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

Example 6 with GenotypeBuilder

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

the class EvaluateCopyNumberTriStateCalls method buildAndAnnotateTruthOverlappingGenotype.

private Genotype buildAndAnnotateTruthOverlappingGenotype(final String sample, final TargetCollection<Target> targets, final Genotype truthGenotype, final int truthCopyNumber, final CopyNumberTriStateAllele truthAllele, final List<Pair<VariantContext, Genotype>> calls) {
    final Set<CopyNumberTriStateAllele> calledAlleles = calls.stream().map(pair -> CopyNumberTriStateAllele.valueOf(pair.getRight().getAllele(0))).collect(Collectors.toSet());
    final Allele calledAllele = calledAlleles.size() == 1 ? calledAlleles.iterator().next() : Allele.NO_CALL;
    final GenotypeBuilder builder = new GenotypeBuilder(sample);
    // Set the call allele.
    builder.alleles(Collections.singletonList(calledAllele));
    // Set the truth allele.
    builder.attribute(VariantEvaluationContext.TRUTH_GENOTYPE_KEY, CopyNumberTriStateAllele.ALL_ALLELES.indexOf(truthAllele));
    // Annotate the genotype with the number of calls.
    builder.attribute(VariantEvaluationContext.CALLED_SEGMENTS_COUNT_KEY, calls.size());
    // When there is more than one qualified type of event we indicate how many.
    builder.attribute(VariantEvaluationContext.CALLED_ALLELE_COUNTS_KEY, CopyNumberTriStateAllele.ALL_ALLELES.stream().mapToInt(allele -> (int) calls.stream().filter(pair -> pair.getRight().getAllele(0).equals(allele, true)).count()).toArray());
    // Calculate the length in targets of the call as the sum across all calls.
    builder.attribute(VariantEvaluationContext.CALLED_TARGET_COUNT_KEY, calls.stream().mapToInt(pair -> getTargetCount(targets, pair.getLeft(), pair.getRight())).sum());
    // Calculate call quality-- if there is more than one overlapping call we take the maximum qual one.
    builder.attribute(VariantEvaluationContext.CALL_QUALITY_KEY, calls.stream().mapToDouble(pair -> GATKProtectedVariantContextUtils.calculateGenotypeQualityFromPLs(pair.getRight())).max().orElse(0.0));
    // Calculate the truth copy fraction.
    builder.attribute(VariantEvaluationContext.TRUTH_COPY_FRACTION_KEY, truthGenotype.getExtendedAttribute(GS_COPY_NUMBER_FRACTION_KEY));
    // Calculate the truth call quality.
    final double truthQuality = calculateTruthQuality(truthGenotype, truthCopyNumber);
    builder.attribute(VariantEvaluationContext.TRUTH_QUALITY_KEY, truthQuality);
    // Set genotype filters:
    final boolean truthPassQualityMinimum = truthQuality >= filterArguments.minimumTruthSegmentQuality;
    builder.filter(truthPassQualityMinimum ? EvaluationFilter.PASS : EvaluationFilter.LowQuality.acronym);
    // Calculate the evaluation class (TP, FN, etc.). Only if there is actually either a truth or a call that is not ref.
    if (calledAlleles.contains(CopyNumberTriStateAllele.DEL) || calledAlleles.contains(CopyNumberTriStateAllele.DUP) || truthAllele != CopyNumberTriStateAllele.REF) {
        final EvaluationClass evaluationClass;
        if (calledAlleles.isEmpty() || (calledAlleles.size() == 1 && calledAlleles.contains(CopyNumberTriStateAllele.REF))) {
            evaluationClass = EvaluationClass.FALSE_NEGATIVE;
        } else if (calledAlleles.size() == 1) {
            evaluationClass = calledAlleles.contains(truthAllele) ? EvaluationClass.TRUE_POSITIVE : truthAllele == CopyNumberTriStateAllele.REF ? EvaluationClass.FALSE_POSITIVE : /* else */
            EvaluationClass.DISCORDANT_POSITIVE;
        } else {
            evaluationClass = truthAllele == CopyNumberTriStateAllele.REF ? EvaluationClass.FALSE_POSITIVE : EvaluationClass.MIXED_POSITIVE;
        }
        builder.attribute(VariantEvaluationContext.EVALUATION_CLASS_KEY, evaluationClass.acronym);
    }
    return builder.make();
}

Example 7 with GenotypeBuilder

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

the class EvaluateCopyNumberTriStateCalls method buildAndAnnotateTruthOverlappingGenotype.

private Genotype buildAndAnnotateTruthOverlappingGenotype(final String sample, final TargetCollection<Target> targets, final Genotype truthGenotype, final int truthCopyNumber, final CopyNumberTriStateAllele truthAllele, final List<Pair<VariantContext, Genotype>> calls) {
    final Set<CopyNumberTriStateAllele> calledAlleles = calls.stream().map(pair -> CopyNumberTriStateAllele.valueOf(pair.getRight().getAllele(0))).collect(Collectors.toSet());
    final Allele calledAllele = calledAlleles.size() == 1 ? calledAlleles.iterator().next() : Allele.NO_CALL;
    final GenotypeBuilder builder = new GenotypeBuilder(sample);
    // Set the call allele.
    builder.alleles(Collections.singletonList(calledAllele));
    // Set the truth allele.
    builder.attribute(VariantEvaluationContext.TRUTH_GENOTYPE_KEY, CopyNumberTriStateAllele.ALL_ALLELES.indexOf(truthAllele));
    // Annotate the genotype with the number of calls.
    builder.attribute(VariantEvaluationContext.CALLED_SEGMENTS_COUNT_KEY, calls.size());
    // When there is more than one qualified type of event we indicate how many.
    builder.attribute(VariantEvaluationContext.CALLED_ALLELE_COUNTS_KEY, CopyNumberTriStateAllele.ALL_ALLELES.stream().mapToInt(allele -> (int) calls.stream().filter(pair -> pair.getRight().getAllele(0).equals(allele, true)).count()).toArray());
    // Calculate the length in targets of the call as the sum across all calls.
    builder.attribute(VariantEvaluationContext.CALLED_TARGET_COUNT_KEY, calls.stream().mapToInt(pair -> getTargetCount(targets, pair.getLeft(), pair.getRight())).sum());
    // Calculate call quality-- if there is more than one overlapping call we take the maximum qual one.
    builder.attribute(VariantEvaluationContext.CALL_QUALITY_KEY, calls.stream().mapToDouble(pair -> GATKProtectedVariantContextUtils.calculateGenotypeQualityFromPLs(pair.getRight())).max().orElse(0.0));
    // Calculate the truth copy fraction.
    builder.attribute(VariantEvaluationContext.TRUTH_COPY_FRACTION_KEY, truthGenotype.getExtendedAttribute(GS_COPY_NUMBER_FRACTION_KEY));
    // Calculate the truth call quality.
    final double truthQuality = calculateTruthQuality(truthGenotype, truthCopyNumber);
    builder.attribute(VariantEvaluationContext.TRUTH_QUALITY_KEY, truthQuality);
    // Set genotype filters:
    final boolean truthPassQualityMinimum = truthQuality >= filterArguments.minimumTruthSegmentQuality;
    builder.filter(truthPassQualityMinimum ? EvaluationFilter.PASS : EvaluationFilter.LowQuality.acronym);
    // Calculate the evaluation class (TP, FN, etc.). Only if there is actually either a truth or a call that is not ref.
    if (calledAlleles.contains(CopyNumberTriStateAllele.DEL) || calledAlleles.contains(CopyNumberTriStateAllele.DUP) || truthAllele != CopyNumberTriStateAllele.REF) {
        final EvaluationClass evaluationClass;
        if (calledAlleles.isEmpty() || (calledAlleles.size() == 1 && calledAlleles.contains(CopyNumberTriStateAllele.REF))) {
            evaluationClass = EvaluationClass.FALSE_NEGATIVE;
        } else if (calledAlleles.size() == 1) {
            evaluationClass = calledAlleles.contains(truthAllele) ? EvaluationClass.TRUE_POSITIVE : truthAllele == CopyNumberTriStateAllele.REF ? EvaluationClass.FALSE_POSITIVE : /* else */
            EvaluationClass.DISCORDANT_POSITIVE;
        } else {
            evaluationClass = truthAllele == CopyNumberTriStateAllele.REF ? EvaluationClass.FALSE_POSITIVE : EvaluationClass.MIXED_POSITIVE;
        }
        builder.attribute(VariantEvaluationContext.EVALUATION_CLASS_KEY, evaluationClass.acronym);
    }
    return builder.make();
}

Example 8 with GenotypeBuilder

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

the class EvaluateCopyNumberTriStateCalls method composeNonTruthOverlappingGenotype.

private Genotype composeNonTruthOverlappingGenotype(final VariantContext enclosingContext, final Genotype genotype) {
    final GenotypeBuilder builder = new GenotypeBuilder(genotype.getSampleName());
    if (genotype.isCalled()) {
        GATKProtectedVariantContextUtils.setGenotypeQualityFromPLs(builder, genotype);
        final int[] PL = genotype.getPL();
        final int callAlleleIndex = GATKProtectedMathUtils.minIndex(PL);
        final double quality = callQuality(genotype);
        builder.alleles(Collections.singletonList(enclosingContext.getAlleles().get(callAlleleIndex)));
        builder.attribute(VariantEvaluationContext.CALL_QUALITY_KEY, quality);
        final boolean discovered = XHMMSegmentGenotyper.DISCOVERY_TRUE.equals(GATKProtectedVariantContextUtils.getAttributeAsString(genotype, XHMMSegmentGenotyper.DISCOVERY_KEY, XHMMSegmentGenotyper.DISCOVERY_FALSE));
        if (callAlleleIndex != 0 && discovered) {
            builder.attribute(VariantEvaluationContext.EVALUATION_CLASS_KEY, EvaluationClass.UNKNOWN_POSITIVE.acronym);
        }
        if (quality < filterArguments.minimumCalledSegmentQuality) {
            builder.filter(EvaluationFilter.LowQuality.acronym);
        } else {
            builder.filter(EvaluationFilter.PASS);
        }
    } else {
        /* assume it is REF */
        /* TODO this is a hack to make Andrey's CODEX vcf work; and in general, VCFs that only include discovered
             * variants and NO_CALL (".") on other samples. The idea is to force the evaluation tool to take it call
             * as REF on all other samples. Otherwise, the effective allele frequency of the variant will be erroneously
             * high and will be filtered. */
        builder.alleles(Collections.singletonList(CopyNumberTriStateAllele.REF));
        builder.attribute(VariantEvaluationContext.CALL_QUALITY_KEY, 100000);
        builder.filter(EvaluationFilter.PASS);
    }
    return builder.make();
}

Example 9 with GenotypeBuilder

use of htsjdk.variant.variantcontext.GenotypeBuilder 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 10 with GenotypeBuilder

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

the class HomRefBlock method createHomRefGenotype.

// create a single Genotype with GQ and DP annotations
private Genotype createHomRefGenotype(String sampleName) {
    final GenotypeBuilder gb = new GenotypeBuilder(sampleName, Collections.nCopies(getPloidy(), getRef()));
    // clear all attributes
    gb.noAD().noPL().noAttributes();
    final int[] minPLs = getMinPLs();
    gb.PL(minPLs);
    gb.GQ(GATKVariantContextUtils.calculateGQFromPLs(minPLs));
    gb.DP(getMedianDP());
    gb.attribute(GATKVCFConstants.MIN_DP_FORMAT_KEY, getMinDP());
    return gb.make();
}