Documentation update for release 2022_12

README.md

@@ -15,7 +15,7 @@ Alternatively, *ngs-bits* can be built from sources. Use git to clone the most r
 
     > git clone --recursive https://github.com/imgag/ngs-bits.git
 	> cd ngs-bits
-	> git checkout 2022_10
+	> git checkout 2022_12
 	> git submodule update --recursive --init
 
 Depending on your operating system, building instructions vary slightly:
@@ -170,17 +170,13 @@ The default output format of the quality control tools is [qcML](https://pubmed.
 
 Changes of master since last release:
 
-* GSvar:
-	* Updated ClinVar upload to new API version
-	* Added support to upload CNVs, SVs and CompHet variants to ClinVar
-
-Changes in release 2022_11:
-* VcfAnnotateConsequence: implemented multi-threading, added much more tests and fixed several bugs.
-* NGSDExportSamples: added filters for HPO terms and ancestry.
-* NGSD:
-	* Added version number to table 'gene_transcript'.
-	* Updated tissue list in table 'sample'.
-	* Added comment field in table 'user'.
-	* Added DRAGEN as caller in table 'sv_callset'.
+* none
+
+Changes in release 2022_12:
+
+* tool VcfAdd added
+* VcfFilter: added option `-remove_invalid`
+* VcfSort: added option `-remove_unused_contigs`
+* VcfAnnotateConsequence: improved error handling and load time for GFF file
 
 For older changes see [releases](https://github.com/imgag/ngs-bits/releases).

doc/tools/NGSDUpdateSvGenotype.md

@@ -0,0 +1,24 @@
+### NGSDUpdateSvGenotype tool help
+	NGSDUpdateSvGenotype (2022_11-72-g9164a905)
+
+	Updates the genotype for a given processed sample.
+
+	Mandatory parameters:
+	  -ps <string> Processed sample id.
+	  -in <file>   Input BEDPE file.
+
+	Optional parameters:
+	  -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'.
+
+### NGSDUpdateSvGenotype changelog
+	NGSDUpdateSvGenotype 2022_11-72-g9164a905
+
+	2022-03-07 Initial commit.
+[back to ngs-bits](https://github.com/imgag/ngs-bits)

doc/tools/SeqPurge.md

@@ -1,5 +1,5 @@
 ### SeqPurge tool help
-	SeqPurge (2022_07-18-gfd880985)
+	SeqPurge (2022_11-72-g9164a905)
 
 	Removes adapter sequences from paired-end sequencing data.
 
@@ -17,7 +17,7 @@
 	  -match_perc <float>      Minimum percentage of matching bases for sequence/adapter matches.
 	                           Default value: '80'
 	  -mep <float>             Maximum error probability of insert and adapter matches.
-	                           Default value: '1e-6'
+	                           Default value: '1e-06'
 	  -qcut <int>              Quality trimming cutoff for trimming from the end of reads using a sliding window approach. Set to 0 to disable.
 	                           Default value: '15'
 	  -qwin <int>              Quality trimming window size.
@@ -56,7 +56,7 @@
 	  --tdx                    Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
 
 ### SeqPurge changelog
-	SeqPurge 2022_07-18-gfd880985
+	SeqPurge 2022_11-72-g9164a905
 
 	2022-07-15 Improved scaling with more than 4 threads and CPU usage.
 	2019-03-26 Added 'compression_level' parameter.

doc/tools/VariantFilterAnnotations.md

@@ -1,5 +1,5 @@
 ### VariantFilterAnnotations tool help
-	VariantFilterAnnotations (2022_04-156-ga57fe9df)
+	VariantFilterAnnotations (2022_11-72-g9164a905)
 
 	Filter a variant list in GSvar format based on variant annotations.
 
@@ -59,7 +59,7 @@
 	                                     min_pli - Minumum ExAC pLI score [default=0.9] [min=0.0] [max=1.0]
 	Gene inheritance                   Filter based on gene inheritance.
 	                                   Parameters:
-	                                     modes - Inheritance mode(s) [valid=AR,AD,XLR,XLD,MT] [non-empty]
+	                                     modes - Inheritance mode(s) [valid=AR,AD,XLR,XLD,MT,n/a] [non-empty]
 	Genes                              Filter that preserves a gene set.
 	                                   Parameters:
 	                                     genes - Gene set [non-empty]
@@ -173,7 +173,7 @@
 	  --tdx           Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
 
 ### VariantFilterAnnotations changelog
-	VariantFilterAnnotations 2022_04-156-ga57fe9df
+	VariantFilterAnnotations 2022_11-72-g9164a905
 
 	2018-07-30 Replaced command-line parameters by INI file and added many new filters.
 	2017-06-14 Refactoring of genotype-based filters: now also supports multi-sample filtering of affected and control samples.