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Bugfixes for the case when no read groups / no samples are available. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3523 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-06-09 18:47:05 +00:00
parent adc4c4e577
commit dbee21a50f
1 changed files with 5 additions and 3 deletions
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8
java/src/org/broadinstitute/sting/gatk/iterators/DownsamplingLocusIteratorByState.java
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@ -279,7 +279,7 @@ 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.getDataSource() != null) if(GenomeAnalysisEngine.instance != null && GenomeAnalysisEngine.instance.getDataSource() != null)
sampleNames.addAll(SampleUtils.getSAMFileSamples(GenomeAnalysisEngine.instance.getSAMFileHeader())); sampleNames.addAll(SampleUtils.getSAMFileSamples(GenomeAnalysisEngine.instance.getSAMFileHeader()));
readStates = new ReadStateManager(samIterator,readInformation.getDownsamplingMethod(),readInformation.getMaxReadsAtLocus(),sampleNames); readStates = new ReadStateManager(samIterator,readInformation.getDownsamplingMethod(),readInformation.getMaxReadsAtLocus(),sampleNames);
this.readInfo = readInformation; this.readInfo = readInformation;
@ -657,7 +657,8 @@ public class DownsamplingLocusIteratorByState extends LocusIterator {
int firstAlignmentStart = iterator.peek().getAlignmentStart(); int firstAlignmentStart = iterator.peek().getAlignmentStart();
while(iterator.hasNext() && iterator.peek().getReferenceIndex() == firstContigIndex && iterator.peek().getAlignmentStart() == firstAlignmentStart) { while(iterator.hasNext() && iterator.peek().getReferenceIndex() == firstContigIndex && iterator.peek().getAlignmentStart() == firstAlignmentStart) {
SAMRecord read = iterator.next(); SAMRecord read = iterator.next();
getAggregator(read.getReadGroup().getSample()).add(read); Collection<SAMRecord> aggregator = getAggregator(read.getReadGroup()!=null ? read.getReadGroup().getSample() : null);
aggregator.add(read);
} }
} }
else { else {
@ -667,7 +668,8 @@ public class DownsamplingLocusIteratorByState extends LocusIterator {
while (iterator.hasNext() && !readIsPastCurrentPosition(iterator.peek())) { while (iterator.hasNext() && !readIsPastCurrentPosition(iterator.peek())) {
SAMRecord read = iterator.next(); SAMRecord read = iterator.next();
getAggregator(read.getReadGroup().getSample()).add(read); Collection<SAMRecord> aggregator = getAggregator(read.getReadGroup()!=null ? read.getReadGroup().getSample() : null);
aggregator.add(read);
} }
} }