docu update

doc/tools/BamToFastq.md

@@ -1,5 +1,5 @@
 ### BamToFastq tool help
-	BamToFastq (2024_08-110-g317f43b9)
+	BamToFastq (2024_11-41-g79ac725e)
 
 	Converts a coordinate-sorted BAM file to FASTQ files.
 
@@ -10,19 +10,20 @@
 	Optional parameters:
 	  -out2 <file>             Read 2 output FASTQ.GZ file (required for pair-end samples).
 	                           Default value: ''
-	  -mode <enum>             Determine if BAM/CRAM contains paired-end or single-end reads (default: paired-end)
-	                           Default value: 'paired-end'
-	                           Valid: 'paired-end,single-end'
 	  -reg <string>            Export only reads in the given region. Format: chr:start-end.
 	                           Default value: ''
-	  -remove_duplicates       Does not export duplicate reads into the FASTQ file.
+	  -remove_duplicates       Does not export reads marked as duplicates in SAM flags into the FASTQ file.
 	                           Default value: 'false'
 	  -compression_level <int> Output FASTQ compression level from 1 (fastest) to 9 (best compression).
 	                           Default value: '1'
 	  -write_buffer_size <int> Output write buffer size (number of FASTQ entry pairs).
 	                           Default value: '100'
 	  -ref <file>              Reference genome for CRAM support (mandatory if CRAM is used).
 	                           Default value: ''
+	  -extend <int>            Extend all reads to the given length. Base 'N' and base qualiy '2' are used for extension.
+	                           Default value: '0'
+	  -fix                     Keep only one read pair if several have the same name (note: needs much memory as read names are kept in memory).
+	                           Default value: 'false'
 
 	Special parameters:
 	  --help                   Shows this help and exits.
@@ -32,8 +33,10 @@
 	  --settings [file]        Settings override file (no other settings files are used).
 
 ### BamToFastq changelog
-	BamToFastq 2024_08-110-g317f43b9
+	BamToFastq 2024_11-41-g79ac725e
 
+	2024-12-13 Added 'fix' parameter.
+	2024-12-09 Added 'extend' parameter.
 	2023-03-22 Added mode for single-end samples (long reads).
 	2020-11-27 Added CRAM support.
 	2020-05-29 Massive speed-up by writing in background. Added 'compression_level' parameter.

doc/tools/NGSDAnnotateSV.md

@@ -1,35 +1,27 @@
 ### NGSDAnnotateSV tool help
-	NGSDAnnotateSV (2024_08-110-g317f43b9)
+	NGSDAnnotateSV (2024_11-41-g79ac725e)
 
-	Annotates the structural variants of a given BEDPE file by the NGSD counts.
-
-	NOTICE: the parameter '-ignore_processing_system' will also use SVs from low quality samples (bad samples).
+	Annotates the structural variants in a given BEDPE file with the count of pathogenic SVs of classes 4 and 5 found in the NGSD.
 
 	Mandatory parameters:
-	  -in <file>                 BEDPE file containing structural variants.
-	  -out <file>                Output BEDPE file containing annotated structural variants.
-	  -ps <string>               Processed sample name.
+	  -in <file>        BEDPE file containing structural variants.
+	  -out <file>       Output BEDPE file containing annotated structural variants.
 
 	Optional parameters:
-	  -test                      Uses the test database instead of on the production database.
-	                             Default value: 'false'
-	  -ignore_processing_system  Use all SVs for annotation (otherwise only SVs from good samples of the same processing system are used)
-	                             Default value: 'false'
-	  -debug                     Provide additional information in STDOUT (e.g. query runtime)
-	                             Default value: 'false'
-	  -use_memory                Creates the temporary tables in memory.
-	                             Default value: 'false'
+	  -test             Uses the test database instead of on the production database.
+	                    Default value: 'false'
 
 	Special parameters:
-	  --help                     Shows this help and exits.
-	  --version                  Prints version and exits.
-	  --changelog                Prints changeloge and exits.
-	  --tdx                      Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
-	  --settings [file]          Settings override file (no other settings files are used).
+	  --help            Shows this help and exits.
+	  --version         Prints version and exits.
+	  --changelog       Prints changeloge and exits.
+	  --tdx             Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
+	  --settings [file] Settings override file (no other settings files are used).
 
 ### NGSDAnnotateSV changelog
-	NGSDAnnotateSV 2024_08-110-g317f43b9
+	NGSDAnnotateSV 2024_11-41-g79ac725e
 
+	2024-12-17 Refactored to only annotate pathogenic SVs from NGSD
 	2020-03-12 Bugfix in match computation for INS and BND
 	2020-03-11 Updated match computation for INS and BND
 	2020-02-27 Added temporary db table with same processing system.

doc/tools/TsvDiff.md

@@ -0,0 +1,34 @@
+### TsvDiff tool help
+	TsvDiff (2024_11-41-g79ac725e)
+
+	Compares TSV files.
+
+	Mandatory parameters:
+	  -in1 <file>                      First input TSV file.
+	  -in2 <file>                      Second input TSV file.
+
+	Optional parameters:
+	  -out <file>                      Output file with differences. If unset, writes to stdout.
+	                                   Default value: ''
+	  -skip_comments                   Do not compare comment lines starting with '##'.
+	                                   Default value: 'false'
+	  -skip_comments_matching <string> Comma-separated list of sub-strings for skipping comment lines (case-sensitive matching).
+	                                   Default value: ''
+	  -skip_cols <string>              Comma-separated list of colums to skip.
+	                                   Default value: ''
+	  -no_error                        Do not exit with error state if differences are detected
+	                                   Default value: 'false'
+	  -debug                           Print debug output to stderr
+	                                   Default value: 'false'
+
+	Special parameters:
+	  --help                           Shows this help and exits.
+	  --version                        Prints version and exits.
+	  --changelog                      Prints changeloge and exits.
+	  --tdx                            Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
+	  --settings [file]                Settings override file (no other settings files are used).
+
+### TsvDiff changelog
+	TsvDiff 2024_11-41-g79ac725e
+
+[back to ngs-bits](https://github.com/imgag/ngs-bits)

doc/tools/VcfBreakMulti.md

@@ -1,5 +1,5 @@
 ### VcfBreakMulti tool help
-	VcfBreakMulti (2024_08-113-g94a3b440)
+	VcfBreakMulti (2024_11-41-g79ac725e)
 
 	Breaks multi-allelic variants into several lines, making sure that allele-specific INFO/SAMPLE fields are still valid.
 
@@ -21,7 +21,8 @@
 	  --settings [file] Settings override file (no other settings files are used).
 
 ### VcfBreakMulti changelog
-	VcfBreakMulti 2024_08-113-g94a3b440
+	VcfBreakMulti 2024_11-41-g79ac725e
 
+	2024-11-21 Implemented handling of phased GT
 	2018-10-18 Initial implementation.
 [back to ngs-bits](https://github.com/imgag/ngs-bits)