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We were still dropping halves of some pairs, in which both reads were assigned to the same position. Fixed. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2885 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2010-02-24 23:13:23 +00:00
parent fef1154fc8
commit 2572c24935
1 changed files with 3 additions and 0 deletions
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3
java/src/org/broadinstitute/sting/gatk/walkers/indels/SAMRecordCoordinateComparatorWithUnmappedReads.java
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@ -50,6 +50,9 @@ public class SAMRecordCoordinateComparatorWithUnmappedReads extends SAMRecordCoo
if ( samRecord1.getDuplicateReadFlag() != samRecord2.getDuplicateReadFlag() )
return (samRecord1.getDuplicateReadFlag()? -1: 1);
if ( samRecord1.getReadPairedFlag() && samRecord2.getReadPairedFlag() && samRecord1.getFirstOfPairFlag() != samRecord2.getFirstOfPairFlag() )
return (samRecord1.getFirstOfPairFlag()? -1: 1);
// such a case was actually observed
return samRecord1.getMappingQuality() - samRecord2.getMappingQuality();
}