Fixed a missing special case in MarkDuplicates ReadsKey code

src/main/java/org/broadinstitute/hellbender/utils/read/markduplicates/sparkrecords/Pair.java

@@ -55,21 +55,39 @@ public Pair(final GATKRead read1, final GATKRead read2, final SAMFileHeader head
         final int read1UnclippedStart = ReadUtils.getStrandedUnclippedStart(read1);
         final int read2UnclippedStart = ReadUtils.getStrandedUnclippedStart(read2);
 
-        if( read1UnclippedStart < read2UnclippedStart ){
+        int read1ReferenceIndex = ReadUtils.getReferenceIndex(read1,header);
+        int read2ReferenceIndex = ReadUtils.getReferenceIndex(read2,header);
+
+        if( read1ReferenceIndex != read2ReferenceIndex ? read1ReferenceIndex < read2ReferenceIndex : read1UnclippedStart <= read2UnclippedStart ){
             first = read1;
             second = read2;
         } else {
             first = read2;
             second = read1;
         }
-        // Keep track of the orientation of read1 and read2 as it is important for optical duplicate marking
-        wasFlipped = second.isFirstOfPair();
-
         firstStartPosition = first.getAssignedStart();
 
+        // if the two read ends are in the same position, pointing in opposite directions,
+        // the orientation is undefined and the procedure above
+        // will depend on the order of the reads in the file.
+        // To avoid this, and match picard's behavior in this case, we ensure the orientation will be FR:
+        if (read1ReferenceIndex == read2ReferenceIndex &&
+                read1UnclippedStart == read2UnclippedStart &&
+                first.isReverseStrand() && !second.isReverseStrand()) {
+            // setting to FR for consistencies sake. (which involves flipping) if both reads had the same unclipped start
+            GATKRead tmp = first;
+            first = second;
+            second = tmp;
+        }
+
+        this.key = ReadsKey.getKeyForPair(header, first, second, headerLibraryMap);
+
         isRead1ReverseStrand = first.isReverseStrand();
         isRead2ReverseStrand = second.isReverseStrand();
 
+        // Keep track of the orientation of read1 and read2 as it is important for optical duplicate marking
+        wasFlipped = second.isFirstOfPair();
+
         this.key = ReadsKey.getKeyForPair(header, first, second, headerLibraryMap);
     }
 

src/test/java/org/broadinstitute/hellbender/tools/walkers/markduplicates/AbstractMarkDuplicatesCommandLineProgramTest.java

@@ -210,6 +210,29 @@ public void testOpticalDuplicatesAndPCRDuplicatesOrientationDifference() {
         tester.runTest();
     }
 
+    @Test
+    // To match picard, when two reads are grouped into a duplicate group and have the same unclipped start position we will unify their orientations
+    // to FR if they point in opposite directions. This test asserts that two pairs of reads that ultimately all map to 93470499-93470499 with clipping
+    // and orientations will ultimately be marked and mapped together even though they have opposite orientations (one is FR while the other is RF).
+    public void testReadSameStartPositionOrientationOverride() {
+        final AbstractMarkDuplicatesTester tester = getTester();
+        tester.setExpectedOpticalDuplicate(0);
+        tester.addMatePair("HJYFJCCXX160204:8:1124:31659:21526",  19, 19, 93470380, 93470499, false, false, false, false, "31S111M9S", "64M87S", true, false, false, false, false, DEFAULT_BASE_QUALITY, "1");  // after clipping these both start on 93470499
+        tester.addMatePair("HJYFJCCXX160204:8:1124:31659:21527",  19, 19, 93470499, 93470380, false, false, true, true, "64M87S", "31S111M9S", false, true, false, false, false, DEFAULT_BASE_QUALITY, "1");  // after clipping these both start on 93470499
+        tester.runTest();
+    }
+
+    @Test
+    // This asserts that we are flipping reads in the Pair object based on both start position and contig index, this does not
+    // make a difference unless the start position is the same across two contigs, so we assert it is handled properly
+    public void testReadsHaveSameStartPositionButDifferentChromosomeNonEquivalence() {
+        final AbstractMarkDuplicatesTester tester = getTester();
+        tester.setExpectedOpticalDuplicate(0);
+        tester.addMatePair("HJYFJCCXX160204:8:1124:31659:21526",  19, 20, 93470380, 93470499, false, false, false, false, "31S111M9S", "64M87S", true, false, false, false, false, DEFAULT_BASE_QUALITY, "1");  // after clipping these both start on 93470499
+        tester.addMatePair("HJYFJCCXX160204:8:1124:31659:21527",  20, 19, 93470499, 93470380, false, false, true, true, "64M87S", "31S111M9S", false, true, false, false, false, DEFAULT_BASE_QUALITY, "1");  // after clipping these both start on 93470499
+        tester.runTest();
+    }
+
     @Test
     public void testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance() {
         final AbstractMarkDuplicatesTester tester = getTester();