From 2572c2493571442112ca5dc0dd805a1e05444145 Mon Sep 17 00:00:00 2001
From: asivache <asivache@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 24 Feb 2010 23:13:23 +0000
Subject: [PATCH] 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
---
 .../indels/SAMRecordCoordinateComparatorWithUnmappedReads.java | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/SAMRecordCoordinateComparatorWithUnmappedReads.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/SAMRecordCoordinateComparatorWithUnmappedReads.java
index 07c23ff13..1fe3fdd04 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/SAMRecordCoordinateComparatorWithUnmappedReads.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/SAMRecordCoordinateComparatorWithUnmappedReads.java
@@ -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();
     }