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More bugfixes for cases where no sample name is present. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3578 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-06-17 16:46:02 +00:00
parent 22abbc0edb
commit c1595a383a
1 changed files with 4 additions and 1 deletions
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5
java/src/org/broadinstitute/sting/gatk/iterators/DownsamplingLocusIteratorByState.java
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@ -276,8 +276,11 @@ public class DownsamplingLocusIteratorByState extends LocusIterator {
public DownsamplingLocusIteratorByState(final Iterator<SAMRecord> samIterator, Reads readInformation, List<LocusIteratorFilter> filters ) { public DownsamplingLocusIteratorByState(final Iterator<SAMRecord> samIterator, Reads readInformation, List<LocusIteratorFilter> filters ) {
// Aggregate all sample names. // Aggregate all sample names.
// TODO: Push in header via constructor // TODO: Push in header via constructor
if(GenomeAnalysisEngine.instance != null && GenomeAnalysisEngine.instance.getDataSource() != null) if(GenomeAnalysisEngine.instance != null && GenomeAnalysisEngine.instance.getDataSource() != null) {
sampleNames.addAll(SampleUtils.getSAMFileSamples(GenomeAnalysisEngine.instance.getSAMFileHeader())); sampleNames.addAll(SampleUtils.getSAMFileSamples(GenomeAnalysisEngine.instance.getSAMFileHeader()));
}
// Add a null sample name as a catch-all for reads without samples
if(!sampleNames.contains(null)) sampleNames.add(null);
readStates = new ReadStateManager(samIterator,readInformation.getDownsamplingMethod(),readInformation.getMaxReadsAtLocus(),sampleNames); readStates = new ReadStateManager(samIterator,readInformation.getDownsamplingMethod(),readInformation.getMaxReadsAtLocus(),sampleNames);
this.readInfo = readInformation; this.readInfo = readInformation;
this.filters = filters; this.filters = filters;