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

Example 36 with Allele

use of htsjdk.variant.variantcontext.Allele 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 37 with Allele

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

the class ValidateVariants method apply.

@Override
public void apply(final VariantContext vc, final ReadsContext readsContext, final ReferenceContext ref, final FeatureContext featureContext) {
    if (DO_NOT_VALIDATE_FILTERED && vc.isFiltered()) {
        return;
    }
    // get the true reference allele
    final Allele reportedRefAllele = vc.getReference();
    final int refLength = reportedRefAllele.length();
    final Allele observedRefAllele = hasReference() ? Allele.create(Arrays.copyOf(ref.getBases(), refLength)) : null;
    final Set<String> rsIDs = getRSIDs(featureContext);
    for (final ValidationType t : validationTypes) {
        try {
            applyValidationType(vc, reportedRefAllele, observedRefAllele, rsIDs, t);
        } catch (TribbleException e) {
            if (WARN_ON_ERROR) {
                logger.warn("***** " + e.getMessage() + " *****");
            } else {
                throw new UserException.FailsStrictValidation(drivingVariantFile, t, e.getMessage());
            }
        }
    }
}

Example 38 with Allele

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

the class SelectVariants method addAnnotations.

/*
     * Add annotations to the new VC
     *
     * @param builder     the new VC to annotate
     * @param originalVC  the original VC
     * @param selectedSampleNames the post-selection list of sample names
     */
private void addAnnotations(final VariantContextBuilder builder, final VariantContext originalVC, final Set<String> selectedSampleNames) {
    if (fullyDecode) {
        // TODO -- annotations are broken with fully decoded data
        return;
    }
    if (keepOriginalChrCounts) {
        final int[] indexOfOriginalAlleleForNewAllele;
        final List<Allele> newAlleles = builder.getAlleles();
        final int numOriginalAlleles = originalVC.getNAlleles();
        // if the alleles already match up, we can just copy the previous list of counts
        if (numOriginalAlleles == newAlleles.size()) {
            indexOfOriginalAlleleForNewAllele = null;
        } else // otherwise we need to parse them and select out the correct ones
        {
            indexOfOriginalAlleleForNewAllele = new int[newAlleles.size() - 1];
            Arrays.fill(indexOfOriginalAlleleForNewAllele, -1);
            // note that we don't care about the reference allele at position 0
            for (int newI = 1; newI < newAlleles.size(); newI++) {
                final Allele newAlt = newAlleles.get(newI);
                for (int oldI = 0; oldI < numOriginalAlleles - 1; oldI++) {
                    if (newAlt.equals(originalVC.getAlternateAllele(oldI), false)) {
                        indexOfOriginalAlleleForNewAllele[newI - 1] = oldI;
                        break;
                    }
                }
            }
        }
        if (originalVC.hasAttribute(VCFConstants.ALLELE_COUNT_KEY)) {
            builder.attribute(GATKVCFConstants.ORIGINAL_AC_KEY, getReorderedAttributes(originalVC.getAttribute(VCFConstants.ALLELE_COUNT_KEY), indexOfOriginalAlleleForNewAllele));
        }
        if (originalVC.hasAttribute(VCFConstants.ALLELE_FREQUENCY_KEY)) {
            builder.attribute(GATKVCFConstants.ORIGINAL_AF_KEY, getReorderedAttributes(originalVC.getAttribute(VCFConstants.ALLELE_FREQUENCY_KEY), indexOfOriginalAlleleForNewAllele));
        }
        if (originalVC.hasAttribute(VCFConstants.ALLELE_NUMBER_KEY)) {
            builder.attribute(GATKVCFConstants.ORIGINAL_AN_KEY, originalVC.getAttribute(VCFConstants.ALLELE_NUMBER_KEY));
        }
    }
    VariantContextUtils.calculateChromosomeCounts(builder, false);
    if (keepOriginalDepth && originalVC.hasAttribute(VCFConstants.DEPTH_KEY)) {
        builder.attribute(GATKVCFConstants.ORIGINAL_DP_KEY, originalVC.getAttribute(VCFConstants.DEPTH_KEY));
    }
    boolean sawDP = false;
    int depth = 0;
    for (final String sample : selectedSampleNames) {
        final Genotype g = originalVC.getGenotype(sample);
        if (!g.isFiltered()) {
            if (g.hasDP()) {
                depth += g.getDP();
                sawDP = true;
            }
        }
    }
    if (sawDP) {
        builder.attribute(VCFConstants.DEPTH_KEY, depth);
    }
}

Example 39 with Allele

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

the class XHMMSegmentGenotyperIntegrationTest method assertVariantsInfoFieldsAreConsistent.

private void assertVariantsInfoFieldsAreConsistent(final List<VariantContext> variants) {
    for (final VariantContext variant : variants) {
        final int expectedAN = variant.getGenotypes().size();
        final int[] expectedAC = new int[CopyNumberTriState.values().length];
        final List<Allele> alleles = variant.getAlleles();
        for (final Genotype genotype : variant.getGenotypes()) {
            Assert.assertEquals(genotype.getAlleles().size(), 1);
            final int alleleIndex = alleles.indexOf(genotype.getAllele(0));
            Assert.assertTrue(alleleIndex >= 0);
            expectedAC[alleleIndex]++;
        }
        Assert.assertEquals(variant.getAlleles(), CopyNumberTriStateAllele.ALL_ALLELES);
        Assert.assertTrue(variant.hasAttribute(XHMMSegmentGenotyper.NUMBER_OF_TARGETS_KEY));
        Assert.assertTrue(variant.hasAttribute(VCFConstants.ALLELE_COUNT_KEY));
        Assert.assertTrue(variant.hasAttribute(VCFConstants.END_KEY));
        Assert.assertTrue(variant.hasAttribute(VCFConstants.ALLELE_FREQUENCY_KEY));
        Assert.assertTrue(variant.hasAttribute(VCFConstants.ALLELE_NUMBER_KEY));
        final int expectedANAnotherWay = IntStream.of(expectedAC).sum();
        Assert.assertEquals(expectedANAnotherWay, expectedAN);
        Assert.assertEquals(variant.getAttributeAsInt(VCFConstants.ALLELE_NUMBER_KEY, -1), expectedAN);
        final double[] expectedAF = IntStream.of(expectedAC).mapToDouble(c -> c / (double) expectedAN).toArray();
        final double[] observedAFWithoutRef = variant.getAttributeAsList(VCFConstants.ALLELE_FREQUENCY_KEY).stream().mapToDouble(o -> Double.parseDouble(String.valueOf(o))).toArray();
        Assert.assertEquals(observedAFWithoutRef.length, expectedAF.length - 1);
        for (int i = 0; i < observedAFWithoutRef.length; i++) {
            Assert.assertEquals(observedAFWithoutRef[i], expectedAF[i + 1], 0.001);
        }
        final int[] observedACWithoutRef = variant.getAttributeAsList(VCFConstants.ALLELE_COUNT_KEY).stream().mapToInt(o -> Integer.parseInt(String.valueOf(o))).toArray();
        Assert.assertEquals(observedACWithoutRef.length, expectedAC.length - 1);
        for (int i = 0; i < observedACWithoutRef.length; i++) {
            Assert.assertEquals(observedACWithoutRef[i], expectedAC[i + 1]);
        }
        Assert.assertEquals(variant.getAttributeAsInt(XHMMSegmentGenotyper.NUMBER_OF_TARGETS_KEY, -1), XHMMSegmentCallerBaseIntegrationTest.REALISTIC_TARGETS.targetCount(variant));
    }
}

Example 40 with Allele

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

the class ReadThreadingAssemblerUnitTest method testAssembleRefAndInsertion.

@Test(dataProvider = "AssembleIntervalsWithVariantData")
public void testAssembleRefAndInsertion(final ReadThreadingAssembler assembler, final SimpleInterval loc, final int nReadsToUse, final int variantSite) {
    final byte[] refBases = seq.getSubsequenceAt(loc.getContig(), loc.getStart(), loc.getEnd()).getBases();
    for (int insertionLength = 1; insertionLength < 10; insertionLength++) {
        final Allele refBase = Allele.create(refBases[variantSite], false);
        final Allele altBase = Allele.create(new String(refBases).substring(variantSite, variantSite + insertionLength + 1), true);
        final VariantContextBuilder vcb = new VariantContextBuilder("x", loc.getContig(), variantSite, variantSite + insertionLength, Arrays.asList(refBase, altBase));
        testAssemblyWithVariant(assembler, refBases, loc, nReadsToUse, vcb.make());
    }
}