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Tie into sequence merging code in the latest version of picard. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@851 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-05-28 21:48:35 +00:00
parent b43deda6c9
commit 0cf90b6f8a
1 changed files with 4 additions and 0 deletions
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4
java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
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@ -184,6 +184,10 @@ public class MergingSamRecordIterator2 implements CloseableIterator<SAMRecord>,
}
record.setHeader(samHeaderMerger.getMergedHeader());
if (this.samHeaderMerger.hasMergedSequenceDictionary()) {
record.setReferenceIndex(this.samHeaderMerger.getNewSequenceMapping(iterator.getReader(),record.getReferenceIndex()));
}
//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());