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added a fix for a bug Andrew found 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@869 348d0f76-0448-11de-a6fe-93d51630548a
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aaron 2009-06-01 16:53:56 +00:00
parent b7defeae83
commit 4edb33788b
1 changed files with 1 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
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@ -184,7 +184,7 @@ public class MergingSamRecordIterator2 implements CloseableIterator<SAMRecord>,
}
record.setHeader(samHeaderMerger.getMergedHeader());
if (this.samHeaderMerger.hasMergedSequenceDictionary()) {
if (this.samHeaderMerger.hasMergedSequenceDictionary() && record.getReferenceIndex() > 0) {
record.setReferenceIndex(this.samHeaderMerger.getNewSequenceMapping(iterator.getReader(),record.getReferenceIndex()));
}