From e1b4c3968f7df4b4f50495b0ee15ab20f7c33ffd Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Tue, 8 Nov 2011 16:50:03 -0500
Subject: [PATCH] Fixing GATKSAMRecord bug

when constructing a GATKSAMRecord from scratch, we should set "mRestOfBinaryData" to null so the BAMRecord doesn't try to retrieve missing information from the non-existent bam file.
---
 .../org/broadinstitute/sting/utils/sam/GATKSAMRecord.java  | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

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 ede75817a..4c1cbf547 100755
--- a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
@@ -24,7 +24,10 @@
 
 package org.broadinstitute.sting.utils.sam;
 
-import net.sf.samtools.*;
+import net.sf.samtools.BAMRecord;
+import net.sf.samtools.SAMFileHeader;
+import net.sf.samtools.SAMReadGroupRecord;
+import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.utils.NGSPlatform;
 
 import java.util.HashMap;
@@ -83,7 +86,7 @@ public class GATKSAMRecord extends BAMRecord {
                 read.getMateReferenceIndex(),
                 read.getMateAlignmentStart(),
                 read.getInferredInsertSize(),
-                new byte[]{});
+                null);
         super.clearAttributes();
     }