From 787c84d68b28b4579a096939be9942c3fa62a61f Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 8 Jul 2009 04:07:08 +0000
Subject: [PATCH] only compare pair position for paired end reads

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1190 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../src/org/broadinstitute/sting/utils/ComparableSAMRecord.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/utils/ComparableSAMRecord.java b/java/src/org/broadinstitute/sting/utils/ComparableSAMRecord.java
index 27540bb77..01e5baba8 100755
--- a/java/src/org/broadinstitute/sting/utils/ComparableSAMRecord.java
+++ b/java/src/org/broadinstitute/sting/utils/ComparableSAMRecord.java
@@ -24,7 +24,7 @@ public class ComparableSAMRecord implements Comparable<ComparableSAMRecord> {
         if ( comparison == 0 )
             comparison = record.getReadName().compareTo(o.getRecord().getReadName());
         // if the read names are the same, use the first of the pair if appropriate
-        if ( comparison == 0 )
+        if ( comparison == 0 && record.getReadPairedFlag() )
             comparison = ( record.getFirstOfPairFlag() ? -1 : 1);
         return comparison;
     }