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

Example 21 with FeatureDataSource

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

the class OrientationBiasFiltererUnitTest method testAnnotateVariantContextWithFilterValuesMultiArtifact.

@Test
public void testAnnotateVariantContextWithFilterValuesMultiArtifact() {
    final FeatureDataSource<VariantContext> featureDataSource = new FeatureDataSource<>(new File(smallM2VcfMore));
    SortedSet<Transition> relevantTransitions = new TreeSet<>();
    relevantTransitions.add(Transition.transitionOf('G', 'T'));
    relevantTransitions.add(Transition.transitionOf('C', 'T'));
    final Map<Transition, Double> preAdapterQFakeScoreMap = new HashMap<>();
    final double amGTPreAdapterQ = 20.0;
    final double amCTPreAdapterQ = 25.0;
    // preAdapterQ suppression will do nothing.
    preAdapterQFakeScoreMap.put(relevantTransitions.first(), amGTPreAdapterQ);
    // preAdapterQ suppression will do nothing.
    preAdapterQFakeScoreMap.put(relevantTransitions.last(), amCTPreAdapterQ);
    final List<VariantContext> updatedVariants = new ArrayList<>();
    for (final VariantContext vc : featureDataSource) {
        final VariantContext updatedVariantContext = OrientationBiasFilterer.annotateVariantContextWithPreprocessingValues(vc, relevantTransitions, preAdapterQFakeScoreMap);
        updatedVariants.add(updatedVariantContext);
    }
    final List<String> sampleNames = updatedVariants.get(0).getSampleNamesOrderedByName();
    // Create a mapping from sample name to a genotype->variant context map
    final Map<String, SortedMap<Genotype, VariantContext>> sampleNameToVariants = OrientationBiasFilterer.createSampleToGenotypeVariantContextSortedMap(sampleNames, updatedVariants);
}

Example 22 with FeatureDataSource

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

the class OrientationBiasUtilsUnitTest method testCountNumUnfiltered.

@Test
public void testCountNumUnfiltered() {
    // Setup the test
    final FeatureDataSource<VariantContext> featureDataSource = new FeatureDataSource<>(new File(smallM2VcfMore));
    final List<VariantContext> variantContexts = getVariantContexts(featureDataSource);
    Assert.assertEquals(OrientationBiasUtils.calculateUnfilteredNonRefGenotypeCount(variantContexts, "TUMOR"), 9);
    Assert.assertEquals(OrientationBiasUtils.calculateUnfilteredNonRefGenotypeCount(variantContexts, "NORMAL"), 0);
}

Example 23 with FeatureDataSource

use of org.broadinstitute.hellbender.engine.FeatureDataSource in project gatk-protected 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 24 with FeatureDataSource

use of org.broadinstitute.hellbender.engine.FeatureDataSource 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 25 with FeatureDataSource

use of org.broadinstitute.hellbender.engine.FeatureDataSource 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);
}