Examples with OrientationSampleTransitionSummary org.broadinstitute.hellbender.tools.exome.orientationbiasvariantfilter.OrientationSampleTransitionSummary used on opensource projects

Example 1 with OrientationSampleTransitionSummary

use of org.broadinstitute.hellbender.tools.exome.orientationbiasvariantfilter.OrientationSampleTransitionSummary 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 2 with OrientationSampleTransitionSummary

use of org.broadinstitute.hellbender.tools.exome.orientationbiasvariantfilter.OrientationSampleTransitionSummary 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);
}

Example 3 with OrientationSampleTransitionSummary

use of org.broadinstitute.hellbender.tools.exome.orientationbiasvariantfilter.OrientationSampleTransitionSummary in project gatk by broadinstitute.

the class FilterByOrientationBiasIntegrationTest method testNoVariantsNoSamplesRun.

@Test
public void testNoVariantsNoSamplesRun() throws IOException {
    final File outputFile = File.createTempFile("ob_no_variants_no_sample", ".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(emptyVcfNoSamples);
    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);
    Assert.assertTrue(FileUtils.sizeOf(outputFile) > 0);
    final File summaryFile = new File(outputFile.getAbsolutePath() + FilterByOrientationBias.SUMMARY_FILE_SUFFIX);
    Assert.assertTrue(summaryFile.exists());
    Assert.assertTrue(FileUtils.sizeOf(summaryFile) > 0);
    final List<OrientationSampleTransitionSummary> summaries = OrientationBiasUtils.readOrientationBiasSummaryTable(summaryFile);
    Assert.assertEquals(summaries.size(), 0);
}

Example 4 with OrientationSampleTransitionSummary

use of org.broadinstitute.hellbender.tools.exome.orientationbiasvariantfilter.OrientationSampleTransitionSummary in project gatk 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);
}

Example 5 with OrientationSampleTransitionSummary

use of org.broadinstitute.hellbender.tools.exome.orientationbiasvariantfilter.OrientationSampleTransitionSummary in project gatk 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);
}