From 586f87fa35c9e56756d2d7ae42d2891dd9a1be7b Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 16 Mar 2010 02:59:26 +0000
Subject: [PATCH] Quick fix

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3007 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../broadinstitute/sting/utils/sam/GATKSAMRecord.java | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java b/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
index fe1feec41..450edca70 100755
--- a/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
+++ b/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
@@ -1,11 +1,8 @@
 package org.broadinstitute.sting.utils.sam;
 
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
 
 import net.sf.samtools.*;
-import net.sf.samtools.util.StringUtil;
 import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
@@ -149,8 +146,10 @@ public class GATKSAMRecord extends SAMRecord {
     public String getBaseQualityString() {
         if ( mQualString == null ) {
             final byte[] quals = getBaseQualities();
-            if ( quals.length > 0 )
-                mQualString = StringUtil.bytesToString(quals);
+	    if ( Arrays.equals(NULL_QUALS, quals) )
+		mQualString = NULL_QUALS_STRING;
+	    else
+		mQualString = SAMUtils.phredToFastq(quals);
         }
         return mQualString;
     }