docu update

doc/GSvar/changelog.md

@@ -1,5 +1,12 @@
 # GSvar change log
 
+## 2024_11-86 (20.01.25)
+
+- general: renamed class 'R*' to 'R' (changed in HerediCare and HerediVar)
+- general: improved opening QC files from GSvarServer
+- variant details: updated allOfUs variant URL
+- NGSD: Added device type 'Revio'
+
 ## 2024_11-50 (07.01.25)
 
 - general: added sample counts dialog (NGSD > Sample counts)

doc/tools/TsvSlice.md

@@ -1,5 +1,5 @@
 ### TsvSlice tool help
-	TsvSlice (2024_08-113-g94a3b440)
+	TsvSlice (2024_11-86-g94c45dea)
 
 	Extracts/reorders columns of a TSV file.
 
@@ -13,6 +13,8 @@
 	                    Default value: ''
 	  -numeric          If set, column names are interpreted as 1-based column numbers.
 	                    Default value: 'false'
+	  -rm               If set, the columns given in 'cols' are removed instead of extracted.
+	                    Default value: 'false'
 
 	Special parameters:
 	  --help            Shows this help and exits.
@@ -22,6 +24,6 @@
 	  --settings [file] Settings override file (no other settings files are used).
 
 ### TsvSlice changelog
-	TsvSlice 2024_08-113-g94a3b440
+	TsvSlice 2024_11-86-g94c45dea
 
 [back to ngs-bits](https://github.com/imgag/ngs-bits)

doc/tools/VariantFilterAnnotations.md

@@ -1,5 +1,5 @@
 ### VariantFilterAnnotations tool help
-	VariantFilterAnnotations (2024_11-59-ge0a7288e)
+	VariantFilterAnnotations (2024_11-86-g94c45dea)
 
 	Filter a variant list in GSvar format based on variant annotations.
 
@@ -27,7 +27,7 @@
 	                                     action - Action to perform [default=KEEP] [valid=KEEP,FILTER]
 	Classification NGSD                Filter for variant classification from NGSD.
 	                                   Parameters:
-	                                     classes - NGSD classes [default=4,5] [valid=1,2,3,4,5,M,R*] [non-empty]
+	                                     classes - NGSD classes [default=4,5] [valid=1,2,3,4,5,M,R] [non-empty]
 	                                     action - Action to perform [default=KEEP] [valid=KEEP,FILTER,REMOVE]
 	Column match                       Filter that matches the content of a column against a perl-compatible regular expression.
 	                                   For details about regular expressions, see http://perldoc.perl.org/perlretut.html
@@ -183,7 +183,7 @@
 	  --settings [file] Settings override file (no other settings files are used).
 
 ### VariantFilterAnnotations changelog
-	VariantFilterAnnotations 2024_11-59-ge0a7288e
+	VariantFilterAnnotations 2024_11-86-g94c45dea
 
 	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.

doc/tools/VcfAdd.md

@@ -1,23 +1,22 @@
 ### VcfAdd tool help
-	VcfAdd (2024_08-110-g317f43b9)
+	VcfAdd (2024_11-86-g94c45dea)
 
-	Appends variants from a VCF file to another VCF file.
+	Merges several VCF files into one VCF by appending one to the other.
 
-	VCF header lines are taken from 'in' only.
+	Variant lines from all other input files are appended to the first input file.
+	VCF header lines are taken from the first input file only.
 
 	Mandatory parameters:
-	  -in2 <file>           Input VCF file that is added to 'in'.
+	  -in <filelist>        Input VCF ro VCG.GZ files to merge.
 
 	Optional parameters:
-	  -in <file>            Input VCF file to add 'in2' to.
+	  -out <file>           Output VCF file with all variants.
 	                        Default value: ''
-	  -out <file>           Output VCF file with variants from 'in' and 'in2'.
-	                        Default value: ''
-	  -filter <string>      Tag variants from 'in2' with this filter entry.
+	  -filter <string>      Tag variants from all but the first input file with this filter entry.
 	                        Default value: ''
 	  -filter_desc <string> Description used in the filter header - use underscore instead of spaces.
 	                        Default value: ''
-	  -skip_duplicates      Skip variants from  'in2' which are also contained in 'in'.
+	  -skip_duplicates      Skip variants if they occur more than once.
 	                        Default value: 'false'
 
 	Special parameters:
@@ -28,7 +27,8 @@
 	  --settings [file]     Settings override file (no other settings files are used).
 
 ### VcfAdd changelog
-	VcfAdd 2024_08-110-g317f43b9
+	VcfAdd 2024_11-86-g94c45dea
 
+	2025-01-17 Added support for gzipped VCFs and removing duplicates if there is only one input file.
 	2022-12-08 Initial implementation.
 [back to ngs-bits](https://github.com/imgag/ngs-bits)