Updated documentation and update.php.

.gitattributes

@@ -4,6 +4,7 @@
 *.cpp text eol=lf
 *.pro text eol=lf
 *.pri text eol=lf
+*.md text eol=lf
 
 *.txt text eol=lf
 *.fa text eol=lf

README.md

@@ -64,13 +64,14 @@ _ngs-bits_ contains a lot of tools that we use for NGS short-read data analysis
 * [ReadQC](doc/tools/ReadQC.md) - Quality control tool for FASTQ files (output is [qcML](https://code.google.com/p/qcml/)).
 * [MappingQC](doc/tools/MappingQC.md) - Quality control tool for a BAM file (output is [qcML](https://code.google.com/p/qcml/)).
 * [VariantQC](doc/tools/VariantQC.md) - Quality control tool for a VCF file (output is [qcML](https://code.google.com/p/qcml/)).
+* [SomaticQC](doc/tools/SomaticQC.md) - Quality control tool for tumor-normal pairs (output is [qcML](https://code.google.com/p/qcml/)).
 * [SampleCorrelation](doc/tools/SampleCorrelation.md) - Calculates the variant overlap and correlation of two VCF/BAM files.
 * [SampleGender](doc/tools/SampleGender.md) - Determines sample gender based on a BAM file.
 * [PERsim](doc/tools/PERsim.md) - Paired-end read simulator for Illumina reads.
 
 ### BAM tools
 
-* [BamClipOverlap](doc/tools/BamClipOverlap.md) - Clips paired-end reads that overlap.
+* [BamClipOverlap](doc/tools/BamClipOverlap.md) - (Soft-)Clips paired-end reads that overlap.
 * [BamDownsample](doc/tools/BamDownsample.md) - Downsamples a BAM file to the given percentage of reads.
 * [BamIndex](doc/tools/BamIndex.md) - Creates a BAI index for a BAM file.
 * [BamLeftAlign](doc/tools/BamLeftAlign.md) - Left-aligns indels in repeat regions.

doc/tools/BamCleanHaloplex.md

@@ -1,5 +1,5 @@
 ### BamCleanHaloplex tool help
-	BamCleanHaloplex (0.1-222-g9be2128)
+	BamCleanHaloplex (0.1-420-g3536bb0)
 
 	BAM cleaning for Haloplex.
 
@@ -18,6 +18,6 @@
 	  --tdx            Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
 
 ### BamCleanHaloplex changelog
-	BamCleanHaloplex 0.1-222-g9be2128
+	BamCleanHaloplex 0.1-420-g3536bb0
 
-[back to ngs-bits](https://github.com/marc-sturm/ngs-bits)
+[back to ngs-bits](https://github.com/imgag/ngs-bits)

doc/tools/BamClipOverlap.md

@@ -1,5 +1,5 @@
 ### BamClipOverlap tool help
-	BamClipOverlap (0.1-222-g9be2128)
+	BamClipOverlap (0.1-420-g3536bb0)
 
 	Softclipping of overlapping reads.
 
@@ -20,6 +20,6 @@
 	  --tdx        Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
 
 ### BamClipOverlap changelog
-	BamClipOverlap 0.1-222-g9be2128
+	BamClipOverlap 0.1-420-g3536bb0
 
-[back to ngs-bits](https://github.com/marc-sturm/ngs-bits)
+[back to ngs-bits](https://github.com/imgag/ngs-bits)

doc/tools/BamDeduplicateByBarcode.md

@@ -0,0 +1,40 @@
+### BamDeduplicateByBarcode tool help
+	BamDeduplicateByBarcode (0.1-420-g3536bb0)
+
+	Removes duplicates from a bam file based on a molecular barcode file.
+
+	Mandatory parameters:
+	  -bam <file>           Input BAM file.
+	  -index <file>         Index FASTQ file.
+	  -out <file>           Output BAM file.
+
+	Optional parameters:
+	  -flag                 flag duplicate reads insteadt of deleting them
+	                        Default value: 'false'
+	  -test                 adjust output for testing purposes
+	                        Default value: 'false'
+	  -min_group <int>      minimal numbers of reads to keep a barcode group.
+	                        Default value: '1'
+	  -dist <int>           edit distance for single read matching .
+	                        Default value: '0'
+	  -mip_file <file>      input file for MIPS (reads are filtered and cut to match only MIP inserts).
+	                        Default value: ''
+	  -hs_file <file>       input file for Haloplex HS amplicons (reads are filtered to match only amplicons).
+	                        Default value: ''
+	  -stats <file>         Output TSV file for statistics).
+	                        Default value: ''
+	  -nomatch_out <file>   Output Bed file for reads not matching any amplicon).
+	                        Default value: ''
+	  -duplicate_out <file> Output Bed file for reads removed as duplicates).
+	                        Default value: ''
+
+	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'.
+
+### BamDeduplicateByBarcode changelog
+	BamDeduplicateByBarcode 0.1-420-g3536bb0
+
+[back to ngs-bits](https://github.com/imgag/ngs-bits)

doc/tools/BamDownsample.md

@@ -1,5 +1,5 @@
 ### BamDownsample tool help
-	BamDownsample (0.1-222-g9be2128)
+	BamDownsample (0.1-420-g3536bb0)
 
 	Downsamples a BAM file to the given percentage of reads.
 
@@ -19,6 +19,6 @@
 	  --tdx             Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
 
 ### BamDownsample changelog
-	BamDownsample 0.1-222-g9be2128
+	BamDownsample 0.1-420-g3536bb0
 
-[back to ngs-bits](https://github.com/marc-sturm/ngs-bits)
+[back to ngs-bits](https://github.com/imgag/ngs-bits)

doc/tools/BamIndex.md

@@ -1,5 +1,5 @@
 ### BamIndex tool help
-	BamIndex (0.1-222-g9be2128)
+	BamIndex (0.1-420-g3536bb0)
 
 	Indexes a sorted BAM file.
 
@@ -13,6 +13,6 @@
 	  --tdx        Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
 
 ### BamIndex changelog
-	BamIndex 0.1-222-g9be2128
+	BamIndex 0.1-420-g3536bb0
 
-[back to ngs-bits](https://github.com/marc-sturm/ngs-bits)
+[back to ngs-bits](https://github.com/imgag/ngs-bits)

doc/tools/BamLeftAlign.md

@@ -1,5 +1,5 @@
 ### BamLeftAlign tool help
-	BamLeftAlign (0.1-222-g9be2128)
+	BamLeftAlign (0.1-420-g3536bb0)
 
 	Iteratively left-aligns and merges the insertions and deletions in all alignments.
 
@@ -22,6 +22,6 @@
 	  --tdx           Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
 
 ### BamLeftAlign changelog
-	BamLeftAlign 0.1-222-g9be2128
+	BamLeftAlign 0.1-420-g3536bb0
 
-[back to ngs-bits](https://github.com/marc-sturm/ngs-bits)
+[back to ngs-bits](https://github.com/imgag/ngs-bits)

doc/tools/BamToFastq.md

@@ -1,5 +1,5 @@
 ### BamToFastq tool help
-	BamToFastq (0.1-350-g2af2ea1)
+	BamToFastq (0.1-420-g3536bb0)
 
 	Converts a coordinate-sorted BAM file to FASTQ files (paired-end only).
 
@@ -15,6 +15,6 @@
 	  --tdx        Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
 
 ### BamToFastq changelog
-	BamToFastq 0.1-350-g2af2ea1
+	BamToFastq 0.1-420-g3536bb0
 
-[back to ngs-bits](https://github.com/marc-sturm/ngs-bits)
+[back to ngs-bits](https://github.com/imgag/ngs-bits)

doc/tools/BedAdd.md

@@ -1,5 +1,5 @@
 ### BedAdd tool help
-	BedAdd (0.1-222-g9be2128)
+	BedAdd (0.1-420-g3536bb0)
 
 	Adds the regions in two BED files.
 
@@ -19,6 +19,6 @@
 	  --tdx        Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
 
 ### BedAdd changelog
-	BedAdd 0.1-222-g9be2128
+	BedAdd 0.1-420-g3536bb0
 
-[back to ngs-bits](https://github.com/marc-sturm/ngs-bits)
+[back to ngs-bits](https://github.com/imgag/ngs-bits)

doc/tools/BedAnnotateFreq.md

@@ -1,5 +1,5 @@
 ### BedAnnotateFreq tool help
-	BedAnnotateFreq (0.1-222-g9be2128)
+	BedAnnotateFreq (0.1-420-g3536bb0)
 
 	Extracts base frequencies for given regions from BAMs files.
 
@@ -19,6 +19,6 @@
 	  --tdx           Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
 
 ### BedAnnotateFreq changelog
-	BedAnnotateFreq 0.1-222-g9be2128
+	BedAnnotateFreq 0.1-420-g3536bb0
 
-[back to ngs-bits](https://github.com/marc-sturm/ngs-bits)
+[back to ngs-bits](https://github.com/imgag/ngs-bits)

doc/tools/BedAnnotateGC.md

@@ -1,5 +1,5 @@
 ### BedAnnotateGC tool help
-	BedAnnotateGC (0.1-222-g9be2128)
+	BedAnnotateGC (0.1-420-g3536bb0)
 
 	Annotates GC content fraction to regions in a BED file.
 
@@ -18,6 +18,6 @@
 	  --tdx        Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
 
 ### BedAnnotateGC changelog
-	BedAnnotateGC 0.1-222-g9be2128
+	BedAnnotateGC 0.1-420-g3536bb0
 
-[back to ngs-bits](https://github.com/marc-sturm/ngs-bits)
+[back to ngs-bits](https://github.com/imgag/ngs-bits)

doc/tools/BedAnnotateGenes.md

@@ -1,5 +1,5 @@
 ### BedAnnotateGenes tool help
-	BedAnnotateGenes (0.1-222-g9be2128)
+	BedAnnotateGenes (0.1-420-g3536bb0)
 
 	Annotates BED file regions with gene names.
 
@@ -20,6 +20,6 @@
 	  --tdx         Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
 
 ### BedAnnotateGenes changelog
-	BedAnnotateGenes 0.1-222-g9be2128
+	BedAnnotateGenes 0.1-420-g3536bb0
 
-[back to ngs-bits](https://github.com/marc-sturm/ngs-bits)
+[back to ngs-bits](https://github.com/imgag/ngs-bits)

doc/tools/BedChunk.md

@@ -1,5 +1,5 @@
 ### BedChunk tool help
-	BedChunk (0.1-222-g9be2128)
+	BedChunk (0.1-420-g3536bb0)
 
 	Splits all regions to chunks of an approximate desired size.
 
@@ -19,6 +19,6 @@
 	  --tdx        Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
 
 ### BedChunk changelog
-	BedChunk 0.1-222-g9be2128
+	BedChunk 0.1-420-g3536bb0
 
-[back to ngs-bits](https://github.com/marc-sturm/ngs-bits)
+[back to ngs-bits](https://github.com/imgag/ngs-bits)

doc/tools/BedCoverage.md

@@ -1,5 +1,5 @@
 ### BedCoverage tool help
-	BedCoverage (0.1-222-g9be2128)
+	BedCoverage (0.1-420-g3536bb0)
 
 	Extracts the average coverage for input regions from one or several BAM file(s).
 
@@ -21,6 +21,6 @@
 	  --tdx           Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
 
 ### BedCoverage changelog
-	BedCoverage 0.1-222-g9be2128
+	BedCoverage 0.1-420-g3536bb0
 
-[back to ngs-bits](https://github.com/marc-sturm/ngs-bits)
+[back to ngs-bits](https://github.com/imgag/ngs-bits)

doc/tools/BedExtend.md

@@ -1,5 +1,5 @@
 ### BedExtend tool help
-	BedExtend (0.1-222-g9be2128)
+	BedExtend (0.1-420-g3536bb0)
 
 	Extends the regions in a BED file.
 
@@ -21,6 +21,6 @@
 	  --tdx        Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
 
 ### BedExtend changelog
-	BedExtend 0.1-222-g9be2128
+	BedExtend 0.1-420-g3536bb0
 
-[back to ngs-bits](https://github.com/marc-sturm/ngs-bits)
+[back to ngs-bits](https://github.com/imgag/ngs-bits)

doc/tools/BedGeneOverlap.md

@@ -1,5 +1,5 @@
 ### BedGeneOverlap tool help
-	BedGeneOverlap (0.1-222-g9be2128)
+	BedGeneOverlap (0.1-420-g3536bb0)
 
 	Calculates how much of each overlapping gene is covered.
 
@@ -22,6 +22,6 @@
 	  --tdx          Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
 
 ### BedGeneOverlap changelog
-	BedGeneOverlap 0.1-222-g9be2128
+	BedGeneOverlap 0.1-420-g3536bb0
 
-[back to ngs-bits](https://github.com/marc-sturm/ngs-bits)
+[back to ngs-bits](https://github.com/imgag/ngs-bits)

doc/tools/BedInfo.md

@@ -1,5 +1,5 @@
 ### BedInfo tool help
-	BedInfo (0.1-222-g9be2128)
+	BedInfo (0.1-420-g3536bb0)
 
 	Prints information about a (merged) BED file.
 
@@ -22,6 +22,6 @@
 	  --tdx        Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
 
 ### BedInfo changelog
-	BedInfo 0.1-222-g9be2128
+	BedInfo 0.1-420-g3536bb0
 
-[back to ngs-bits](https://github.com/marc-sturm/ngs-bits)
+[back to ngs-bits](https://github.com/imgag/ngs-bits)

doc/tools/BedIntersect.md

@@ -1,5 +1,5 @@
 ### BedIntersect tool help
-	BedIntersect (0.1-222-g9be2128)
+	BedIntersect (0.1-420-g3536bb0)
 
 	Intersects the regions in two BED files.
 
@@ -22,6 +22,6 @@
 	  --tdx        Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
 
 ### BedIntersect changelog
-	BedIntersect 0.1-222-g9be2128
+	BedIntersect 0.1-420-g3536bb0
 
-[back to ngs-bits](https://github.com/marc-sturm/ngs-bits)
+[back to ngs-bits](https://github.com/imgag/ngs-bits)

doc/tools/BedLowCoverage.md

@@ -1,5 +1,5 @@
 ### BedLowCoverage tool help
-	BedLowCoverage (0.1-350-g2af2ea1)
+	BedLowCoverage (0.1-420-g3536bb0)
 
 	Detects low-coverage regions from a BAM file.
 
@@ -24,7 +24,7 @@
 	  --tdx           Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
 
 ### BedLowCoverage changelog
-	BedLowCoverage 0.1-350-g2af2ea1
+	BedLowCoverage 0.1-420-g3536bb0
 
 	2016-06-09 The BED line name if the input BED file is now passed on to the output BED file.
-[back to ngs-bits](https://github.com/marc-sturm/ngs-bits)
+[back to ngs-bits](https://github.com/imgag/ngs-bits)

doc/tools/BedMerge.md

@@ -1,5 +1,5 @@
 ### BedMerge tool help
-	BedMerge (0.1-222-g9be2128)
+	BedMerge (0.1-420-g3536bb0)
 
 	Merges overlapping regions in a BED file.
 
@@ -20,6 +20,6 @@
 	  --tdx         Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
 
 ### BedMerge changelog
-	BedMerge 0.1-222-g9be2128
+	BedMerge 0.1-420-g3536bb0
 
-[back to ngs-bits](https://github.com/marc-sturm/ngs-bits)
+[back to ngs-bits](https://github.com/imgag/ngs-bits)