Innocuous housekeeping changes in the partially determined haplotypes code

src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/PartiallyDeterminedHaplotypeComputationEngine.java

@@ -420,18 +420,15 @@ private static List<List<Event>> smithWatermanRealignPairsOfVariantsForEquivalen
      * at the same base.
      *
      */
+    @VisibleForTesting
     static boolean eventsOverlapForPDHapsCode(Event e1, Event e2){
         if (!e1.getContig().equals(e2.getContig())) {
             return false;
         }
 
-        double start1 = dragenStart(e1);
         double end1 = e1.getEnd() + (e1.isSimpleInsertion() ? 0.5 : 0);
-        double start2 = dragenStart(e2);
         double end2 = e2.getEnd() + (e2.isSimpleInsertion() ? 0.5 : 0);
-
-        //Pulled directly from CoordMath.java (not using here because of doubles)
-        return (start2 >= start1 && start2 <= end1) || (end2 >=start1 && end2 <= end1) || start1 >= start2 && end1 <= end2;
+        return !(dragenStart(e1) > end2 || dragenStart(e2) > end1);
     }
 
 

src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/PartiallyDeterminedHaplotypeComputationEngineUnitTest.java

@@ -16,6 +16,7 @@
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.List;
+import java.util.function.BiPredicate;
 
 public class PartiallyDeterminedHaplotypeComputationEngineUnitTest extends GATKBaseTest {
 
@@ -214,4 +215,42 @@ public void testDeletionUnderlapingDeterminedBases() {
         Assert.assertEquals(result.getCigar(), TextCigarCodec.decode("10M"));
         Assert.assertEquals(result.getDeterminedPosition(), DEL_AA_105.getStart());
     }
+
+    @Test
+    public void testEventsOverlapForPDHapsCode() {
+        final BiPredicate<Event, Event> overlaps = ((e1, e2) -> PartiallyDeterminedHaplotypeComputationEngine.eventsOverlapForPDHapsCode(e1,e2));
+
+        // easy SNP cases
+        Assert.assertFalse(overlaps.test(SNP_C_100, SNP_G_101));
+        Assert.assertFalse(overlaps.test(SNP_C_100, SNP_G_102));
+        Assert.assertFalse(overlaps.test(SNP_C_107, SNP_G_105));
+        Assert.assertTrue(overlaps.test(SNP_C_105, SNP_G_105));
+        Assert.assertTrue(overlaps.test(SNP_T_106, SNP_T_106));
+
+        // overlap of SNP and deletion -- note that we add 1 to deletion start but not to deletion end
+        Assert.assertFalse(overlaps.test(DEL_AAA_102, SNP_G_101));
+        Assert.assertFalse(overlaps.test(DEL_AAA_102, SNP_G_102));
+        Assert.assertTrue(overlaps.test(DEL_AAA_102, SNP_C_104));
+        Assert.assertFalse(overlaps.test(DEL_AAA_102, SNP_C_105));
+
+        // overlap of SNP and insertion -- note that we add 0.5 to insertion start and end
+        Assert.assertFalse(overlaps.test(SNP_G_102, INS_TT_103));
+        Assert.assertFalse(overlaps.test(SNP_C_104, INS_TT_103));
+        Assert.assertFalse(overlaps.test(SNP_C_105, INS_TT_105));
+
+        // two insertions should overlap only if they occur at the same position
+        Assert.assertTrue(overlaps.test(INS_TT_105, INS_TT_105));
+        Assert.assertFalse(overlaps.test(INS_TT_105, INS_GGG_106));
+
+        // two deletions
+        Assert.assertTrue(overlaps.test(DEL_AAAAAAA_102, DEL_AAA_102));
+        Assert.assertTrue(overlaps.test(DEL_AA_105, DEL_AAAAAAA_102));
+        Assert.assertFalse(overlaps.test(DEL_AA_100, DEL_AAA_102));
+
+        // deletion and insertion
+        Assert.assertFalse(overlaps.test(INS_TT_105, DEL_AA_105));  // add 1 to deletion start but only 0.5 to insertion end
+        Assert.assertFalse(overlaps.test(INS_TT_103, DEL_AA_105));
+        Assert.assertTrue(overlaps.test(DEL_AAAAAAA_102, INS_GGG_106));
+        Assert.assertTrue(overlaps.test(INS_TT_103, DEL_AAA_102));
+    }
 }