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

Example 11 with VariantContext

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

the class AnnotateVcfWithExpectedAlleleFraction method apply.

@Override
public void apply(final VariantContext vc, final ReadsContext readsContext, final ReferenceContext refContext, final FeatureContext fc) {
    final double[] weights = vc.getGenotypes().stream().mapToDouble(g -> weight(g)).toArray();
    final double expectedAlleleFraction = MathUtils.sum(MathArrays.ebeMultiply(weights, mixingFractionsInSampleOrder));
    vcfWriter.add(new VariantContextBuilder(vc).attribute(EXPECTED_ALLELE_FRACTION_NAME, expectedAlleleFraction).make());
}

Example 12 with VariantContext

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

the class CalculateMixingFractions method apply.

@Override
public void apply(final VariantContext vc, final ReadsContext readsContext, final ReferenceContext refContext, final FeatureContext fc) {
    if (!isBiallelicSingletonHetSnp(vc)) {
        return;
    }
    final Optional<String> variantSample = StreamSupport.stream(vc.getGenotypes().spliterator(), false).filter(genotype -> genotype.isHet()).map(genotype -> genotype.getSampleName()).findFirst();
    if (!variantSample.isPresent()) {
        return;
    }
    final List<GATKRead> reads = new ArrayList<>();
    final List<Integer> offsets = new ArrayList<>();
    for (final GATKRead read : readsContext) {
        if (read.failsVendorQualityCheck()) {
            continue;
        }
        final AlignmentStateMachine asm = new AlignmentStateMachine(read);
        while (asm.stepForwardOnGenome() != null && asm.getGenomePosition() < vc.getStart()) {
        }
        if (asm.getGenomePosition() == vc.getStart()) {
            reads.add(read);
            offsets.add(asm.getReadOffset());
        }
    }
    final ReadPileup pileup = new ReadPileup(vc, reads, offsets);
    final byte altBase = vc.getAlternateAllele(0).getBases()[0];
    final long altCount = StreamSupport.stream(pileup.spliterator(), false).filter(pe -> pe.getBase() == altBase).count();
    final long totalCount = pileup.size();
    sampleCounts.get(variantSample.get()).addCounts(altCount, totalCount);
}

Example 13 with VariantContext

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

the class CalculateGenotypePosteriors method apply.

@Override
public void apply(final VariantContext variant, final ReadsContext readsContext, final ReferenceContext referenceContext, final FeatureContext featureContext) {
    final Collection<VariantContext> vcs = featureContext.getValues(getDrivingVariantsFeatureInput());
    final Collection<VariantContext> otherVCs = featureContext.getValues(supportVariants);
    final int missing = supportVariants.size() - otherVCs.size();
    for (final VariantContext vc : vcs) {
        final VariantContext vc_familyPriors;
        final VariantContext vc_bothPriors;
        //do family priors first (if applicable)
        final VariantContextBuilder builder = new VariantContextBuilder(vc);
        //only compute family priors for biallelelic sites
        if (!skipFamilyPriors && vc.isBiallelic()) {
            final GenotypesContext gc = famUtils.calculatePosteriorGLs(vc);
            builder.genotypes(gc);
        }
        VariantContextUtils.calculateChromosomeCounts(builder, false);
        vc_familyPriors = builder.make();
        if (!skipPopulationPriors) {
            vc_bothPriors = PosteriorProbabilitiesUtils.calculatePosteriorProbs(vc_familyPriors, otherVCs, missing * numRefIfMissing, globalPrior, !ignoreInputSamples, defaultToAC, useACoff);
        } else {
            final VariantContextBuilder builder2 = new VariantContextBuilder(vc_familyPriors);
            VariantContextUtils.calculateChromosomeCounts(builder, false);
            vc_bothPriors = builder2.make();
        }
        vcfWriter.add(vc_bothPriors);
    }
}

Example 14 with VariantContext

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

the class FilterMutectCalls method onTraversalSuccess.

@Override
public Object onTraversalSuccess() {
    final String tumorSample = getHeaderForVariants().getMetaDataLine(Mutect2Engine.TUMOR_SAMPLE_KEY_IN_VCF_HEADER).getValue();
    final Mutect2FilteringEngine filteringEngine = new Mutect2FilteringEngine(MTFAC, tumorSample);
    // TODO: implement sophisticated filtering
    for (final VariantContext vc : unfilteredCalls) {
        final VariantContextBuilder vcb = new VariantContextBuilder(vc);
        vcb.filters(filteringEngine.calculateFilters(MTFAC, vc));
        vcfWriter.add(vcb.make());
    }
    return "SUCCESS";
}

Example 15 with VariantContext

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

the class ReferenceBasesUnitTest method test.

@Test
public void test() {
    final File refFasta = new File(b37_reference_20_21);
    final ReferenceDataSource refDataSource = new ReferenceFileSource(refFasta);
    final ReferenceContext ref = new ReferenceContext(refDataSource, new SimpleInterval("20", 10_000_000, 10_000_200));
    final VariantContext vc = new VariantContextBuilder("source", "20", 10_000_100, 10_000_100, Collections.singleton(Allele.create((byte) 'A', true))).make();
    final String refBases = (String) new ReferenceBases().annotate(ref, vc, null).get(ReferenceBases.REFERENCE_BASES_KEY);
    Assert.assertEquals(refBases, "ACTGCATCCCTTGCATTTCC");
}