Package htsjdk.variant.variantcontext

Examples of htsjdk.variant.variantcontext.Allele

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                                                                               final int haplotypeSize,
                                                                               final int numPrefBases) {

        LinkedHashMap<Allele,Haplotype> haplotypeMap = new LinkedHashMap<Allele,Haplotype>();

        Allele refAllele = null;

        for (Allele a:alleleList) {
            if (a.isReference()) {
                refAllele = a;
                break;
            }
        }

        if (refAllele == null)
            throw new ReviewedGATKException("BUG: no ref alleles in input to makeHaplotypeListfrom Alleles at loc: "+ startPos);

        final byte[] refBases = ref.getBases();

        final int startIdxInReference = 1 + startPos - numPrefBases - ref.getWindow().getStart();
        final String basesBeforeVariant = new String(Arrays.copyOfRange(refBases, startIdxInReference, startIdxInReference + numPrefBases));

        // protect against long events that overrun available reference context
        final int startAfter = Math.min(startIdxInReference + numPrefBases + refAllele.getBases().length - 1, refBases.length);
        final String basesAfterVariant = new String(Arrays.copyOfRange(refBases, startAfter, refBases.length));

        // Create location for all haplotypes
        final int startLoc = ref.getWindow().getStart() + startIdxInReference;
        final int stopLoc = startLoc + haplotypeSize-1;
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        final byte[] largerAllele = Utils.dupBytes((byte) 'A', size+1);
        final byte[] smallerAllele = Utils.dupBytes((byte) 'A', 1);

        final List<Allele> alleles = new ArrayList<Allele>(2);
        final Allele ref = Allele.create(op.equals("I") ? smallerAllele : largerAllele, true);
        final Allele alt = Allele.create(op.equals("D") ? smallerAllele : largerAllele, false);
        alleles.add(ref);
        alleles.add(alt);
        if ( otherSize > 0 && otherSize != size ) {
            final Allele otherAlt = Allele.create(op.equals("D") ? Utils.dupBytes((byte) 'A', size-otherSize+1) : Utils.dupBytes((byte) 'A', otherSize+1), false);
            alleles.add(otherAlt);
        }

        final VariantContext vc = new VariantContextBuilder("test", "1", 10, 10 + ref.length() - 1, alleles).make();
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        basicInsertTest("G", "C", 17, h1Cigar, bases, h1bases);
    }

    private void basicInsertTest(String ref, String alt, int loc, Cigar cigar, String hap, String newHap) {
        final Haplotype h = new Haplotype(hap.getBytes());
        final Allele h1refAllele = Allele.create(ref, true);
        final Allele h1altAllele = Allele.create(alt, false);
        final ArrayList<Allele> alleles = new ArrayList<Allele>();
        alleles.add(h1refAllele);
        alleles.add(h1altAllele);
        final VariantContext vc = new VariantContextBuilder().alleles(alleles).loc("1", loc, loc + h1refAllele.getBases().length - 1).make();
        h.setAlignmentStartHapwrtRef(0);
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    private void validate(VariantContext vc, RefMetaDataTracker tracker, ReferenceContext ref) {
        if ( DO_NOT_VALIDATE_FILTERED && vc.isFiltered() )
            return;

        // get the true reference allele
        final Allele reportedRefAllele = vc.getReference();
        final int refLength = reportedRefAllele.length();
        if ( refLength > 100 ) {
            logger.info(String.format("Reference allele is too long (%d) at position %s:%d; skipping that record.", refLength, vc.getChr(), vc.getStart()));
            return;
        }

        final byte[] observedRefBases = new byte[refLength];
        System.arraycopy(ref.getBases(), 0, observedRefBases, 0, refLength);
        final Allele observedRefAllele = Allele.create(observedRefBases);

        // get the RS IDs
        Set<String> rsIDs = null;
        if ( tracker.hasValues(dbsnp.dbsnp) ) {
            rsIDs = new HashSet<String>();
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        if ( comp.getType() != eval.getType() )
            return EvalCompMatchType.NO_MATCH;

        // find the comp which matches both the reference allele and alternate allele from eval
        final Allele altEval = eval.getAlternateAlleles().size() == 0 ? null : eval.getAlternateAllele(0);
        final Allele altComp = comp.getAlternateAlleles().size() == 0 ? null : comp.getAlternateAllele(0);
        if ((altEval == null && altComp == null) || (altEval != null && altEval.equals(altComp) && eval.getReference().equals(comp.getReference())))
            return EvalCompMatchType.STRICT;
        else
            return requireStrictAlleleMatch ? EvalCompMatchType.NO_MATCH : EvalCompMatchType.LENIENT;
    }
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            for (final Map.Entry<GATKSAMRecord,Map<Allele,Double>> readEntry : sampleEntry.getValue().getLikelihoodReadMap().entrySet()) {
                final GATKSAMRecord read = readEntry.getKey();
                final int readIndex = sampleMatrix.readIndex(read);
                final Map<Allele,Double> alleleToLikelihoodMap = readEntry.getValue();
                for (int a = 0; a < alleleCount; a++) {
                    final Allele allele = alleleList.alleleAt(a);
                    final Double likelihood = alleleToLikelihoodMap.get(allele);
                    if (likelihood == null)
                        throw new IllegalArgumentException("there is no likelihood for allele " + allele + " and read " + read);
                    sampleMatrix.set(a,readIndex,likelihood);
                }
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            final byte[] overallGCP = gcp.get(read);

            // peak at the next haplotype in the list (necessary to get nextHaplotypeBases, which is required for caching in the array implementation)
            final boolean isFirstHaplotype = true;
            for (int a = 0; a < alleleCount; a++) {
                final Allele allele = alleles.get(a);
                final byte[] alleleBases = allele.getBases();
                final byte[] nextAlleleBases = a == alleles.size() - 1 ? null : alleles.get(a + 1).getBases();
                final double lk = computeReadLikelihoodGivenHaplotypeLog10(alleleBases,
                        readBases, readQuals, readInsQuals, readDelQuals, overallGCP, isFirstHaplotype, nextAlleleBases);
                likelihoods.set(a, readIndex, lk);
                mLikelihoodArray[idx++] = lk;
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        };
        // Rebuild a new set of unit test data with all permutations of alleles.
        final List<Object[]> allPermutationUnitTestDataList = new ArrayList<Object[]>();
        for (final Object[] unitTestData : originalUnitTestData) {
            allPermutationUnitTestDataList.add(unitTestData);
            final Allele truthAllele1 = (Allele) unitTestData[0];
            final Allele truthAllele2 = (Allele) unitTestData[1];
            final TruthState expectedTruthState = (TruthState) unitTestData[2];
            final Allele callAllele1 = (Allele) unitTestData[3];
            final Allele callAllele2 = (Allele) unitTestData[4];
            final CallState expectedCallState = (CallState) unitTestData[5];
            if (!callAllele1.equals(callAllele2)) {
                allPermutationUnitTestDataList.add(new Object[]{truthAllele1, truthAllele2, expectedTruthState, callAllele2, callAllele1, expectedCallState});
            }
            if (!truthAllele1.equals(truthAllele2)) {
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Related Classes of htsjdk.variant.variantcontext.Allele

  • bcbio.gatk.tools.walkers.annotator.FisherStrand
  • bcbio.variation.annotate.AlleleBalanceConfidenceInterval
  • bcbio.variation.annotate.MostProbableGenotype
  • org.broadinstitute.gatk.tools.walkers.annotator.InbreedingCoeff
  • org.broadinstitute.gatk.tools.walkers.annotator.StrandBiasTest
  • org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.StateTracker
  • org.broadinstitute.gatk.tools.walkers.genotyper.AlleleListUtilsUnitTest
  • org.broadinstitute.gatk.tools.walkers.genotyper.ErrorModel
  • org.broadinstitute.gatk.tools.walkers.genotyper.GeneralPloidyIndelGenotypeLikelihoods
  • org.broadinstitute.gatk.tools.walkers.genotyper.GeneralPloidySNPGenotypeLikelihoods
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