fix: Add QNAME in pair identification

samtools · Sep 22, 2017 · 3c01a88 · 3c01a88
1 parent 7843453
commit 3c01a88
Show file tree

Hide file tree

Showing 2 changed files with 3 additions and 0 deletions.
diff --git a/src/main/java/htsjdk/samtools/SAMRecord.java b/src/main/java/htsjdk/samtools/SAMRecord.java
@@ -338,6 +338,7 @@ private boolean hasReferenceName() {
  */
  public boolean isPair(final SAMRecord record) {
  return record != null
+ && Objects.equals(this.getReadName(), record.getReadName())
  && this.getMateAlignmentStart() == record.getAlignmentStart()
  && record.getMateAlignmentStart() == this.getAlignmentStart()
  && !NO_ALIGNMENT_REFERENCE_NAME.equals(this.getMateReferenceName())

diff --git a/src/test/java/htsjdk/samtools/SAMRecordUnitTest.java b/src/test/java/htsjdk/samtools/SAMRecordUnitTest.java
@@ -1124,9 +1124,11 @@ public void testRecordsArePairIfTheyLinkEachOtherInMateFields() {
  @Test
  public void testRecordsArePairIfTheyHaveNoMateFields() {
  final SAMRecord first = new SAMRecord(new SAMFileHeader(new SAMSequenceDictionary()));
+ first.setReadName("example1");
  first.setAlignmentStart(42);
  first.setReferenceName("chrm1");
  final SAMRecord second = new SAMRecord(new SAMFileHeader(new SAMSequenceDictionary()));
+ first.setReadName("example1");
  second.setAlignmentStart(142);
  second.setReferenceName("chrm2");