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Bug fix. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3526 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-06-10 01:53:26 +00:00
parent ca4eab1d23
commit f55f32d4ee
1 changed files with 3 additions and 3 deletions
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6
java/src/org/broadinstitute/sting/gatk/iterators/DownsamplingLocusIteratorByState.java
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@ -612,15 +612,15 @@ public class DownsamplingLocusIteratorByState extends LocusIterator {
// nextReadState != null indicates that we haven't returned this value from the next() method yet. // nextReadState != null indicates that we haven't returned this value from the next() method yet.
if(nextReadState != null) if(nextReadState != null)
return; return;
if(alignmentStartIterator!=null&&alignmentStartIterator.hasNext()) { while(alignmentStartIterator!=null&&alignmentStartIterator.hasNext()) {
nextReadState = alignmentStartIterator.next(); nextReadState = alignmentStartIterator.next();
} }
else if(sampleIterator!=null&&sampleIterator.hasNext()) { while(nextReadState==null&&sampleIterator!=null&&sampleIterator.hasNext()) {
currentAlignmentStart = sampleIterator.next(); currentAlignmentStart = sampleIterator.next();
alignmentStartIterator = currentAlignmentStart!=null ? currentAlignmentStart.iterator() : null; alignmentStartIterator = currentAlignmentStart!=null ? currentAlignmentStart.iterator() : null;
nextReadState = alignmentStartIterator!=null&&alignmentStartIterator.hasNext() ? alignmentStartIterator.next() : null; nextReadState = alignmentStartIterator!=null&&alignmentStartIterator.hasNext() ? alignmentStartIterator.next() : null;
} }
else if(sampleIterators.hasNext()) { while(nextReadState==null&&sampleIterators.hasNext()) {
sampleIterator = sampleIterators.next(); sampleIterator = sampleIterators.next();
currentAlignmentStart = sampleIterator!=null&&sampleIterator.hasNext() ? sampleIterator.next() : null; currentAlignmentStart = sampleIterator!=null&&sampleIterator.hasNext() ? sampleIterator.next() : null;
alignmentStartIterator = currentAlignmentStart!=null ? currentAlignmentStart.iterator() : null; alignmentStartIterator = currentAlignmentStart!=null ? currentAlignmentStart.iterator() : null;