From 84af1fc75f524669a5688b17cd6f29ab3499fb29 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Wed, 23 Jul 2014 15:31:03 -0400
Subject: [PATCH] The copy constructor for a GATKSAMRecord (used for testing
 only) should use the actual read's contig index, not its mate's.

---
 .../java/org/broadinstitute/gatk/utils/sam/GATKSAMRecord.java  | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecord.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecord.java
index 18a91b3df..0080f01df 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecord.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecord.java
@@ -92,7 +92,8 @@ public class GATKSAMRecord extends BAMRecord implements Cloneable {
      * @param read
      */
     public GATKSAMRecord(final SAMRecord read) {
-        super(read.getHeader(), read.getMateReferenceIndex(),
+        super(read.getHeader(),
+                read.getReferenceIndex(),
                 read.getAlignmentStart(),
                 read.getReadName() != null ? (short)read.getReadNameLength() : 0,
                 (short)read.getMappingQuality(),