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* fixed bug where the merged header was not being set on the read (although the read group was) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@445 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kcibul 2009-04-16 12:53:07 +00:00
parent 240eb18564
commit d35a542bb9
1 changed files with 1 additions and 0 deletions
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java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
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@ -134,6 +134,7 @@ public class MergingSamRecordIterator2 implements CloseableIterator<SAMRecord>,
record.setAttribute(SAMTag.PG.toString(), newProgramGroupId);
}
record.setHeader(samHeaderMerger.getMergedHeader());
//System.out.printf("NEXT = %s %s %d%n", record.getReadName(), record.getReferenceName(), record.getAlignmentStart());
//System.out.printf("PEEK = %s %s %d%n", this.pq.peek().peek().getReadName(), this.pq.peek().peek().getReferenceName(), this.pq.peek().peek().getAlignmentStart());
return record;