From 940816f16a6de33c35789ec73f5de02618b647f6 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Fri, 21 Dec 2012 10:50:56 -0500
Subject: [PATCH] GATKSamRecord now checks that the read group is a
 GATKReadGroupRecord, and if not makes one

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

diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
index ebb3c1ad0..cf06c59e8 100755
--- a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
@@ -154,7 +154,8 @@ public class GATKSAMRecord extends BAMRecord {
     @Override
     public GATKSAMReadGroupRecord getReadGroup() {
         if ( ! retrievedReadGroup ) {
-            mReadGroup = (GATKSAMReadGroupRecord)super.getReadGroup();
+            final SAMReadGroupRecord rg = super.getReadGroup();
+            mReadGroup = rg instanceof GATKSAMReadGroupRecord ? (GATKSAMReadGroupRecord)rg : new GATKSAMReadGroupRecord(rg);
             retrievedReadGroup = true;
         }
         return mReadGroup;