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

Example 1 with VariantContextBuilder

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

the class SVVariantConsensusDiscovery method discoverVariantsFromConsensus.

// TODO: 12/12/16 does not handle translocation yet
/**
     * Produces a VC from a {@link NovelAdjacencyReferenceLocations} (consensus among different assemblies if they all point to the same breakpoint).
     *
     * @param breakpointPairAndItsEvidence      consensus among different assemblies if they all point to the same breakpoint
     * @param broadcastReference                broadcasted reference
     * @throws IOException                      due to read operations on the reference
     */
public static VariantContext discoverVariantsFromConsensus(final Tuple2<NovelAdjacencyReferenceLocations, Iterable<ChimericAlignment>> breakpointPairAndItsEvidence, final Broadcast<ReferenceMultiSource> broadcastReference) throws IOException {
    final NovelAdjacencyReferenceLocations novelAdjacencyReferenceLocations = breakpointPairAndItsEvidence._1;
    final Iterable<ChimericAlignment> evidence = breakpointPairAndItsEvidence._2();
    final String contig = novelAdjacencyReferenceLocations.leftJustifiedLeftRefLoc.getContig();
    final int start = novelAdjacencyReferenceLocations.leftJustifiedLeftRefLoc.getEnd();
    final int end = novelAdjacencyReferenceLocations.leftJustifiedRightRefLoc.getStart();
    Utils.validateArg(start <= end, "An identified breakpoint pair has left breakpoint positioned to the right of right breakpoint: " + novelAdjacencyReferenceLocations.toString());
    final SvType variant = getType(novelAdjacencyReferenceLocations);
    final VariantContextBuilder vcBuilder = new VariantContextBuilder().chr(contig).start(start).stop(end).alleles(produceAlleles(novelAdjacencyReferenceLocations, broadcastReference.getValue(), variant)).id(variant.getVariantId()).attribute(VCFConstants.END_KEY, end).attribute(GATKSVVCFHeaderLines.SVTYPE, variant.toString()).attribute(GATKSVVCFHeaderLines.SVLEN, variant.getSVLength());
    variant.getTypeSpecificAttributes().forEach(vcBuilder::attribute);
    parseComplicationsAndMakeThemAttributeMap(novelAdjacencyReferenceLocations).forEach(vcBuilder::attribute);
    getEvidenceRelatedAnnotations(evidence).forEach(vcBuilder::attribute);
    return vcBuilder.make();
}

Example 2 with VariantContextBuilder

use of htsjdk.variant.variantcontext.VariantContextBuilder 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 3 with VariantContextBuilder

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

the class FilterApplyingVariantIterator method next.

/**
     * Provides the next record from the underlying iterator after applying filter strings generated
     * by the set of filters in use by the iterator.
     */
@Override
public VariantContext next() {
    final VariantContext ctx = this.iterator.next();
    final Set<String> filterStrings = new HashSet<>();
    // Collect variant level filters
    for (final VariantFilter filter : this.filters) {
        final String val = filter.filter(ctx);
        if (val != null)
            filterStrings.add(val);
    }
    // Collect genotype level filters in a Map of Sample -> List<filter string>
    final ListMap<String, String> gtFilterStrings = new ListMap<>();
    final Set<String> variantSamples = new HashSet<>();
    for (final Genotype gt : ctx.getGenotypes()) {
        if (gt.isCalled() && !gt.isHomRef())
            variantSamples.add(gt.getSampleName());
        for (final GenotypeFilter filter : gtFilters) {
            final String filterString = filter.filter(ctx, gt);
            if (filterString != null)
                gtFilterStrings.add(gt.getSampleName(), filterString);
        }
    }
    // If all genotypes are filtered apply a site level filter
    if (gtFilterStrings.keySet().containsAll(variantSamples)) {
        filterStrings.add(ALL_GTS_FILTERED);
    }
    // Make a builder and set the site level filter appropriately
    final VariantContextBuilder builder = new VariantContextBuilder(ctx);
    if (filterStrings.isEmpty()) {
        builder.passFilters();
    } else {
        builder.filters(filterStrings);
    }
    // Apply filters to the necessary genotypes
    builder.noGenotypes();
    final List<Genotype> newGenotypes = new ArrayList<>(ctx.getNSamples());
    for (final Genotype gt : ctx.getGenotypes()) {
        final GenotypeBuilder gtBuilder = new GenotypeBuilder(gt);
        final List<String> filters = gtFilterStrings.get(gt.getSampleName());
        if (filters == null || filters.isEmpty()) {
            gtBuilder.filter(PASS_FILTER);
        } else {
            gtBuilder.filters(filters);
        }
        newGenotypes.add(gtBuilder.make());
    }
    builder.genotypes(newGenotypes);
    return builder.make();
}

Example 4 with VariantContextBuilder

use of htsjdk.variant.variantcontext.VariantContextBuilder in project gatk 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 5 with VariantContextBuilder

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

the class HomRefBlock method toVariantContext.

/**
     * Convert a HomRefBlock into a VariantContext
     *
     * @param sampleName sample name to give this variant context
     * @return a VariantContext representing the gVCF encoding for this block.
     * It will return {@code null} if input {@code block} is {@code null}, indicating that there
     * is no variant-context to be output into the VCF.
     */
public VariantContext toVariantContext(String sampleName) {
    final VariantContextBuilder vcb = new VariantContextBuilder(getStartingVC());
    // clear the attributes
    vcb.attributes(new LinkedHashMap<>(2));
    vcb.stop(getEnd());
    vcb.attribute(VCFConstants.END_KEY, getEnd());
    final Genotype genotype = createHomRefGenotype(sampleName);
    return vcb.genotypes(genotype).make();
}