fixed an issue where the logic for suffix ends was incorrect for dang…

…ling tails

src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/readthreading/AbstractReadThreadingGraph.java

@@ -588,7 +588,7 @@ final int mergeDanglingTail(final DanglingChainMergeHelper danglingTailMergeResu
 
         final int lastRefIndex = danglingTailMergeResult.cigar.getReferenceLength() - 1;
         final int matchingSuffix = Math.min(longestSuffixMatch(danglingTailMergeResult.referencePathString, danglingTailMergeResult.danglingPathString, lastRefIndex), lastElement.getLength());
-        if (matchingSuffix == 0 && matchingSuffix >= minMatchingBasesToDangingEndRecovery ) {
+        if (minMatchingBasesToDangingEndRecovery >= 0 ? matchingSuffix < minMatchingBasesToDangingEndRecovery : matchingSuffix == 0 ) {
             return 0;
         }
 

src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/readthreading/ReadThreadingGraphUnitTest.java

@@ -339,6 +339,53 @@ public void testDanglingTails(final String refEnd,
         }
     }
 
+    @Test
+    public void testForkedDanglingEndsWithSuffixCode() {
+
+        final int kmerSize = 15;
+
+        // construct the haplotypes
+        final String commonPrefix = "AAAAAAAAAACCCCCCCCCCGGGGGGGGGGTTTTTTTTTT";
+        final String refEnd = "GCTAGCTAATCGTTAAGCTTTAAC";
+        final String altEnd1 = "GCTAGCTAA"+ "GGCG";// two mismatches compared to the reference
+        final String altEnd2 = "GCTAGCTAA"+ "GCCGATGGCT";
+        final String ref = commonPrefix + refEnd;
+        final String alt1 = commonPrefix + altEnd1;
+        final String alt2 = commonPrefix + altEnd2;
+
+        // create the graph and populate it
+        final ReadThreadingGraph rtgraph = new ReadThreadingGraph(kmerSize);
+        rtgraph.addSequence("ref", ref.getBytes(), true);
+        final GATKRead read1 = ArtificialReadUtils.createArtificialRead(alt1.getBytes(), Utils.dupBytes((byte) 30, alt1.length()), alt1.length() + "M");
+        final GATKRead read2 = ArtificialReadUtils.createArtificialRead(alt2.getBytes(), Utils.dupBytes((byte) 30, alt2.length()), alt2.length() + "M");
+        final SAMFileHeader header = ArtificialReadUtils.createArtificialSamHeader();
+        rtgraph.setMinMatchingBasesToDangingEndRecovery(1);
+        rtgraph.addRead(read2, header);
+        rtgraph.addRead(read1, header);
+        rtgraph.buildGraphIfNecessary();
+
+        Assert.assertEquals(rtgraph.getSinks().size(), 3);
+
+        // Testing a degenerate case where the wrong "reference" path is selected and assuring that when
+        for (final MultiDeBruijnVertex altSink : rtgraph.getSinks()) {
+            if (rtgraph.isReferenceNode(altSink) || !altSink.getSequenceString().equals("GCTAAGCCGATGGCT")) {
+                continue;
+            }
+
+            // confirm that the SW alignment agrees with our expectations
+            final ReadThreadingGraph.DanglingChainMergeHelper result = rtgraph.generateCigarAgainstDownwardsReferencePath(altSink,
+                    0, 2, false, SmithWatermanJavaAligner.getInstance());
+            Assert.assertNotNull(result);
+            Assert.assertTrue(ReadThreadingGraph.cigarIsOkayToMerge(result.cigar, false, true));
+
+            Assert.assertEquals(Math.min(AbstractReadThreadingGraph.longestSuffixMatch(result.referencePathString, result.danglingPathString, result.cigar.getReferenceLength() - 1), result.cigar.getCigarElement(0).getLength()), 0);
+
+            // confirm that the tail merging works as expected
+            final int mergeResult = rtgraph.mergeDanglingTail(result);
+            Assert.assertTrue(mergeResult == 0);
+        }
+    }
+
     @Test
     public void testForkedDanglingEnds() {
 

src/test/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2IntegrationTest.java

@@ -14,6 +14,7 @@
 import org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection;
 import org.broadinstitute.hellbender.engine.FeatureDataSource;
 import org.broadinstitute.hellbender.testutils.ArgumentsBuilder;
+import org.broadinstitute.hellbender.testutils.IntegrationTestSpec;
 import org.broadinstitute.hellbender.testutils.VariantContextTestUtils;
 import org.broadinstitute.hellbender.tools.walkers.annotator.AnnotationUtils;
 import org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection;
@@ -549,6 +550,42 @@ public Object[][] vcfsForFiltering() {
         };
     }
 
+    @Test
+    public void testThing() {
+        Utils.resetRandomGenerator();
+
+        //NOTE: AlleleSpecific support in the VCF mode is implemented but bogus for now.
+        // This test should not be treated as a strict check of correctness.
+        final File output = createTempFile("testVCFModeIsConsistentWithPastResults", ".vcf");
+//        final File expected = new File(TEST_FILES_DIR + "expected.testVCFMode.gatk4.alleleSpecific.vcf");
+
+//        final String outputPath = UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS ? expected.getAbsolutePath() : output.getAbsolutePath();
+
+        final String[] args = {
+                "-R",
+                "gs://broad-dsp-spec-ops/scratch/andrea/mtb/Mycobacterium_tuberculosis_H37Rv.fasta",
+                "-I",
+                "gs://broad-dsp-spec-ops-cromwell-execution/MicrobialGenomePipeline/3625b1d1-38a1-40de-a810-23b347d51b14/call-AlignToRef/MicrobialAlignmentPipeline/87d3ba55-4497-474c-9232-44144c7c3ef4/call-AlignAndMarkDuplicates/D1CLVACXX.1.Solexa-125092.aligned.realigned.bam",
+                "-O", output.getAbsolutePath(),
+                "-L", "/Users/emeryj/hellbender/UserLiason/debugM2Graph/Mycobacterium_tuberculosis_H37Rv.intervals",
+                "--annotation","StrandBiasBySample",
+                "--num-matching-bases-in-dangling-end-to-recover",
+                "1",
+                "--max-reads-per-alignment-start",
+                "75",
+                "--max-mnp-distance",
+                "0"};
+
+        runCommandLine(args);
+
+        // Test for an exact match against past results
+//        if ( ! UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS ) {
+//            IntegrationTestSpec.assertEqualTextFiles(output, expected);
+//        }
+
+    }
+
+
     @Test(dataProvider = "vcfsForFiltering")
     public void testFilterMitochondria(File unfiltered, final double minAlleleFraction, final List<String> intervals, List<Set<String>> expectedFilters, List<List<String>> expectedASFilters)  {
         final File filteredVcf = createTempFile("filtered", ".vcf");