @@ -10,7 +10,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/biopython_version.py b/bin/biopython_version.py index ed58aef..906cbcb 100755 --- a/bin/biopython_version.py +++ b/bin/biopython_version.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/blat-filter-fusion.py b/bin/blat-filter-fusion.py index 2ebb377..631faee 100755 --- a/bin/blat-filter-fusion.py +++ b/bin/blat-filter-fusion.py @@ -9,7 +9,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/blat_parallel.py b/bin/blat_parallel.py index 528f6ca..5bc429e 100755 --- a/bin/blat_parallel.py +++ b/bin/blat_parallel.py @@ -14,7 +14,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/bootstrap.py b/bin/bootstrap.py index a705f75..426f1f5 100755 --- a/bin/bootstrap.py +++ b/bin/bootstrap.py @@ -10,7 +10,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/build_ig.py b/bin/build_ig.py index 6994edc..f1f33ca 100755 --- a/bin/build_ig.py +++ b/bin/build_ig.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/build_report_fusions_map.py b/bin/build_report_fusions_map.py index 0c2a2d0..1713dce 100755 --- a/bin/build_report_fusions_map.py +++ b/bin/build_report_fusions_map.py @@ -9,7 +9,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/build_report_fusions_psl.py b/bin/build_report_fusions_psl.py index 3de469d..957e530 100755 --- a/bin/build_report_fusions_psl.py +++ b/bin/build_report_fusions_psl.py @@ -9,7 +9,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/build_report_fusions_psl2.py b/bin/build_report_fusions_psl2.py index 0a4fc8a..8064d78 100755 --- a/bin/build_report_fusions_psl2.py +++ b/bin/build_report_fusions_psl2.py @@ -9,7 +9,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/build_summary.py b/bin/build_summary.py index 4d815c6..9717755 100755 --- a/bin/build_summary.py +++ b/bin/build_summary.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/clean_bed.py b/bin/clean_bed.py index 93d5b86..29ecbb0 100755 --- a/bin/clean_bed.py +++ b/bin/clean_bed.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/clip_quality.py b/bin/clip_quality.py index 4443e3e..d9a5a30 100755 --- a/bin/clip_quality.py +++ b/bin/clip_quality.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/compress-reads-ids.py b/bin/compress-reads-ids.py index d40b6f5..9eb0a0c 100755 --- a/bin/compress-reads-ids.py +++ b/bin/compress-reads-ids.py @@ -8,7 +8,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/concatenate.py b/bin/concatenate.py index 12896fc..f4e7a9a 100755 --- a/bin/concatenate.py +++ b/bin/concatenate.py @@ -9,7 +9,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/configuration.py b/bin/configuration.py index 5001978..255135a 100755 --- a/bin/configuration.py +++ b/bin/configuration.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/convert_pairs_symbols.py b/bin/convert_pairs_symbols.py index fce30de..6925876 100755 --- a/bin/convert_pairs_symbols.py +++ b/bin/convert_pairs_symbols.py @@ -8,7 +8,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/droppe.py b/bin/droppe.py index e525f92..f4acd5d 100755 --- a/bin/droppe.py +++ b/bin/droppe.py @@ -6,7 +6,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. @@ -75,7 +75,7 @@ def format_epilog(self, formatter): Author: Daniel Nicorici Email: Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici """ diff --git a/bin/enlarge_genes.py b/bin/enlarge_genes.py index 4c760a8..00a66a4 100755 --- a/bin/enlarge_genes.py +++ b/bin/enlarge_genes.py @@ -6,7 +6,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/extract_fusion_genes.py b/bin/extract_fusion_genes.py index dd60573..9199bf1 100755 --- a/bin/extract_fusion_genes.py +++ b/bin/extract_fusion_genes.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/extract_reads_ids.py b/bin/extract_reads_ids.py index 645ce39..f15a599 100755 --- a/bin/extract_reads_ids.py +++ b/bin/extract_reads_ids.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/extract_short_reads.py b/bin/extract_short_reads.py index 6ec2234..bccfc81 100755 --- a/bin/extract_short_reads.py +++ b/bin/extract_short_reads.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/extract_transcripts.py b/bin/extract_transcripts.py index 414d27b..856105e 100755 --- a/bin/extract_transcripts.py +++ b/bin/extract_transcripts.py @@ -8,7 +8,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/fasta2reads.py b/bin/fasta2reads.py index 8695a24..07b9264 100755 --- a/bin/fasta2reads.py +++ b/bin/fasta2reads.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/fastq2fasta.py b/bin/fastq2fasta.py index 13ac7b9..8366a32 100755 --- a/bin/fastq2fasta.py +++ b/bin/fastq2fasta.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/fastq_b2n.py b/bin/fastq_b2n.py index 5df22e9..b66cd79 100755 --- a/bin/fastq_b2n.py +++ b/bin/fastq_b2n.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/fc2vcf.py b/bin/fc2vcf.py index 4956a6b..bfd64ff 100755 --- a/bin/fc2vcf.py +++ b/bin/fc2vcf.py @@ -6,7 +6,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/filter-wiggle.py b/bin/filter-wiggle.py index 2611491..8734beb 100755 --- a/bin/filter-wiggle.py +++ b/bin/filter-wiggle.py @@ -5,7 +5,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. @@ -69,7 +69,7 @@ def format_epilog(self, formatter): Author: Daniel Nicorici Email: Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici """ diff --git a/bin/filter_fusion_sequences.py b/bin/filter_fusion_sequences.py index d5ab6c5..99d1ade 100755 --- a/bin/filter_fusion_sequences.py +++ b/bin/filter_fusion_sequences.py @@ -5,7 +5,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. @@ -73,7 +73,7 @@ def format_epilog(self, formatter): Author: Daniel Nicorici Email: Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici """ diff --git a/bin/filter_map_pre-splitting.py b/bin/filter_map_pre-splitting.py index 00502df..438f46b 100755 --- a/bin/filter_map_pre-splitting.py +++ b/bin/filter_map_pre-splitting.py @@ -5,7 +5,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. @@ -84,7 +84,7 @@ def format_epilog(self, formatter): Author: Daniel Nicorici Email: Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici """ diff --git a/bin/filter_pairs.py b/bin/filter_pairs.py index 6658cd4..234390a 100755 --- a/bin/filter_pairs.py +++ b/bin/filter_pairs.py @@ -5,7 +5,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. @@ -96,7 +96,7 @@ def format_epilog(self, formatter): Author: Daniel Nicorici Email: Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici """ diff --git a/bin/filter_splits.py b/bin/filter_splits.py index 7ef7a59..fe1ddf6 100755 --- a/bin/filter_splits.py +++ b/bin/filter_splits.py @@ -5,7 +5,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. @@ -75,7 +75,7 @@ def format_epilog(self, formatter): Author: Daniel Nicorici Email: Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici """ diff --git a/bin/find_fusion_genes_map.py b/bin/find_fusion_genes_map.py index a91dba9..5a8fd7d 100755 --- a/bin/find_fusion_genes_map.py +++ b/bin/find_fusion_genes_map.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/find_fusion_genes_psl.py b/bin/find_fusion_genes_psl.py index c65c9da..ac5f6a7 100755 --- a/bin/find_fusion_genes_psl.py +++ b/bin/find_fusion_genes_psl.py @@ -9,7 +9,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/find_fusion_genes_psl2.py b/bin/find_fusion_genes_psl2.py index b92a48b..8672233 100755 --- a/bin/find_fusion_genes_psl2.py +++ b/bin/find_fusion_genes_psl2.py @@ -9,7 +9,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/find_homolog_genes.py b/bin/find_homolog_genes.py index bb2e03c..18ead05 100755 --- a/bin/find_homolog_genes.py +++ b/bin/find_homolog_genes.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/fix.py b/bin/fix.py index 4b80f7f..b018342 100755 --- a/bin/fix.py +++ b/bin/fix.py @@ -5,7 +5,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. @@ -74,7 +74,7 @@ def format_epilog(self, formatter): Author: Daniel Nicorici Email: Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici """ diff --git a/bin/fragment_fastq.py b/bin/fragment_fastq.py index e527713..c80cf91 100755 --- a/bin/fragment_fastq.py +++ b/bin/fragment_fastq.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. @@ -397,7 +397,7 @@ def format_epilog(self, formatter): Author: Daniel Nicorici Email: Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici """ diff --git a/bin/fragments_fusion_genes.py b/bin/fragments_fusion_genes.py index 2c8fd23..c34d9ea 100755 --- a/bin/fragments_fusion_genes.py +++ b/bin/fragments_fusion_genes.py @@ -6,7 +6,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/fusioncatcher-batch.py b/bin/fusioncatcher-batch.py index 2cb5528..bf6a691 100755 --- a/bin/fusioncatcher-batch.py +++ b/bin/fusioncatcher-batch.py @@ -23,7 +23,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. @@ -329,7 +329,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici It is a wrapper for 'fusioncatcher.py' which allows to run 'fusioncatcher.py' in batch mode where the input is a directory which contains the directories for diff --git a/bin/fusioncatcher-build.py b/bin/fusioncatcher-build.py index 28d5dcb..062d667 100755 --- a/bin/fusioncatcher-build.py +++ b/bin/fusioncatcher-build.py @@ -9,7 +9,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. @@ -126,7 +126,7 @@ def format_epilog(self, formatter): epilog = ("\n" + "Author: Daniel Nicorici \n" + "Email: Daniel.Nicorici@gmail.com \n" + - "Copyright (c) 2009-2020 Daniel Nicorici \n " + + "Copyright (c) 2009-2021 Daniel Nicorici \n " + "\n") description = ("FusionCatcher-build downloads data from Ensembl database and "+ diff --git a/bin/fusioncatcher.py b/bin/fusioncatcher.py index 3eb819a..2440e97 100755 --- a/bin/fusioncatcher.py +++ b/bin/fusioncatcher.py @@ -11,7 +11,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. @@ -241,7 +241,7 @@ def is_known_extension(something): epilog = ("\n" + "Author: Daniel Nicorici \n" + "Email: Daniel.Nicorici@gmail.com \n" + - "Copyright (c) 2009-2020, Daniel Nicorici \n " + + "Copyright (c) 2009-2021, Daniel Nicorici \n " + "\n") description = ("FusionCatcher searches for novel and known somatic gene fusions in RNA-seq \n"+ diff --git a/bin/generate_1000genomes.py b/bin/generate_1000genomes.py index fa543d0..662d63c 100755 --- a/bin/generate_1000genomes.py +++ b/bin/generate_1000genomes.py @@ -13,7 +13,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/generate_18cancers.py b/bin/generate_18cancers.py index 1f6ed2a..55b2da9 100755 --- a/bin/generate_18cancers.py +++ b/bin/generate_18cancers.py @@ -13,7 +13,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/generate_adjacent_genes.py b/bin/generate_adjacent_genes.py index 432268a..168df1c 100755 --- a/bin/generate_adjacent_genes.py +++ b/bin/generate_adjacent_genes.py @@ -10,7 +10,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/generate_banned.py b/bin/generate_banned.py index a43903e..982136d 100755 --- a/bin/generate_banned.py +++ b/bin/generate_banned.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/generate_banned_seq.py b/bin/generate_banned_seq.py index 82dd8d3..07fd64e 100755 --- a/bin/generate_banned_seq.py +++ b/bin/generate_banned_seq.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/generate_bodymap2.py b/bin/generate_bodymap2.py index b36d4ce..c085f3c 100755 --- a/bin/generate_bodymap2.py +++ b/bin/generate_bodymap2.py @@ -9,7 +9,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/generate_ccle3.py b/bin/generate_ccle3.py index cafb844..3aa4e54 100755 --- a/bin/generate_ccle3.py +++ b/bin/generate_ccle3.py @@ -14,7 +14,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/generate_chrom_lens.py b/bin/generate_chrom_lens.py index e4fd930..0976e25 100755 --- a/bin/generate_chrom_lens.py +++ b/bin/generate_chrom_lens.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/generate_cortex.py b/bin/generate_cortex.py index c8ef0fe..5203cd7 100755 --- a/bin/generate_cortex.py +++ b/bin/generate_cortex.py @@ -9,7 +9,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/generate_enlarge.py b/bin/generate_enlarge.py index f868924..60bc0e7 100755 --- a/bin/generate_enlarge.py +++ b/bin/generate_enlarge.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/generate_exon-exon_junctions.py b/bin/generate_exon-exon_junctions.py index 03c768d..d3a3ea0 100755 --- a/bin/generate_exon-exon_junctions.py +++ b/bin/generate_exon-exon_junctions.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/generate_exons.py b/bin/generate_exons.py index c485551..cc4167a 100755 --- a/bin/generate_exons.py +++ b/bin/generate_exons.py @@ -8,7 +8,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/generate_gene-gene_junctions.py b/bin/generate_gene-gene_junctions.py index e800c6c..1b5659f 100755 --- a/bin/generate_gene-gene_junctions.py +++ b/bin/generate_gene-gene_junctions.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/generate_genes.py b/bin/generate_genes.py index 2a3c253..39e938f 100755 --- a/bin/generate_genes.py +++ b/bin/generate_genes.py @@ -8,7 +8,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/generate_genes_symbols.py b/bin/generate_genes_symbols.py index 0b4adf6..7fc4dda 100755 --- a/bin/generate_genes_symbols.py +++ b/bin/generate_genes_symbols.py @@ -8,7 +8,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/generate_genes_with_no_proteins.py b/bin/generate_genes_with_no_proteins.py index cbf0031..2d7cdde 100755 --- a/bin/generate_genes_with_no_proteins.py +++ b/bin/generate_genes_with_no_proteins.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/generate_gliomas.py b/bin/generate_gliomas.py index 54469d9..9fb45b9 100755 --- a/bin/generate_gliomas.py +++ b/bin/generate_gliomas.py @@ -14,7 +14,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/generate_healthy.py b/bin/generate_healthy.py index 2410ce7..b720e2a 100755 --- a/bin/generate_healthy.py +++ b/bin/generate_healthy.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/generate_hpa.py b/bin/generate_hpa.py index f379b24..e06c601 100755 --- a/bin/generate_hpa.py +++ b/bin/generate_hpa.py @@ -10,7 +10,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/generate_known.py b/bin/generate_known.py index f650275..c304746 100755 --- a/bin/generate_known.py +++ b/bin/generate_known.py @@ -8,7 +8,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/generate_labels_descriptions.py b/bin/generate_labels_descriptions.py index 1565469..e224242 100755 --- a/bin/generate_labels_descriptions.py +++ b/bin/generate_labels_descriptions.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/generate_metastasis.py b/bin/generate_metastasis.py index 9522850..a748322 100755 --- a/bin/generate_metastasis.py +++ b/bin/generate_metastasis.py @@ -13,7 +13,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/generate_nontumor.py b/bin/generate_nontumor.py index da28caa..5aed796 100755 --- a/bin/generate_nontumor.py +++ b/bin/generate_nontumor.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/generate_oesophagus.py b/bin/generate_oesophagus.py index f802dcb..acda36f 100755 --- a/bin/generate_oesophagus.py +++ b/bin/generate_oesophagus.py @@ -12,7 +12,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/generate_overlapping_genes.py b/bin/generate_overlapping_genes.py index 3b17a30..6d78d3f 100755 --- a/bin/generate_overlapping_genes.py +++ b/bin/generate_overlapping_genes.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/generate_pairs_pseudogenes.py b/bin/generate_pairs_pseudogenes.py index 873167a..be56335 100755 --- a/bin/generate_pairs_pseudogenes.py +++ b/bin/generate_pairs_pseudogenes.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/generate_rrna_unit.py b/bin/generate_rrna_unit.py index 0014338..01f6f1e 100755 --- a/bin/generate_rrna_unit.py +++ b/bin/generate_rrna_unit.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/generate_tcga.py b/bin/generate_tcga.py index a792cc5..e3fceb5 100755 --- a/bin/generate_tcga.py +++ b/bin/generate_tcga.py @@ -8,7 +8,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/generate_tcga3.py b/bin/generate_tcga3.py index 592376b..c79abdd 100755 --- a/bin/generate_tcga3.py +++ b/bin/generate_tcga3.py @@ -14,7 +14,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/generate_transcripts.py b/bin/generate_transcripts.py index 82937fa..692b06e 100755 --- a/bin/generate_transcripts.py +++ b/bin/generate_transcripts.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/generate_tumor-genes.py b/bin/generate_tumor-genes.py index de6177d..3e9f02f 100755 --- a/bin/generate_tumor-genes.py +++ b/bin/generate_tumor-genes.py @@ -8,7 +8,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/get_biotypes.py b/bin/get_biotypes.py index dfb978a..31c1870 100755 --- a/bin/get_biotypes.py +++ b/bin/get_biotypes.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/get_cacg.py b/bin/get_cacg.py index 9ca3157..363dd3c 100755 --- a/bin/get_cacg.py +++ b/bin/get_cacg.py @@ -8,7 +8,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/get_cancer-genes.py b/bin/get_cancer-genes.py index 7f2d4a5..53daadf 100755 --- a/bin/get_cancer-genes.py +++ b/bin/get_cancer-genes.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/get_ccle.py b/bin/get_ccle.py index 018709a..f2e10c4 100755 --- a/bin/get_ccle.py +++ b/bin/get_ccle.py @@ -8,7 +8,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/get_ccle2.py b/bin/get_ccle2.py index 77e2a04..4dd5a80 100755 --- a/bin/get_ccle2.py +++ b/bin/get_ccle2.py @@ -9,7 +9,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/get_cgp.py b/bin/get_cgp.py index 1177c39..d3b0758 100755 --- a/bin/get_cgp.py +++ b/bin/get_cgp.py @@ -8,7 +8,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/get_chimerdb2.py b/bin/get_chimerdb2.py index 82d3b82..20ac1bc 100755 --- a/bin/get_chimerdb2.py +++ b/bin/get_chimerdb2.py @@ -11,7 +11,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/get_chimerdb3.py b/bin/get_chimerdb3.py index 863db17..6bd96b4 100755 --- a/bin/get_chimerdb3.py +++ b/bin/get_chimerdb3.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/get_chimerdb4.py b/bin/get_chimerdb4.py index a9b8d31..565bffb 100755 --- a/bin/get_chimerdb4.py +++ b/bin/get_chimerdb4.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/get_civic.py b/bin/get_civic.py index cb8f52a..9a1d8c5 100755 --- a/bin/get_civic.py +++ b/bin/get_civic.py @@ -8,7 +8,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/get_conjoing.py b/bin/get_conjoing.py index 94de0bf..864cfa7 100755 --- a/bin/get_conjoing.py +++ b/bin/get_conjoing.py @@ -10,7 +10,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/get_cosmic.py b/bin/get_cosmic.py index c2b2559..c12400d 100755 --- a/bin/get_cosmic.py +++ b/bin/get_cosmic.py @@ -9,7 +9,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/get_dgd.py b/bin/get_dgd.py index b200e79..56114f0 100755 --- a/bin/get_dgd.py +++ b/bin/get_dgd.py @@ -8,7 +8,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/get_exons_positions.py b/bin/get_exons_positions.py index 3cbc8af..f11f201 100755 --- a/bin/get_exons_positions.py +++ b/bin/get_exons_positions.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/get_gencode.py b/bin/get_gencode.py index cf31f53..f841e42 100755 --- a/bin/get_gencode.py +++ b/bin/get_gencode.py @@ -8,7 +8,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/get_genes_descriptions.py b/bin/get_genes_descriptions.py index 14720db..6b1a6d9 100755 --- a/bin/get_genes_descriptions.py +++ b/bin/get_genes_descriptions.py @@ -8,7 +8,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/get_genome.py b/bin/get_genome.py index 8a58ba2..d06d0c4 100755 --- a/bin/get_genome.py +++ b/bin/get_genome.py @@ -8,7 +8,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/get_gtex.py b/bin/get_gtex.py index 1c6be81..38c2812 100755 --- a/bin/get_gtex.py +++ b/bin/get_gtex.py @@ -9,7 +9,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/get_gtf.py b/bin/get_gtf.py index f10acf8..a3a8268 100755 --- a/bin/get_gtf.py +++ b/bin/get_gtf.py @@ -6,7 +6,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/get_hla.py b/bin/get_hla.py index 175fe30..fc0aed4 100755 --- a/bin/get_hla.py +++ b/bin/get_hla.py @@ -13,7 +13,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/get_hla2.py b/bin/get_hla2.py index a0c36d5..8af4e8a 100755 --- a/bin/get_hla2.py +++ b/bin/get_hla2.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/get_mitelman.py b/bin/get_mitelman.py index 589eb77..1c7749b 100755 --- a/bin/get_mitelman.py +++ b/bin/get_mitelman.py @@ -8,7 +8,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/get_mtrna.py b/bin/get_mtrna.py index 731c69a..ff6a323 100755 --- a/bin/get_mtrna.py +++ b/bin/get_mtrna.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/get_noncancer.py b/bin/get_noncancer.py index 114b3fd..265af4b 100755 --- a/bin/get_noncancer.py +++ b/bin/get_noncancer.py @@ -9,7 +9,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/get_oncogenes.py b/bin/get_oncogenes.py index 082f898..e9b05d5 100755 --- a/bin/get_oncogenes.py +++ b/bin/get_oncogenes.py @@ -11,7 +11,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/get_oncokb.py b/bin/get_oncokb.py index 7139fd2..64b1e77 100755 --- a/bin/get_oncokb.py +++ b/bin/get_oncokb.py @@ -8,7 +8,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/get_pancreases.py b/bin/get_pancreases.py index 17cc848..35d6195 100755 --- a/bin/get_pancreases.py +++ b/bin/get_pancreases.py @@ -9,7 +9,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/get_paralogs.py b/bin/get_paralogs.py index db8223f..9f1b4f7 100755 --- a/bin/get_paralogs.py +++ b/bin/get_paralogs.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/get_pcawg.py b/bin/get_pcawg.py index 60735ca..049d968 100755 --- a/bin/get_pcawg.py +++ b/bin/get_pcawg.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/get_phix174.py b/bin/get_phix174.py index e4bc20e..ee81ac5 100755 --- a/bin/get_phix174.py +++ b/bin/get_phix174.py @@ -8,7 +8,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/get_prostate_cancer.py b/bin/get_prostate_cancer.py index 1c1afce..b4ffcb6 100755 --- a/bin/get_prostate_cancer.py +++ b/bin/get_prostate_cancer.py @@ -9,7 +9,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/get_refseq.py b/bin/get_refseq.py index 749cfd9..44817a3 100755 --- a/bin/get_refseq.py +++ b/bin/get_refseq.py @@ -8,7 +8,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/get_refseq_ensembl.py b/bin/get_refseq_ensembl.py index 6906fff..25c3e01 100755 --- a/bin/get_refseq_ensembl.py +++ b/bin/get_refseq_ensembl.py @@ -8,7 +8,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/get_rrna.py b/bin/get_rrna.py index a25f6fd..43e2dde 100755 --- a/bin/get_rrna.py +++ b/bin/get_rrna.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/get_rtcircrna.py b/bin/get_rtcircrna.py index 6ca04dc..227d3d4 100755 --- a/bin/get_rtcircrna.py +++ b/bin/get_rtcircrna.py @@ -9,7 +9,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/get_synonyms.py b/bin/get_synonyms.py index ff6d617..adc339f 100755 --- a/bin/get_synonyms.py +++ b/bin/get_synonyms.py @@ -8,7 +8,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/get_tcga.py b/bin/get_tcga.py index 8c7103d..1439d93 100755 --- a/bin/get_tcga.py +++ b/bin/get_tcga.py @@ -9,7 +9,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/get_tcga2.py b/bin/get_tcga2.py index bcc0913..cf38597 100755 --- a/bin/get_tcga2.py +++ b/bin/get_tcga2.py @@ -9,7 +9,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/get_ticdb.py b/bin/get_ticdb.py index 58526a9..e67c32f 100755 --- a/bin/get_ticdb.py +++ b/bin/get_ticdb.py @@ -9,7 +9,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/get_trna.py b/bin/get_trna.py index 782f940..52441c4 100755 --- a/bin/get_trna.py +++ b/bin/get_trna.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/get_ucsc.py b/bin/get_ucsc.py index e132e9b..5af0525 100755 --- a/bin/get_ucsc.py +++ b/bin/get_ucsc.py @@ -8,7 +8,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/get_viruses.py b/bin/get_viruses.py index edbc4d4..1c683a4 100755 --- a/bin/get_viruses.py +++ b/bin/get_viruses.py @@ -8,7 +8,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/inspect_fusion_sequences.py b/bin/inspect_fusion_sequences.py index 24dabea..ea81c95 100755 --- a/bin/inspect_fusion_sequences.py +++ b/bin/inspect_fusion_sequences.py @@ -5,7 +5,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. @@ -256,7 +256,7 @@ def format_epilog(self, formatter): Author: Daniel Nicorici Email: Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici """ diff --git a/bin/join_homolog_genes.py b/bin/join_homolog_genes.py index 3522d69..3494be0 100755 --- a/bin/join_homolog_genes.py +++ b/bin/join_homolog_genes.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/label_ambiguous_fusion_genes.py b/bin/label_ambiguous_fusion_genes.py index 66a33d1..f796c9e 100755 --- a/bin/label_ambiguous_fusion_genes.py +++ b/bin/label_ambiguous_fusion_genes.py @@ -8,7 +8,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/label_exonexon.py b/bin/label_exonexon.py index 98975b6..a48aa84 100755 --- a/bin/label_exonexon.py +++ b/bin/label_exonexon.py @@ -5,7 +5,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. @@ -179,7 +179,7 @@ def format_epilog(self, formatter): Author: Daniel Nicorici Email: Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici """ diff --git a/bin/label_found_fusions.py b/bin/label_found_fusions.py index 9b289bc..0539d17 100755 --- a/bin/label_found_fusions.py +++ b/bin/label_found_fusions.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/label_fusion_genes.py b/bin/label_fusion_genes.py index 167fd3e..a0b55b2 100755 --- a/bin/label_fusion_genes.py +++ b/bin/label_fusion_genes.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/label_fusion_genes_trim2.py b/bin/label_fusion_genes_trim2.py index c262a25..6d877b8 100755 --- a/bin/label_fusion_genes_trim2.py +++ b/bin/label_fusion_genes_trim2.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/label_multi.py b/bin/label_multi.py index 3cb3f6e..6437e32 100755 --- a/bin/label_multi.py +++ b/bin/label_multi.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/label_rtcircrna.py b/bin/label_rtcircrna.py index e4a5dcd..7a53b8e 100755 --- a/bin/label_rtcircrna.py +++ b/bin/label_rtcircrna.py @@ -5,7 +5,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. @@ -103,7 +103,7 @@ def format_epilog(self, formatter): Author: Daniel Nicorici Email: Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici """ diff --git a/bin/lengths_reads.py b/bin/lengths_reads.py index d7b6cc7..d4af7ee 100755 --- a/bin/lengths_reads.py +++ b/bin/lengths_reads.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/liftover.py b/bin/liftover.py index be1436f..ffa001f 100755 --- a/bin/liftover.py +++ b/bin/liftover.py @@ -8,7 +8,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/merge-reads.py b/bin/merge-reads.py index 0265824..42272ec 100755 --- a/bin/merge-reads.py +++ b/bin/merge-reads.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/merge-sam.py b/bin/merge-sam.py index 896c4cd..221276e 100755 --- a/bin/merge-sam.py +++ b/bin/merge-sam.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/merge_reports.py b/bin/merge_reports.py index 042fbba..cd49969 100755 --- a/bin/merge_reports.py +++ b/bin/merge_reports.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/overlap.py b/bin/overlap.py index c187fa2..4208304 100755 --- a/bin/overlap.py +++ b/bin/overlap.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/padding-fastq.py b/bin/padding-fastq.py index 60c210c..6b5f04e 100755 --- a/bin/padding-fastq.py +++ b/bin/padding-fastq.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/pair8removal.py b/bin/pair8removal.py index f25c6a9..2795b2a 100755 --- a/bin/pair8removal.py +++ b/bin/pair8removal.py @@ -8,7 +8,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. @@ -72,7 +72,7 @@ def format_epilog(self, formatter): Author: Daniel Nicorici Email: Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici """ diff --git a/bin/phred.py b/bin/phred.py index 6022290..b666b56 100755 --- a/bin/phred.py +++ b/bin/phred.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/predict_frame.py b/bin/predict_frame.py index eeb2994..9dfd15c 100755 --- a/bin/predict_frame.py +++ b/bin/predict_frame.py @@ -6,7 +6,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. @@ -386,7 +386,7 @@ def format_epilog(self, formatter): Author: Daniel Nicorici Email: Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici """ diff --git a/bin/prep-1by1.py b/bin/prep-1by1.py index 8ad0024..6cda180 100755 --- a/bin/prep-1by1.py +++ b/bin/prep-1by1.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/psl_best_unique_contigs.py b/bin/psl_best_unique_contigs.py index 42a86ae..7f6901a 100755 --- a/bin/psl_best_unique_contigs.py +++ b/bin/psl_best_unique_contigs.py @@ -8,7 +8,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/python_version.py b/bin/python_version.py index 1c855bc..2f64df4 100755 --- a/bin/python_version.py +++ b/bin/python_version.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/reads_from_map.py b/bin/reads_from_map.py index 7238063..4df941e 100755 --- a/bin/reads_from_map.py +++ b/bin/reads_from_map.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/remove-adapter.py b/bin/remove-adapter.py index 4a8e1f6..6887dd2 100755 --- a/bin/remove-adapter.py +++ b/bin/remove-adapter.py @@ -10,7 +10,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. @@ -1107,7 +1107,7 @@ def format_epilog(self, formatter): Author: Daniel Nicorici Email: Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici """ diff --git a/bin/remove-bad-illumina.py b/bin/remove-bad-illumina.py index 88f87ca..db276f8 100755 --- a/bin/remove-bad-illumina.py +++ b/bin/remove-bad-illumina.py @@ -8,7 +8,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/remove_custom_feature.py b/bin/remove_custom_feature.py index 7466281..70b9c55 100755 --- a/bin/remove_custom_feature.py +++ b/bin/remove_custom_feature.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/remove_reads_exon_exon_fastq.py b/bin/remove_reads_exon_exon_fastq.py index b407161..af286b3 100755 --- a/bin/remove_reads_exon_exon_fastq.py +++ b/bin/remove_reads_exon_exon_fastq.py @@ -10,7 +10,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/remove_reads_exon_exon_map.py b/bin/remove_reads_exon_exon_map.py index d048f91..2a4a9e3 100755 --- a/bin/remove_reads_exon_exon_map.py +++ b/bin/remove_reads_exon_exon_map.py @@ -10,7 +10,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/remove_reads_exon_exon_psl.py b/bin/remove_reads_exon_exon_psl.py index 2be195d..9f721ed 100755 --- a/bin/remove_reads_exon_exon_psl.py +++ b/bin/remove_reads_exon_exon_psl.py @@ -10,7 +10,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/remove_reads_genome_transcriptome.py b/bin/remove_reads_genome_transcriptome.py index c824af2..cb77146 100755 --- a/bin/remove_reads_genome_transcriptome.py +++ b/bin/remove_reads_genome_transcriptome.py @@ -9,7 +9,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/remove_shorter_reads.py b/bin/remove_shorter_reads.py index 5a8ade5..b1bca5e 100755 --- a/bin/remove_shorter_reads.py +++ b/bin/remove_shorter_reads.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/remove_str.py b/bin/remove_str.py index c01524a..c6326e3 100755 --- a/bin/remove_str.py +++ b/bin/remove_str.py @@ -9,7 +9,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/sam2psl.py b/bin/sam2psl.py index 7b4bdae..563dff8 100755 --- a/bin/sam2psl.py +++ b/bin/sam2psl.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/shebang.py b/bin/shebang.py index 01a40d4..bb41b09 100755 --- a/bin/shebang.py +++ b/bin/shebang.py @@ -5,7 +5,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. @@ -72,7 +72,7 @@ def format_epilog(self, formatter): Author: Daniel Nicorici Email: Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici """ diff --git a/bin/shield_genes.py b/bin/shield_genes.py index faa1b3d..34129e0 100755 --- a/bin/shield_genes.py +++ b/bin/shield_genes.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/shuffle.py b/bin/shuffle.py index 5b90aa9..c5d1703 100755 --- a/bin/shuffle.py +++ b/bin/shuffle.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/sliding-read.py b/bin/sliding-read.py index f618c1e..c6bac59 100755 --- a/bin/sliding-read.py +++ b/bin/sliding-read.py @@ -6,7 +6,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/smoothing_fusions_psl.py b/bin/smoothing_fusions_psl.py index 1394ddc..b937ed9 100755 --- a/bin/smoothing_fusions_psl.py +++ b/bin/smoothing_fusions_psl.py @@ -9,7 +9,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/solexa18to15.py b/bin/solexa18to15.py index bdf2dee..14d861d 100755 --- a/bin/solexa18to15.py +++ b/bin/solexa18to15.py @@ -10,7 +10,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/sort_ttdb.py b/bin/sort_ttdb.py index 1e43feb..f84f618 100755 --- a/bin/sort_ttdb.py +++ b/bin/sort_ttdb.py @@ -8,7 +8,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/split-fasta.py b/bin/split-fasta.py index cce86da..4849d90 100755 --- a/bin/split-fasta.py +++ b/bin/split-fasta.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/split-reads.py b/bin/split-reads.py index b29a0d2..9c0f473 100755 --- a/bin/split-reads.py +++ b/bin/split-reads.py @@ -8,7 +8,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/sra2illumina.py b/bin/sra2illumina.py index cb82417..a66df4a 100755 --- a/bin/sra2illumina.py +++ b/bin/sra2illumina.py @@ -9,7 +9,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/symbols.py b/bin/symbols.py index 68f1e2b..fda8543 100755 --- a/bin/symbols.py +++ b/bin/symbols.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/trim_poly_tails.py b/bin/trim_poly_tails.py index a77c200..d06f38f 100755 --- a/bin/trim_poly_tails.py +++ b/bin/trim_poly_tails.py @@ -6,7 +6,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/trim_reads.py b/bin/trim_reads.py index fed955f..e40a60b 100755 --- a/bin/trim_reads.py +++ b/bin/trim_reads.py @@ -7,7 +7,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/unshuffle.py b/bin/unshuffle.py index 1b7a6ad..f1e6a25 100755 --- a/bin/unshuffle.py +++ b/bin/unshuffle.py @@ -6,7 +6,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/update-config.py b/bin/update-config.py index eb4f1ee..57038a7 100755 --- a/bin/update-config.py +++ b/bin/update-config.py @@ -10,7 +10,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. diff --git a/bin/workflow.py b/bin/workflow.py index 5da506f..c649389 100755 --- a/bin/workflow.py +++ b/bin/workflow.py @@ -12,7 +12,7 @@ Author: Daniel Nicorici, Daniel.Nicorici@gmail.com -Copyright (c) 2009-2020 Daniel Nicorici +Copyright (c) 2009-2021 Daniel Nicorici This file is part of FusionCatcher. @@ -395,7 +395,7 @@ class pipeline: """ __version__ = '0.98.3 beta' __author__ = 'Daniel Nicorici' - __copyright__ = "Copyright (c) 2009-2020 Daniel Nicorici" + __copyright__ = "Copyright (c) 2009-2021 Daniel Nicorici" __credits__ = ["Henrikki Almusa"] __license__ = "GPL v3.0" __maintainer__ = "Daniel Nicorici"