Examples with VariantContext htsjdk.variant.variantcontext.VariantContext used on opensource projects

Example 1 with VariantContext

use of htsjdk.variant.variantcontext.VariantContext in project gatk by broadinstitute.

the class FilterByOrientationBias method apply.

/**
     *  Just adds the Pre Adapter Q annotation to the variant and creates a new variant.
     *
     *  Note: the writing of the VCF is not done here, since we need to aggregate once we have OxoQ scores.
     *  Note:  No variant is dropped, if no additional annotation was needed, then the original format field is
     *   preserved
     * @param variant See {@link VariantWalker}
     * @param readsContext See {@link VariantWalker}
     * @param referenceContext See {@link VariantWalker}
     * @param featureContext See {@link VariantWalker}
     */
@Override
public void apply(VariantContext variant, ReadsContext readsContext, ReferenceContext referenceContext, FeatureContext featureContext) {
    final VariantContext updatedVariant = OrientationBiasFilterer.annotateVariantContextWithPreprocessingValues(variant, relevantTransitions, transitionToPreAdapterScoreMap);
    firstPassVariants.add(updatedVariant);
// See onTraversalSuccess for the actual filtering.
}

Example 2 with VariantContext

use of htsjdk.variant.variantcontext.VariantContext in project gatk 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 3 with VariantContext

use of htsjdk.variant.variantcontext.VariantContext in project gatk by broadinstitute.

the class SVVCFWriter method writeVCF.

/**
     * FASTA and Broadcast references are both required because 2bit Broadcast references currently order their
     * sequence dictionaries in a scrambled order, see https://github.com/broadinstitute/gatk/issues/2037.
     */
public static void writeVCF(final PipelineOptions pipelineOptions, final String vcfFileName, final String fastaReference, final JavaRDD<VariantContext> variantContexts, final Logger logger) {
    final SAMSequenceDictionary referenceSequenceDictionary = new ReferenceMultiSource(pipelineOptions, fastaReference, ReferenceWindowFunctions.IDENTITY_FUNCTION).getReferenceSequenceDictionary(null);
    final List<VariantContext> sortedVariantsList = sortVariantsByCoordinate(variantContexts.collect(), referenceSequenceDictionary);
    logNumOfVarByTypes(sortedVariantsList, logger);
    writeVariants(pipelineOptions, vcfFileName, sortedVariantsList, referenceSequenceDictionary);
}

Example 4 with VariantContext

use of htsjdk.variant.variantcontext.VariantContext in project gatk by broadinstitute.

the class GenotypingEngineUnitTest method init.

@BeforeTest
public void init() {
    genotypingEngine = getGenotypingEngine();
    final int deletionSize = refAllele.length() - altT.length();
    final int start = 1;
    final VariantContext deletionVC = new VariantContextBuilder("testDeletion", "1", start, start + deletionSize, allelesDel).make();
    genotypingEngine.recordDeletion(deletionSize, deletionVC);
}

Example 5 with VariantContext

use of htsjdk.variant.variantcontext.VariantContext in project gatk by broadinstitute.

the class ApplyVQSRIntegrationTest method testApplyRecalibrationSnpAndIndelTogetherExcludeFiltered.

@Test
public void testApplyRecalibrationSnpAndIndelTogetherExcludeFiltered() throws Exception {
    ArgumentsBuilder args = new ArgumentsBuilder();
    File tempOut = createTempFile("testApplyRecalibrationSnpAndIndelTogetherExcludeFiltered", ".vcf");
    args.add("--variant");
    args.add(new File(getToolTestDataDir() + "VQSR.mixedTest.input.vcf"));
    args.add("-L");
    args.add("20:1000100-1000500");
    args.add("-mode");
    args.add("BOTH");
    args.add("--excludeFiltered");
    args.add("-ts_filter_level");
    args.add("90.0");
    args.add("-tranchesFile ");
    args.add(getToolTestDataDir() + "VQSR.mixedTest.tranches");
    args.add("-recalFile");
    args.add(getToolTestDataDir() + "VQSR.mixedTest.recal.vcf");
    args.addOutput(tempOut);
    runCommandLine(args);
    try (FeatureDataSource<VariantContext> featureSource = new FeatureDataSource<>(tempOut)) {
        for (VariantContext feature : featureSource) {
            // there should only be unfiltered records in the output VCF file
            Assert.assertTrue(feature.isNotFiltered());
        }
    }
}