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Quick fix 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3007 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-03-16 02:59:26 +00:00
parent 202231141c
commit 586f87fa35
1 changed files with 5 additions and 6 deletions
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11
java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
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@ -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;
}