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Loosen a restriction on isOriginalRead() 

* no longer needs to satisfy ReadAndIntervalOverlap.OVERLAP_CONTAINED
This commit is contained in:
Joel Thibault 2012-07-13 15:24:46 -04:00
parent 07822d6c0f
commit 6c6a324583
1 changed files with 1 additions and 1 deletions
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protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsWalker.java
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@ -663,7 +663,7 @@ public class ReduceReadsWalker extends ReadWalker<LinkedList<GATKSAMRecord>, Red
* @return Returns true if the read is the original read that went through map(). * @return Returns true if the read is the original read that went through map().
*/ */
private boolean isOriginalRead(LinkedList<GATKSAMRecord> list, GATKSAMRecord read) { private boolean isOriginalRead(LinkedList<GATKSAMRecord> list, GATKSAMRecord read) {
return isWholeGenome() || (list.getFirst().equals(read) && ReadUtils.getReadAndIntervalOverlapType(read, intervalList.first()) == ReadUtils.ReadAndIntervalOverlap.OVERLAP_CONTAINED); return isWholeGenome() || list.getFirst().equals(read);
} }
/** /**