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

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