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

Example 81 with Allele

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

the class CoverageUnitTest method testLikelihoods.

@Test
public void testLikelihoods() {
    final Allele REF = Allele.create("T", true);
    final Allele ALT = Allele.create("A");
    final int refDepth = 5;
    final int altDepth = 3;
    final List<GATKRead> refReads = IntStream.range(0, refDepth).mapToObj(n -> makeRead()).collect(Collectors.toList());
    final List<GATKRead> altReads = IntStream.range(0, altDepth).mapToObj(n -> makeRead()).collect(Collectors.toList());
    final ReadLikelihoods<Allele> likelihoods = AnnotationArtificialData.makeLikelihoods("sample1", refReads, altReads, -100.0, -100.0, REF, ALT);
    final VariantContext vc = makeVC();
    final ReferenceContext referenceContext = null;
    final Map<String, Object> annotate = new Coverage().annotate(referenceContext, vc, likelihoods);
    Assert.assertEquals(annotate.size(), 1, "size");
    Assert.assertEquals(annotate.keySet(), Collections.singleton(VCFConstants.DEPTH_KEY), "annots");
    final int m = altDepth + refDepth;
    Assert.assertEquals(annotate.get(VCFConstants.DEPTH_KEY), String.valueOf(m));
}

Example 82 with Allele

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

the class CoverageUnitTest method makeVC.

private VariantContext makeVC() {
    final GenotypesContext testGC = GenotypesContext.create(2);
    final Allele refAllele = Allele.create("A", true);
    final Allele altAllele = Allele.create("T");
    return (new VariantContextBuilder()).alleles(Arrays.asList(refAllele, altAllele)).chr("1").start(15L).stop(15L).genotypes(testGC).make();
}

Example 83 with Allele

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

the class MappingQualityZeroUnitTest method testLikelihoods.

@Test
public void testLikelihoods() {
    final Allele REF = Allele.create("T", true);
    final Allele ALT = Allele.create("A");
    final int refDepth = 5;
    final int altDepth = 3;
    final int refMQ = 10;
    final int altMQ = 0;
    final List<GATKRead> refReads = IntStream.range(0, refDepth).mapToObj(i -> makeRead(refMQ)).collect(Collectors.toList());
    final List<GATKRead> altReads = IntStream.range(0, altDepth).mapToObj(i -> makeRead(altMQ)).collect(Collectors.toList());
    final ReadLikelihoods<Allele> likelihoods = AnnotationArtificialData.makeLikelihoods("sample1", refReads, altReads, -1.0, -1.0, REF, ALT);
    final VariantContext vc = makeVC();
    final ReferenceContext referenceContext = null;
    final Map<String, Object> annotate = new MappingQualityZero().annotate(referenceContext, vc, likelihoods);
    Assert.assertEquals(annotate.size(), 1, "size");
    Assert.assertEquals(annotate.keySet(), Collections.singleton(VCFConstants.MAPPING_QUALITY_ZERO_KEY), "annots");
    Assert.assertEquals(annotate.get(VCFConstants.MAPPING_QUALITY_ZERO_KEY), String.valueOf(altDepth));
}

Example 84 with Allele

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

the class ReadThreadingAssembler method composeGivenHaplotypes.

/**
     * Create the list of artificial GGA-mode haplotypes by injecting each of the provided alternate alleles into the reference haplotype
     *
     * @param refHaplotype the reference haplotype
     * @param givenHaplotypes the list of alternate alleles in VariantContexts
     * @param activeRegionWindow the window containing the reference haplotype
     *
     * @return a non-null list of haplotypes
     */
private static List<Haplotype> composeGivenHaplotypes(final Haplotype refHaplotype, final List<VariantContext> givenHaplotypes, final SimpleInterval activeRegionWindow) {
    Utils.nonNull(refHaplotype, "the reference haplotype cannot be null");
    Utils.nonNull(givenHaplotypes, "given haplotypes cannot be null");
    Utils.nonNull(activeRegionWindow, "active region window cannot be null");
    Utils.validateArg(activeRegionWindow.size() == refHaplotype.length(), "inconsistent reference haplotype and active region window");
    final Set<Haplotype> returnHaplotypes = new LinkedHashSet<>();
    final int activeRegionStart = refHaplotype.getAlignmentStartHapwrtRef();
    for (final VariantContext compVC : givenHaplotypes) {
        Utils.validateArg(GATKVariantContextUtils.overlapsRegion(compVC, activeRegionWindow), " some variant provided does not overlap with active region window");
        for (final Allele compAltAllele : compVC.getAlternateAlleles()) {
            final Haplotype insertedRefHaplotype = refHaplotype.insertAllele(compVC.getReference(), compAltAllele, activeRegionStart + compVC.getStart() - activeRegionWindow.getStart(), compVC.getStart());
            if (insertedRefHaplotype != null) {
                // can be null if the requested allele can't be inserted into the haplotype
                returnHaplotypes.add(insertedRefHaplotype);
            }
        }
    }
    return new ArrayList<>(returnHaplotypes);
}

Example 85 with Allele

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

the class GermlineProbabilityCalculator method calculateAnnotations.

public static Map<String, Object> calculateAnnotations(List<VariantContext> germlineResourceVariants, final List<Allele> altAlleles, final double[] tumorLog10Odds, final Optional<double[]> normalLog10Odds, final double afOfAllelesNotInGermlineResource, final double log10PriorProbOfSomaticEvent) {
    final double[] normalLog10OddsOrFlat = normalLog10Odds.orElseGet(() -> MathUtils.applyToArray(tumorLog10Odds, x -> 0));
    final Optional<VariantContext> germlineVC = germlineResourceVariants.isEmpty() ? Optional.empty() : // assume only one VC per site
    Optional.of(germlineResourceVariants.get(0));
    final double[] populationAlleleFrequencies = getGermlineAltAlleleFrequencies(altAlleles, germlineVC, afOfAllelesNotInGermlineResource);
    // note the minus sign required because Mutect has the convention that this is log odds of allele *NOT* being in the normal
    final double[] germlineLog10Posteriors = new IndexRange(0, altAlleles.size()).mapToDouble(n -> log10PosteriorProbabilityOfGermlineVariant(-normalLog10OddsOrFlat[n], tumorLog10Odds[n], populationAlleleFrequencies[n], log10PriorProbOfSomaticEvent));
    return ImmutableMap.of(POPULATION_AF_VCF_ATTRIBUTE, populationAlleleFrequencies, GERMLINE_POSTERIORS_VCF_ATTRIBUTE, germlineLog10Posteriors);
}