Examples with Transition org.broadinstitute.hellbender.tools.picard.analysis.artifacts.Transition used on opensource projects

Example 21 with Transition

use of org.broadinstitute.hellbender.tools.picard.analysis.artifacts.Transition in project gatk-protected by broadinstitute.

the class FilterByOrientationBias method onTraversalSuccess.

@Override
public Object onTraversalSuccess() {
    logger.info("Tagging whether genotypes are in one of the artifact modes.");
    // Calculate how many artifacts need to be cut
    double fdrThreshold = 0.01;
    final List<VariantContext> finalVariants = OrientationBiasFilterer.annotateVariantContextsWithFilterResults(fdrThreshold, relevantTransitions, firstPassVariants, transitionToPreAdapterScoreMap);
    logger.info("Writing variants to VCF...");
    finalVariants.forEach(vcfWriter::add);
    logger.info("Writing a simple summary table...");
    List<String> sampleNames = new ArrayList<>();
    if (finalVariants.size() != 0) {
        sampleNames = finalVariants.get(0).getSampleNamesOrderedByName();
    }
    final List<Pair<String, Transition>> sampleTransitionCombinations = new ArrayList<>();
    for (Transition relevantTransition : relevantTransitions) {
        for (String sampleName : sampleNames) {
            sampleTransitionCombinations.add(Pair.of(sampleName, relevantTransition));
        }
    }
    OrientationBiasUtils.writeOrientationBiasSummaryTable(sampleTransitionCombinations, finalVariants, transitionToPreAdapterScoreMap, new File(outputFile.getAbsolutePath() + SUMMARY_FILE_SUFFIX));
    return null;
}

Example 22 with Transition

use of org.broadinstitute.hellbender.tools.picard.analysis.artifacts.Transition in project gatk by broadinstitute.

the class OrientationBiasFiltererUnitTest method assertArtifact.

private boolean assertArtifact(double amPreAdapterQ, final Genotype genotypeTumor, final Transition transition) {
    final Transition transitionComplement = transition.complement();
    boolean result = false;
    // Check whether this genotype is reverse complement or actual artifact mode
    if (genotypeTumor.getAllele(0).basesMatch(String.valueOf(transition.ref())) && genotypeTumor.getAllele(1).basesMatch(String.valueOf(transition.call()))) {
        // not complement (i.e. artifact mode)
        Assert.assertTrue(genotypeTumor.getExtendedAttribute(OrientationBiasFilterConstants.PRE_ADAPTER_METRIC_RC_FIELD_NAME).equals(OrientationBiasFilterer.PRE_ADAPTER_METRIC_NOT_ARTIFACT_SCORE));
        Assert.assertTrue(genotypeTumor.getExtendedAttribute(OrientationBiasFilterConstants.PRE_ADAPTER_METRIC_FIELD_NAME).equals(amPreAdapterQ));
        Assert.assertEquals(genotypeTumor.getExtendedAttribute(OrientationBiasFilterConstants.IS_ORIENTATION_BIAS_ARTIFACT_MODE), String.valueOf(true));
        Assert.assertEquals(genotypeTumor.getExtendedAttribute(OrientationBiasFilterConstants.IS_ORIENTATION_BIAS_RC_ARTIFACT_MODE), String.valueOf(false));
        result = true;
    } else if (genotypeTumor.getAllele(0).basesMatch(String.valueOf(transitionComplement.ref())) && genotypeTumor.getAllele(1).basesMatch(String.valueOf(transitionComplement.call()))) {
        //complement
        Assert.assertTrue(genotypeTumor.getExtendedAttribute(OrientationBiasFilterConstants.PRE_ADAPTER_METRIC_RC_FIELD_NAME).equals(amPreAdapterQ));
        Assert.assertTrue(genotypeTumor.getExtendedAttribute(OrientationBiasFilterConstants.PRE_ADAPTER_METRIC_FIELD_NAME).equals(OrientationBiasFilterer.PRE_ADAPTER_METRIC_NOT_ARTIFACT_SCORE));
        Assert.assertEquals(genotypeTumor.getExtendedAttribute(OrientationBiasFilterConstants.IS_ORIENTATION_BIAS_ARTIFACT_MODE), String.valueOf(false));
        Assert.assertEquals(genotypeTumor.getExtendedAttribute(OrientationBiasFilterConstants.IS_ORIENTATION_BIAS_RC_ARTIFACT_MODE), String.valueOf(true));
        result = true;
    }
    return result;
}

Example 23 with Transition

use of org.broadinstitute.hellbender.tools.picard.analysis.artifacts.Transition in project gatk by broadinstitute.

the class OrientationBiasFiltererUnitTest method testHighPloidy.

@Test(description = "This test just confirms that the OB filterer does not throw an exception if confronted with high ploidy call.  Also test that it is a superset of the original variant context.")
public void testHighPloidy() {
    final FeatureDataSource<VariantContext> featureDataSource = new FeatureDataSource<>(new File(smallM2HighPloidy));
    // Dummy values for relevant transitions and preAdapter Map
    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);
    for (final VariantContext vc : featureDataSource) {
        final VariantContext updatedVariantContext = OrientationBiasFilterer.annotateVariantContextWithPreprocessingValues(vc, relevantTransitions, preAdapterQFakeScoreMap);
        final Set<String> originalGenotypeAttributes = vc.getGenotype("TUMOR1").getExtendedAttributes().keySet();
        final Set<String> newGenotypeAttributes = updatedVariantContext.getGenotype("TUMOR1").getExtendedAttributes().keySet();
        Assert.assertTrue(newGenotypeAttributes.containsAll(originalGenotypeAttributes));
        Assert.assertTrue(newGenotypeAttributes.size() == (originalGenotypeAttributes.size() + 2));
        for (final String ga : originalGenotypeAttributes) {
            Assert.assertEquals(updatedVariantContext.getGenotype("TUMOR1").getExtendedAttributes().get(ga), vc.getGenotype("TUMOR1").getExtendedAttributes().get(ga));
        }
    }
}

Example 24 with Transition

use of org.broadinstitute.hellbender.tools.picard.analysis.artifacts.Transition in project gatk by broadinstitute.

the class OrientationBiasFiltererUnitTest method testAnnotateVariantContextWithPreprocessingValuesMultiArtifact.

@Test
public void testAnnotateVariantContextWithPreprocessingValuesMultiArtifact() {
    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);
    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");
        // This is mostly just to make sure that nobody breaks the test itself.  I.e. that this test will test all tumor genotype paths be artifact or non-artifact.
        boolean wasGenotypeTumorTested = false;
        // Check whether this genotype is reverse complement or actual artifact mode
        wasGenotypeTumorTested |= assertArtifact(amGTPreAdapterQ, genotypeTumor, relevantTransitions.first());
        wasGenotypeTumorTested |= assertArtifact(amCTPreAdapterQ, genotypeTumor, relevantTransitions.last());
        // Check any variants that are not an artifact mode but are SNP
        if (!OrientationBiasUtils.isGenotypeInTransitionsWithComplement(genotypeTumor, relevantTransitions)) {
            assertNotTransition(genotypeTumor);
            wasGenotypeTumorTested = true;
        } else {
            // Check attributes common to all variants in artifact mode
            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);
        }
        // The NORMAL is always ref/ref in the example file.
        assertNormal(genotypeNormal);
        Assert.assertTrue(wasGenotypeTumorTested, "The test seems to be broken...  A variant context was tested, but it had no tumor genotype.");
    }
}

Example 25 with Transition

use of org.broadinstitute.hellbender.tools.picard.analysis.artifacts.Transition in project gatk by broadinstitute.

the class PreAdapterOrientationScorerUnitTest method testBasicScoring.

/**
     * Note that (due to raw data), this test includes collapsing over libraries (not just the contexts).
     * @throws IOException
     */
@Test
public void testBasicScoring() throws IOException {
    final MetricsFile<SequencingArtifactMetrics.PreAdapterDetailMetrics, Comparable<?>> mf = new MetricsFile<>();
    mf.read(new FileReader(testPreAdapterDetailsMetrics));
    final Map<Transition, Double> scoreMap = PreAdapterOrientationScorer.scoreOrientationBiasMetricsOverContext(mf.getMetrics());
    Assert.assertNotNull(scoreMap);
    Assert.assertEquals(scoreMap.keySet().size(), 12);
    // Ground truth values painstakingly derived manually
    Assert.assertEquals(scoreMap.get(Transition.transitionOf('A', 'C')), 100.0, 1e-6);
    Assert.assertEquals(scoreMap.get(Transition.transitionOf('A', 'G')), 50.5788416297570, 1e-6);
    Assert.assertEquals(scoreMap.get(Transition.transitionOf('A', 'T')), 100.0, 1e-6);
    Assert.assertEquals(scoreMap.get(Transition.transitionOf('C', 'A')), 100.0, 1e-6);
    Assert.assertEquals(scoreMap.get(Transition.transitionOf('C', 'G')), 100.0, 1e-6);
    Assert.assertEquals(scoreMap.get(Transition.transitionOf('C', 'T')), 58.0641821538479, 1e-6);
}