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

Example 11 with Genotype

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

the class GenotypeConcordanceTest method testGenotypeConcordanceDetermineStateGq.

@Test
public void testGenotypeConcordanceDetermineStateGq() throws Exception {
    final List<Allele> allelesNormal = makeUniqueListOfAlleles(Aref, C);
    final Genotype gtNormal = GenotypeBuilder.create(TRUTH_SAMPLE_NAME, Arrays.asList(Aref, C));
    final VariantContext vcNormal = new VariantContextBuilder("test", snpLoc, snpLocStart, snpLocStop, allelesNormal).genotypes(gtNormal).make();
    final List<Allele> allelesLowGq = makeUniqueListOfAlleles(Aref, C);
    final Genotype gtLowGq = new GenotypeBuilder(TRUTH_SAMPLE_NAME, Arrays.asList(Aref, C)).GQ(4).make();
    final VariantContext vcLowGq = new VariantContextBuilder("test", snpLoc, snpLocStart, snpLocStop, allelesLowGq).genotypes(gtLowGq).make();
    testGenotypeConcordanceDetermineState(vcLowGq, TruthState.LOW_GQ, vcNormal, CallState.HET_REF_VAR1, 20, 0);
    testGenotypeConcordanceDetermineState(vcLowGq, TruthState.HET_REF_VAR1, vcLowGq, CallState.HET_REF_VAR1, 2, 0);
    testGenotypeConcordanceDetermineState(vcNormal, TruthState.HET_REF_VAR1, vcLowGq, CallState.LOW_GQ, 20, 0);
    testGenotypeConcordanceDetermineState(vcNormal, TruthState.HET_REF_VAR1, vcLowGq, CallState.HET_REF_VAR1, 2, 0);
    testGenotypeConcordanceDetermineState(vcLowGq, TruthState.LOW_GQ, vcLowGq, CallState.LOW_GQ, 20, 0);
    testGenotypeConcordanceDetermineState(vcLowGq, TruthState.HET_REF_VAR1, vcLowGq, CallState.HET_REF_VAR1, 2, 0);
}

Example 12 with Genotype

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

the class HaplotypeCallerSparkIntegrationTest method testFastGenotypeIsSerializable.

@Test
public void testFastGenotypeIsSerializable() {
    Genotype genotype = GenotypeBuilder.create("sample1", Collections.nCopies(2, Allele.create("C", false)));
    SparkTestUtils.roundTripInKryo(genotype, genotype.getClass(), SparkContextFactory.getTestSparkContext().getConf());
}

Example 13 with Genotype

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

the class IndependentAllelesDiploidExactAFCalculatorUnitTest method testCombineGLsPrecise.

@Test(enabled = true, dataProvider = "TestCombineGLs")
public void testCombineGLsPrecise(final int altIndex, final int nAlts, final Genotype testg, final Genotype expected) {
    final Genotype combined = IndependentAllelesDiploidExactAFCalculator.combineGLsPrecise(testg, altIndex, nAlts);
    Assert.assertEquals(combined.getPL(), expected.getPL(), "Combined PLs " + Utils.join(",", combined.getPL()) + " != expected " + Utils.join(",", expected.getPL()));
}

Example 14 with Genotype

use of htsjdk.variant.variantcontext.Genotype 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 15 with Genotype

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

the class EvaluateCopyNumberTriStateCalls method updateSampleStats.

private void updateSampleStats(final Map<String, EvaluationSampleSummaryRecord> sampleStats, final VariantEvaluationContext vc) {
    // ignore filtered out variants.
    if (vc.getFilters().stream().anyMatch(f -> !VCFConstants.PASSES_FILTERS_v4.equals(f))) {
        return;
    }
    for (final Genotype genotype : vc.getGenotypes()) {
        final Set<String> filters = genotype.getFilters() == null ? Collections.emptySet() : Stream.of(genotype.getFilters().split(VCFConstants.INFO_FIELD_ARRAY_SEPARATOR)).collect(Collectors.toSet());
        if (filters.stream().anyMatch(s -> !s.equals(VCFConstants.PASSES_FILTERS_v4))) {
            continue;
        }
        final String sample = genotype.getSampleName();
        final String evalClassString = GATKProtectedVariantContextUtils.getAttributeAsString(genotype, VariantEvaluationContext.EVALUATION_CLASS_KEY, null);
        if (evalClassString != null) {
            final EvaluationClass evalClass = EvaluationClass.parseString(evalClassString);
            sampleStats.get(sample).increase(evalClass);
        }
    }
}