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Repopulating rodsToSamples. Code reviewed by Eric. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4027 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kshakir 2010-08-13 17:07:18 +00:00
parent cb144734c0
commit 80a70ccf03
1 changed files with 5 additions and 1 deletions
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6
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BatchedCallsMerger.java
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@ -83,8 +83,12 @@ public class BatchedCallsMerger extends LocusWalker<VariantContext, Integer> imp
// get all of the sample names and meta data // get all of the sample names and meta data
Map<String, VCFHeader> headers = VCFUtils.getVCFHeadersFromRods(getToolkit(), targetRods); Map<String, VCFHeader> headers = VCFUtils.getVCFHeadersFromRods(getToolkit(), targetRods);
Set<String> samples = SampleUtils.getSampleList(headers); Set<String> samples = SampleUtils.getSampleList(headers);
for ( VCFHeader header : headers.values() ) for ( String rodName : headers.keySet() ) {
VCFHeader header = headers.get(rodName);
headerLines.addAll(header.getMetaData()); headerLines.addAll(header.getMetaData());
HashSet<String> mySamples = new HashSet<String>(header.getGenotypeSamples());
rodsToSamples.put(rodName, mySamples);
}
// update the engine // update the engine
UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, writer, null, null); UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, writer, null, null);