integration test for new interpretation tool SvDiscoverFromLocalAssem…

…blyContigAlignmentsSpark

src/main/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/SvDiscoverFromLocalAssemblyContigAlignmentsSpark.java

@@ -126,11 +126,11 @@ public final class SvDiscoverFromLocalAssemblyContigAlignmentsSpark extends GATK
             fullName = "write-sam", optional = true)
     private boolean writeSAMFiles;
 
-    static final String SIMPLE_CHIMERA_VCF_FILE_NAME = "NonComplex.vcf";
-    static final String COMPLEX_CHIMERA_VCF_FILE_NAME = "Complex.vcf";
-    static final String REINTERPRETED_1_SEG_CALL_VCF_FILE_NAME = "cpx_reinterpreted_simple_1_seg.vcf";
-    static final String REINTERPRETED_MULTI_SEG_CALL_VCF_FILE_NAME = "cpx_reinterpreted_simple_multi_seg.vcf";
-    static final String MERGED_VCF_FILE_NAME = "merged_simple.vcf";
+    public static final String SIMPLE_CHIMERA_VCF_FILE_NAME = "NonComplex.vcf";
+    public static final String COMPLEX_CHIMERA_VCF_FILE_NAME = "Complex.vcf";
+    public static final String REINTERPRETED_1_SEG_CALL_VCF_FILE_NAME = "cpx_reinterpreted_simple_1_seg.vcf";
+    public static final String REINTERPRETED_MULTI_SEG_CALL_VCF_FILE_NAME = "cpx_reinterpreted_simple_multi_seg.vcf";
+    public static final String MERGED_VCF_FILE_NAME = "merged_simple.vcf";
 
     @Override
     public boolean requiresReference() {

src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/StructuralVariationDiscoveryPipelineSparkIntegrationTest.java

@@ -180,14 +180,20 @@ static void svDiscoveryVCFEquivalenceTest(final String generatedVCFPath, final S
                                               final String experimentalOutputPathForNonComplex,
                                               final List<String> attributesToIgnore, final boolean onHDFS) throws Exception {
 
-        List<VariantContext> expectedVcs;
-        try (final VCFFileReader fileReader = new VCFFileReader(new File(expectedVCFPath), false) ) {
-            try (final CloseableIterator<VariantContext> iterator = fileReader.iterator()) {
-                expectedVcs = Utils.stream(iterator).collect(Collectors.toList());
+        final List<VariantContext> expectedVcs;
+        if (expectedVCFPath == null) {
+            expectedVcs = Collections.emptyList();
+        } else {
+            try (final VCFFileReader fileReader = new VCFFileReader(new File(expectedVCFPath), false)) {
+                try (final CloseableIterator<VariantContext> iterator = fileReader.iterator()) {
+                    expectedVcs = Utils.stream(iterator).collect(Collectors.toList());
+                }
             }
         }
 
         List<VariantContext> actualVcs = extractActualVCs(generatedVCFPath, onHDFS);
+        if (expectedVCFPath == null)
+            Assert.assertTrue(actualVcs.isEmpty());
 
         GATKBaseTest.assertCondition(actualVcs, expectedVcs,
                 (a, e) -> VariantContextTestUtils.assertVariantContextsAreEqual(a, e, attributesToIgnore));

src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest.java

@@ -0,0 +1,152 @@
+package org.broadinstitute.hellbender.tools.spark.sv.integration;
+
+import org.broadinstitute.hellbender.CommandLineProgramTest;
+import org.broadinstitute.hellbender.GATKBaseTest;
+import org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoverFromLocalAssemblyContigAlignmentsSpark;
+import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
+
+public class SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest extends CommandLineProgramTest {
+
+    private static final String REFERENCE = largeFileTestDir + "/Homo_sapiens_assembly38.20.21.2bit";
+    private static final String NON_CANONICAL_CHROMOSOMES = toolsTestDir + "spark/sv/integration/inputs/Homo_sapiens_assembly38.kill.alts";
+
+    private static final String THIS_TEST_DIR = largeFileTestDir + "/sv/";
+    private static final String TEST_SAMPLE_NAME = "SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTestSample";
+
+    // TODO: 8/15/18 this split between cases of BND variant and "symbolic" variants is temporary because of restraint placed by access to only chr20 and chr21 (BND variant are lacking cases); in the long run we'd prefer to merge them
+    private static final String SYMBOLIC_ASSEMBLY_BAM = THIS_TEST_DIR + "SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest.bam";
+    private static final String SYMBOLIC_EXPECTED_SIMPLE_CHIMERA_VCF = THIS_TEST_DIR + "SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest_NonComplex.vcf";
+    private static final String SYMBOLIC_EXPECTED_COMPLEX_CHIMERA_VCF = THIS_TEST_DIR + "SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest_Complex.vcf";
+    private static final String SYMBOLIC_EXPECTED_CPX_RETERINTERPRETATION_1_SEG_VCF = THIS_TEST_DIR + "SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest_cpx_reinterpreted_simple_1_seg.vcf";
+    private static final String SYMBOLIC_EXPECTED_CPX_RETERINTERPRETATION_MULTI_SEG_VCF = THIS_TEST_DIR + "SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest_cpx_reinterpreted_simple_multi_seg.vcf";
+    private static final String SYMBOLIC_EXPECTED_MERGED_SIMPLE_VCF = THIS_TEST_DIR + "SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest_merged_simple.vcf";
+
+    private static final String BND_ASSEMBLY_BAM = THIS_TEST_DIR + "forBND_SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest.bam";
+    private static final String BND_EXPECTED_SIMPLE_CHIMERA_VCF = THIS_TEST_DIR + "forBND_SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest_NonComplex.vcf";
+    private static final String BND_EXPECTED_MERGED_SIMPLE_VCF = THIS_TEST_DIR + "forBND_SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest_merged_simple.vcf";
+
+    private static final class TestArgs {
+
+        final String outputDir;
+        final String twoBitReference;
+        final String altContigsFile;
+        final String assemblyBam;
+        final String cnvCallsLoc;
+
+        TestArgs(final String workingDir, final String twoBitReference, final String altContigsFile, final String assemblyBam, final String cnvCallsLoc) {
+            this.outputDir = workingDir.endsWith("/") ? workingDir : workingDir + "/";
+            this.twoBitReference = twoBitReference;
+            this.altContigsFile = altContigsFile;
+            this.assemblyBam = assemblyBam;
+            this.cnvCallsLoc = cnvCallsLoc;
+        }
+
+        String getCommandLine() {
+            return  " --debug-mode " +
+                    " -R " + twoBitReference +
+                    " -I " + assemblyBam +
+                    " -O " + outputDir +
+                    (altContigsFile == null ? "" : " -alt-tigs " + altContigsFile) +
+                    (cnvCallsLoc == null ? "" : " --cnv-calls " + cnvCallsLoc);
+        }
+
+        String getOutputDir() {
+            return outputDir;
+        }
+    }
+
+    @DataProvider(name = "svDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest")
+    public Object[][] createTestData() {
+        final File tempDir = GATKBaseTest.createTempDir("symb");
+        tempDir.deleteOnExit();
+
+        final List<Object[]> tests = new ArrayList<>(2);
+        final TestArgs testArgs = new TestArgs(tempDir.getAbsolutePath(), REFERENCE, NON_CANONICAL_CHROMOSOMES,
+                SYMBOLIC_ASSEMBLY_BAM, null);
+        tests.add(new Object[]{testArgs,
+                SYMBOLIC_EXPECTED_SIMPLE_CHIMERA_VCF,
+                SYMBOLIC_EXPECTED_COMPLEX_CHIMERA_VCF,
+                SYMBOLIC_EXPECTED_CPX_RETERINTERPRETATION_1_SEG_VCF,
+                SYMBOLIC_EXPECTED_CPX_RETERINTERPRETATION_MULTI_SEG_VCF,
+                SYMBOLIC_EXPECTED_MERGED_SIMPLE_VCF
+        });
+
+        final File tempDir1 = GATKBaseTest.createTempDir("bnd");
+        tempDir1.deleteOnExit();
+        final TestArgs testArgs1 = new TestArgs(tempDir1.getAbsolutePath(), REFERENCE, NON_CANONICAL_CHROMOSOMES,
+                BND_ASSEMBLY_BAM, null);
+        tests.add(new Object[]{testArgs1,
+                BND_EXPECTED_SIMPLE_CHIMERA_VCF,
+                null,
+                null,
+                null,
+                BND_EXPECTED_MERGED_SIMPLE_VCF
+        });
+
+        return tests.toArray(new Object[][]{});
+    }
+
+    @Test(dataProvider = "svDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest", groups = "sv")
+    public void testDiscoverVariantsRunnableLocal(final TestArgs params, final String expectedSimpleChimeraFilePath,
+                                                  final String expectedComplexFilePath, final String expectedReInterpretationOneSegFilePath, final String expectedReInterPretationMultiSegFilePath,
+                                                  final String expectedMergedSimpleFilePath) throws Exception {
+
+        final List<String> args = Arrays.asList( new ArgumentsBuilder().add(params.getCommandLine()).getArgsArray() );
+        runCommandLine(args);
+
+        final String outputDir = params.getOutputDir();
+
+        final String simpleChimeraVCF = outputDir + TEST_SAMPLE_NAME + "_" + SvDiscoverFromLocalAssemblyContigAlignmentsSpark.SIMPLE_CHIMERA_VCF_FILE_NAME;
+        StructuralVariationDiscoveryPipelineSparkIntegrationTest
+                .svDiscoveryVCFEquivalenceTest(
+                        simpleChimeraVCF,
+                        expectedSimpleChimeraFilePath,
+                        null,
+                        Collections.emptyList(),
+                        false);
+
+        final String complexChimeraVCF = outputDir + TEST_SAMPLE_NAME + "_" + SvDiscoverFromLocalAssemblyContigAlignmentsSpark.COMPLEX_CHIMERA_VCF_FILE_NAME;
+        StructuralVariationDiscoveryPipelineSparkIntegrationTest
+                .svDiscoveryVCFEquivalenceTest(
+                        complexChimeraVCF,
+                        expectedComplexFilePath,
+                        null,
+                        Collections.emptyList(),
+                        false);
+
+        final String cpxReInterpretOneSegVCF = outputDir + TEST_SAMPLE_NAME + "_" + SvDiscoverFromLocalAssemblyContigAlignmentsSpark.REINTERPRETED_1_SEG_CALL_VCF_FILE_NAME;
+        StructuralVariationDiscoveryPipelineSparkIntegrationTest
+                .svDiscoveryVCFEquivalenceTest(
+                        cpxReInterpretOneSegVCF,
+                        expectedReInterpretationOneSegFilePath,
+                        null,
+                        Collections.emptyList(),
+                        false);
+
+        final String cpxReInterpretMultiSegVCF = outputDir + TEST_SAMPLE_NAME + "_" + SvDiscoverFromLocalAssemblyContigAlignmentsSpark.REINTERPRETED_MULTI_SEG_CALL_VCF_FILE_NAME;
+        StructuralVariationDiscoveryPipelineSparkIntegrationTest
+                .svDiscoveryVCFEquivalenceTest(
+                        cpxReInterpretMultiSegVCF,
+                        expectedReInterPretationMultiSegFilePath,
+                        null,
+                        Collections.emptyList(),
+                        false);
+
+        final String mergedSimpleVCF = outputDir + TEST_SAMPLE_NAME + "_" + SvDiscoverFromLocalAssemblyContigAlignmentsSpark.MERGED_VCF_FILE_NAME;
+        StructuralVariationDiscoveryPipelineSparkIntegrationTest
+                .svDiscoveryVCFEquivalenceTest(
+                        mergedSimpleVCF,
+                        expectedMergedSimpleFilePath,
+                        null,
+                        Collections.emptyList(),
+                        false);
+    }
+}