Examples with FeatureDataSource org.broadinstitute.hellbender.engine.FeatureDataSource used on opensource projects

Example 6 with FeatureDataSource

use of org.broadinstitute.hellbender.engine.FeatureDataSource in project gatk by broadinstitute.

the class OrientationBiasFiltererUnitTest method testAnnotateVariantContextWithPreprocessingValues.

@Test
public void testAnnotateVariantContextWithPreprocessingValues() {
    final FeatureDataSource<VariantContext> featureDataSource = new FeatureDataSource<>(new File(smallM2Vcf));
    SortedSet<Transition> relevantTransitions = new TreeSet<>();
    relevantTransitions.add(Transition.transitionOf('G', 'T'));
    final Map<Transition, Double> preAdapterQFakeScoreMap = new HashMap<>();
    final double amGTPreAdapterQ = 20.0;
    // preAdapterQ suppression will do nothing.
    preAdapterQFakeScoreMap.put(Transition.transitionOf('G', 'T'), amGTPreAdapterQ);
    for (final VariantContext vc : featureDataSource) {
        final VariantContext updatedVariantContext = OrientationBiasFilterer.annotateVariantContextWithPreprocessingValues(vc, relevantTransitions, preAdapterQFakeScoreMap);
        final Genotype genotypeTumor = updatedVariantContext.getGenotype("TUMOR");
        final Genotype genotypeNormal = updatedVariantContext.getGenotype("NORMAL");
        Assert.assertNotEquals(genotypeTumor.getExtendedAttribute(OrientationBiasFilterConstants.FOB, VCFConstants.EMPTY_ALLELE), VCFConstants.EMPTY_ALLELE);
        Assert.assertNotEquals(genotypeTumor.getExtendedAttribute(OrientationBiasFilterConstants.P_ARTIFACT_FIELD_NAME, VCFConstants.EMPTY_ALLELE), VCFConstants.EMPTY_ALLELE);
        assertArtifact(amGTPreAdapterQ, genotypeTumor, Transition.transitionOf('G', 'T'));
        // The NORMAL is always ref/ref in the example file.
        assertNormal(genotypeNormal);
    }
}

Example 7 with FeatureDataSource

use of org.broadinstitute.hellbender.engine.FeatureDataSource in project gatk by broadinstitute.

the class OrientationBiasUtilsUnitTest method testCountNumTransition.

@Test
public void testCountNumTransition() {
    // Setup the test
    final FeatureDataSource<VariantContext> featureDataSource = new FeatureDataSource<>(new File(smallM2VcfMore));
    SortedSet<Transition> relevantTransitions = new TreeSet<>();
    relevantTransitions.add(Transition.transitionOf('T', 'A'));
    final List<VariantContext> variantContexts = getVariantContexts(featureDataSource);
    // Should be one, since one of the variants was filtered.
    Assert.assertEquals(OrientationBiasUtils.calculateNumTransition("TUMOR", variantContexts, relevantTransitions.first()), 1);
    Assert.assertEquals(OrientationBiasUtils.calculateNumTransition("NORMAL", variantContexts, relevantTransitions.first()), 0);
}

Example 8 with FeatureDataSource

use of org.broadinstitute.hellbender.engine.FeatureDataSource in project gatk by broadinstitute.

the class HaplotypeCallerIntegrationTest method calculateConcordance.

/*
     * Calculate rough concordance between two vcfs, comparing only the positions, alleles, and the first genotype.
     */
public static double calculateConcordance(final File actual, final File expected) {
    final Set<String> actualVCFKeys = new HashSet<>();
    final Set<String> expectedVCFKeys = new HashSet<>();
    int concordant = 0;
    int discordant = 0;
    try (final FeatureDataSource<VariantContext> actualSource = new FeatureDataSource<>(actual);
        final FeatureDataSource<VariantContext> expectedSource = new FeatureDataSource<>(expected)) {
        for (final VariantContext vc : actualSource) {
            actualVCFKeys.add(keyForVariant(vc));
        }
        for (final VariantContext vc : expectedSource) {
            expectedVCFKeys.add(keyForVariant(vc));
        }
        for (final String vcKey : actualVCFKeys) {
            if (!expectedVCFKeys.contains(vcKey)) {
                ++discordant;
            } else {
                ++concordant;
            }
        }
        for (final String vcKey : expectedVCFKeys) {
            if (!actualVCFKeys.contains(vcKey)) {
                ++discordant;
            }
        }
    }
    return (double) concordant / (double) (concordant + discordant);
}

Example 9 with FeatureDataSource

use of org.broadinstitute.hellbender.engine.FeatureDataSource in project gatk-protected by broadinstitute.

the class FilterByOrientationBiasIntegrationTest method testRun.

@Test
public void testRun() throws IOException {
    final File outputFile = File.createTempFile("ob_", ".vcf");
    final List<String> arguments = new ArrayList<>();
    arguments.add("-" + FilterByOrientationBias.PRE_ADAPTER_METRICS_DETAIL_FILE_SHORT_NAME);
    arguments.add(preAdapterQFile);
    arguments.add("-" + StandardArgumentDefinitions.VARIANT_SHORT_NAME);
    arguments.add(smallM2VcfMore);
    arguments.add("-" + StandardArgumentDefinitions.OUTPUT_SHORT_NAME);
    arguments.add(outputFile.getAbsolutePath());
    runCommandLine(arguments);
    Assert.assertTrue(outputFile.exists());
    final File summaryFile = new File(outputFile.getAbsolutePath() + FilterByOrientationBias.SUMMARY_FILE_SUFFIX);
    Assert.assertTrue(summaryFile.exists());
    final List<VariantContext> variantContexts = new ArrayList<>();
    final FeatureDataSource<VariantContext> featureDataSource = new FeatureDataSource<>(outputFile);
    for (final VariantContext vc : featureDataSource) {
        variantContexts.add(vc);
    }
    Assert.assertEquals(variantContexts.size(), 11);
    Assert.assertTrue(FileUtils.sizeOf(outputFile) > 0);
    Assert.assertTrue(FileUtils.sizeOf(summaryFile) > 0);
    boolean is_variant_context_tested = false;
    //  Also, make sure that the variant context has the filter as well.  Not just the genotypes.
    for (final VariantContext vc : variantContexts) {
        final Genotype tumorGenotype = vc.getGenotype("TUMOR");
        Assert.assertTrue((tumorGenotype.getFilters() == null) || (tumorGenotype.getFilters().contains(OrientationBiasFilterConstants.IS_ORIENTATION_BIAS_CUT)) || !OrientationBiasUtils.isGenotypeInTransitionWithComplement(tumorGenotype, Transition.transitionOf('G', 'T')));
        // If we see a filtered genotype, make sure the variant context was filtered as well.
        if ((tumorGenotype.getFilters() != null) && (tumorGenotype.getFilters().contains(OrientationBiasFilterConstants.IS_ORIENTATION_BIAS_CUT))) {
            Assert.assertTrue(vc.getFilters().contains(OrientationBiasFilterConstants.IS_ORIENTATION_BIAS_CUT));
            is_variant_context_tested = true;
        }
        final Genotype normalGenotype = vc.getGenotype("NORMAL");
        Assert.assertTrue((normalGenotype.getFilters() == null) || normalGenotype.getFilters().equals(VCFConstants.UNFILTERED) || normalGenotype.getFilters().equals(VCFConstants.PASSES_FILTERS_v4));
    }
    Assert.assertTrue(is_variant_context_tested, "Unit test may be broken.  Should have tested that variant context contained filter as well as genotype fields.");
    final List<OrientationSampleTransitionSummary> summaries = OrientationBiasUtils.readOrientationBiasSummaryTable(summaryFile);
    Assert.assertEquals(summaries.size(), 2);
    Assert.assertEquals(summaries.stream().filter(s -> s.getSample().equals("NORMAL")).count(), 1);
    Assert.assertEquals(summaries.stream().filter(s -> s.getSample().equals("TUMOR")).count(), 1);
    Assert.assertEquals(summaries.stream().filter(s -> s.getSample().equals("NORMAL")).map(s -> s.getArtifactMode()).filter(am -> am.equals(Transition.GtoT)).count(), 1);
    Assert.assertEquals(summaries.stream().filter(s -> s.getSample().equals("NORMAL")).map(s -> s.getArtifactModeComplement()).filter(am -> am.equals(Transition.CtoA)).count(), 1);
    Assert.assertEquals(summaries.stream().filter(s -> s.getSample().equals("TUMOR")).map(s -> s.getArtifactMode()).filter(am -> am.equals(Transition.GtoT)).count(), 1);
    Assert.assertEquals(summaries.stream().filter(s -> s.getSample().equals("TUMOR")).map(s -> s.getArtifactModeComplement()).filter(am -> am.equals(Transition.CtoA)).count(), 1);
    Assert.assertEquals(summaries.stream().filter(s -> s.getArtifactModeComplement().equals(s.getArtifactMode().complement())).count(), summaries.size());
    Assert.assertEquals(summaries.stream().filter(s -> s.getSample().equals("TUMOR")).map(s -> s.getArtifactModeComplement()).filter(am -> am.equals(Transition.CtoA)).count(), 1);
}

Example 10 with FeatureDataSource

use of org.broadinstitute.hellbender.engine.FeatureDataSource in project gatk-protected by broadinstitute.

the class FilterByOrientationBiasIntegrationTest method testNoVariantsRun.

@Test
public void testNoVariantsRun() throws IOException {
    final File outputFile = File.createTempFile("ob_no_variants", ".vcf");
    final List<String> arguments = new ArrayList<>();
    arguments.add("-" + FilterByOrientationBias.PRE_ADAPTER_METRICS_DETAIL_FILE_SHORT_NAME);
    arguments.add(preAdapterQFile);
    arguments.add("-" + StandardArgumentDefinitions.VARIANT_SHORT_NAME);
    arguments.add(emptyVcf);
    arguments.add("-" + StandardArgumentDefinitions.OUTPUT_SHORT_NAME);
    arguments.add(outputFile.getAbsolutePath());
    runCommandLine(arguments);
    Assert.assertTrue(outputFile.exists());
    final List<VariantContext> variantContexts = new ArrayList<>();
    final FeatureDataSource<VariantContext> featureDataSource = new FeatureDataSource<>(outputFile);
    for (final VariantContext vc : featureDataSource) {
        variantContexts.add(vc);
    }
    Assert.assertEquals(variantContexts.size(), 0);
    final File summaryFile = new File(outputFile.getAbsolutePath() + FilterByOrientationBias.SUMMARY_FILE_SUFFIX);
    Assert.assertTrue(summaryFile.exists());
    Assert.assertTrue(FileUtils.sizeOf(outputFile) > 0);
    Assert.assertTrue(FileUtils.sizeOf(summaryFile) > 0);
    final List<OrientationSampleTransitionSummary> summaries = OrientationBiasUtils.readOrientationBiasSummaryTable(summaryFile);
    Assert.assertEquals(summaries.size(), 0);
}