From 0d8983feee7655bca60db3657268902ddaece21c Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Wed, 9 Nov 2011 23:34:29 -0500
Subject: [PATCH] outputting the RG information

setReadGroup now sets the read group attribute for the GATKSAMRecord
---
 .../src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java    | 1 +
 1 file changed, 1 insertion(+)

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 d95570d9b..3fe1060dd 100755
--- a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
@@ -167,6 +167,7 @@ public class GATKSAMRecord extends BAMRecord {
     public void setReadGroup( final GATKSAMReadGroupRecord readGroup ) {
         mReadGroup = readGroup;
         retrievedReadGroup = true;
+        setAttribute("RG", mReadGroup.getId());       // todo -- this should be standardized, but we don't have access to SAMTagUtils!
     }
 
     ///////////////////////////////////////////////////////////////////////////////