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inconsequential change in string constants printed into the vcf which noone uses anyway...

This commit is contained in:
Andrey Sivachenko 2011-09-30 16:40:21 -04:00
parent 010899f886
commit c7898a9be7
1 changed files with 3 additions and 3 deletions
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6
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java
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@ -265,7 +265,7 @@ public class SomaticIndelDetectorWalker extends ReadWalker<Integer,Integer> {
Set<VCFHeaderLine> headerInfo = new HashSet<VCFHeaderLine>();
// first, the basic info
headerInfo.add(new VCFHeaderLine("source", "IndelGenotyperV2"));
headerInfo.add(new VCFHeaderLine("source", "SomaticIndelDetector"));
headerInfo.add(new VCFHeaderLine("reference", getToolkit().getArguments().referenceFile.getName()));
// FORMAT and INFO fields
@ -283,10 +283,10 @@ public class SomaticIndelDetectorWalker extends ReadWalker<Integer,Integer> {
args.addAll(getToolkit().getFilters());
Map<String,String> commandLineArgs = getToolkit().getApproximateCommandLineArguments(args);
for ( Map.Entry<String, String> commandLineArg : commandLineArgs.entrySet() )
headerInfo.add(new VCFHeaderLine(String.format("IGv2_%s", commandLineArg.getKey()), commandLineArg.getValue()));
headerInfo.add(new VCFHeaderLine(String.format("SID_%s", commandLineArg.getKey()), commandLineArg.getValue()));
// also, the list of input bams
for ( String fileName : getToolkit().getArguments().samFiles )
headerInfo.add(new VCFHeaderLine("IGv2_bam_file_used", fileName));
headerInfo.add(new VCFHeaderLine("SID_bam_file_used", fileName));
return headerInfo;
}