From f9530e07683250cc2da6e2b178dc3d07230dce00 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Wed, 9 Nov 2011 12:37:14 -0500
Subject: [PATCH] Clean unnecessary attributes from the read

this gives on average 40% file size reduction.
---
 .../org/broadinstitute/sting/utils/sam/GATKSAMRecord.java   | 6 ++++++
 1 file changed, 6 insertions(+)

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 63a618aed..d36ec3411 100755
--- a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
@@ -241,4 +241,10 @@ public class GATKSAMRecord extends BAMRecord {
     public boolean isEmpty() {
         return this.getReadLength() == 0;
     }
+
+    public void simplify () {
+        GATKSAMReadGroupRecord rg = getReadGroup();
+        this.clearAttributes();
+        setReadGroup(rg);
+    }
 }