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The copy constructor for a GATKSAMRecord (used for testing only) should use the actual read's contig index, not its mate's.

This commit is contained in:
Eric Banks 2014-07-23 15:31:03 -04:00
parent 0798a4b768
commit 84af1fc75f
1 changed files with 2 additions and 1 deletions
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3
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecord.java
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@ -92,7 +92,8 @@ public class GATKSAMRecord extends BAMRecord implements Cloneable {
* @param read * @param read
*/ */
public GATKSAMRecord(final SAMRecord read) { public GATKSAMRecord(final SAMRecord read) {
super(read.getHeader(), read.getMateReferenceIndex(), super(read.getHeader(),
read.getReferenceIndex(),
read.getAlignmentStart(), read.getAlignmentStart(),
read.getReadName() != null ? (short)read.getReadNameLength() : 0, read.getReadName() != null ? (short)read.getReadNameLength() : 0,
(short)read.getMappingQuality(), (short)read.getMappingQuality(),