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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.
This commit is contained in:
Mauricio Carneiro 2011-11-08 16:50:03 -05:00
parent 8e519e7d5d
commit e1b4c3968f
1 changed files with 5 additions and 2 deletions
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7
public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
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@ -24,7 +24,10 @@
package org.broadinstitute.sting.utils.sam; 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 org.broadinstitute.sting.utils.NGSPlatform;
import java.util.HashMap; import java.util.HashMap;
@ -83,7 +86,7 @@ public class GATKSAMRecord extends BAMRecord {
read.getMateReferenceIndex(), read.getMateReferenceIndex(),
read.getMateAlignmentStart(), read.getMateAlignmentStart(),
read.getInferredInsertSize(), read.getInferredInsertSize(),
new byte[]{}); null);
super.clearAttributes(); super.clearAttributes();
} }