From f5c1478f4a6225ea520c7e942d4f7f4e7c05d921 Mon Sep 17 00:00:00 2001 From: Steve Huang Date: Wed, 18 Apr 2018 09:15:18 -0400 Subject: [PATCH] integration test for new interpretation tool SvDiscoverFromLocalAssemblyContigAlignmentsSpark --- ...romLocalAssemblyContigAlignmentsSpark.java | 10 +- ...DiscoveryPipelineSparkIntegrationTest.java | 14 +- ...yContigAlignmentsSparkIntegrationTest.java | 152 ++++++++++++++++++ .../large/Homo_sapiens_assembly38.20.21.2bit | 3 + .../Homo_sapiens_assembly38.20.21.fasta.img | 3 + ...lyContigAlignmentsSparkIntegrationTest.bam | 3 + ...ntigAlignmentsSparkIntegrationTest.bam.bai | 3 + ...AlignmentsSparkIntegrationTest_Complex.vcf | 3 + ...gnmentsSparkIntegrationTest_NonComplex.vcf | 3 + ...ionTest_cpx_reinterpreted_simple_1_seg.vcf | 3 + ...est_cpx_reinterpreted_simple_multi_seg.vcf | 3 + ...entsSparkIntegrationTest_merged_simple.vcf | 3 + ...lyContigAlignmentsSparkIntegrationTest.bam | 3 + ...gnmentsSparkIntegrationTest_NonComplex.vcf | 3 + ...entsSparkIntegrationTest_merged_simple.vcf | 3 + 15 files changed, 203 insertions(+), 9 deletions(-) create mode 100644 src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest.java create mode 100644 src/test/resources/large/Homo_sapiens_assembly38.20.21.2bit create mode 100644 src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta.img create mode 100644 src/test/resources/large/sv/SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest.bam create mode 100644 src/test/resources/large/sv/SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest.bam.bai create mode 100644 src/test/resources/large/sv/SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest_Complex.vcf create mode 100644 src/test/resources/large/sv/SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest_NonComplex.vcf create mode 100644 src/test/resources/large/sv/SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest_cpx_reinterpreted_simple_1_seg.vcf create mode 100644 src/test/resources/large/sv/SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest_cpx_reinterpreted_simple_multi_seg.vcf create mode 100644 src/test/resources/large/sv/SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest_merged_simple.vcf create mode 100644 src/test/resources/large/sv/forBND_SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest.bam create mode 100644 src/test/resources/large/sv/forBND_SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest_NonComplex.vcf create mode 100644 src/test/resources/large/sv/forBND_SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest_merged_simple.vcf diff --git a/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/SvDiscoverFromLocalAssemblyContigAlignmentsSpark.java b/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/SvDiscoverFromLocalAssemblyContigAlignmentsSpark.java index 4d8a51ca1c0..c745a4cadbe 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/SvDiscoverFromLocalAssemblyContigAlignmentsSpark.java +++ b/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() { diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/StructuralVariationDiscoveryPipelineSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/StructuralVariationDiscoveryPipelineSparkIntegrationTest.java index d9fa304cd5e..787417cfe6e 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/StructuralVariationDiscoveryPipelineSparkIntegrationTest.java +++ b/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 attributesToIgnore, final boolean onHDFS) throws Exception { - List expectedVcs; - try (final VCFFileReader fileReader = new VCFFileReader(new File(expectedVCFPath), false) ) { - try (final CloseableIterator iterator = fileReader.iterator()) { - expectedVcs = Utils.stream(iterator).collect(Collectors.toList()); + final List expectedVcs; + if (expectedVCFPath == null) { + expectedVcs = Collections.emptyList(); + } else { + try (final VCFFileReader fileReader = new VCFFileReader(new File(expectedVCFPath), false)) { + try (final CloseableIterator iterator = fileReader.iterator()) { + expectedVcs = Utils.stream(iterator).collect(Collectors.toList()); + } } } List actualVcs = extractActualVCs(generatedVCFPath, onHDFS); + if (expectedVCFPath == null) + Assert.assertTrue(actualVcs.isEmpty()); GATKBaseTest.assertCondition(actualVcs, expectedVcs, (a, e) -> VariantContextTestUtils.assertVariantContextsAreEqual(a, e, attributesToIgnore)); diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest.java new file mode 100644 index 00000000000..43479bc3493 --- /dev/null +++ b/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 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 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); + } +} diff --git a/src/test/resources/large/Homo_sapiens_assembly38.20.21.2bit b/src/test/resources/large/Homo_sapiens_assembly38.20.21.2bit new file mode 100644 index 00000000000..72c4c41e5c9 --- /dev/null +++ b/src/test/resources/large/Homo_sapiens_assembly38.20.21.2bit @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:30547cea0b580cbce65fabaebb0e50467936add7abafadfcd1e91101d8229936 +size 28124856 diff --git a/src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta.img b/src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta.img new file mode 100644 index 00000000000..4eeae4705c2 --- /dev/null +++ b/src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta.img @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:8025332f14722f86977761d192955d50bb76c7d00720b4fd3c983c895c7073ad +size 196868832 diff --git a/src/test/resources/large/sv/SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest.bam b/src/test/resources/large/sv/SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest.bam new file mode 100644 index 00000000000..ba54a28e278 --- /dev/null +++ b/src/test/resources/large/sv/SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest.bam @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid 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b/src/test/resources/large/sv/SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest_Complex.vcf @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a071b7cbecfbd3719209e4f7f881e84a41b7c03a15c50aed25d83bbf8b74438e +size 232077 diff --git a/src/test/resources/large/sv/SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest_NonComplex.vcf b/src/test/resources/large/sv/SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest_NonComplex.vcf new file mode 100644 index 00000000000..2a185c96b9d --- /dev/null +++ b/src/test/resources/large/sv/SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest_NonComplex.vcf @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:7934d1b33d4da513fc371fc0afd143ab2134c8bb35479b1b481496e82838c527 +size 229044 diff --git a/src/test/resources/large/sv/SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest_cpx_reinterpreted_simple_1_seg.vcf b/src/test/resources/large/sv/SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest_cpx_reinterpreted_simple_1_seg.vcf new file mode 100644 index 00000000000..685836bb09f --- /dev/null +++ b/src/test/resources/large/sv/SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest_cpx_reinterpreted_simple_1_seg.vcf @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:46a0df6c2e30dfad47c281177828aff2fe55f4fbaddf5aa341bbd14b8265ca5e +size 218475 diff --git a/src/test/resources/large/sv/SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest_cpx_reinterpreted_simple_multi_seg.vcf b/src/test/resources/large/sv/SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest_cpx_reinterpreted_simple_multi_seg.vcf new file mode 100644 index 00000000000..bdd3c497211 --- /dev/null +++ b/src/test/resources/large/sv/SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest_cpx_reinterpreted_simple_multi_seg.vcf @@ -0,0 +1,3 @@ +version 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