From 3c01a887d7e9abb272da500b742937821c4fbd00 Mon Sep 17 00:00:00 2001
From: Denis Verkhoturov <denis_verkhoturov@epam.com>
Date: Fri, 22 Sep 2017 16:01:10 +0300
Subject: [PATCH] fix: Add QNAME in pair identification

---
 src/main/java/htsjdk/samtools/SAMRecord.java         | 1 +
 src/test/java/htsjdk/samtools/SAMRecordUnitTest.java | 2 ++
 2 files changed, 3 insertions(+)

diff --git a/src/main/java/htsjdk/samtools/SAMRecord.java b/src/main/java/htsjdk/samtools/SAMRecord.java
index d08a16e5fe..d47ff9d82c 100644
--- 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
index f2618c2509..a91a403161 100644
--- 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");