Package org.broadinstitute.gatk.utils.haplotype

Examples of org.broadinstitute.gatk.utils.haplotype.EventMap

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        final Allele altC = Allele.create("C", false);
        final Allele altT = Allele.create("T", false);

        final Haplotype AtoC1 = new Haplotype("AACAA".getBytes());
        final VariantContext vc1 = new VariantContextBuilder().chr("20").start(3).stop(3).alleles(Arrays.asList(ref, altC)).make();
        AtoC1.setEventMap(new EventMap(Arrays.asList(vc1)));
        AtoC1.getEventMap().put(3, vc1);
        haplotypes.add(AtoC1);

        final Haplotype AtoC2 = new Haplotype("AAACA".getBytes());
        final VariantContext vc2 = new VariantContextBuilder().chr("20").start(4).stop(4).alleles(Arrays.asList(ref, altT)).make();
        AtoC2.setEventMap(new EventMap(Arrays.asList(vc2)));
        AtoC2.getEventMap().put(4, vc2);
        haplotypes.add(AtoC2);

        tests.add(new Object[]{vc1, haplotypes, AtoC1});
        tests.add(new Object[]{vc2, haplotypes, AtoC2});
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        final VariantContext vc3 = new VariantContextBuilder().chr("20").start(3).stop(3).alleles(Arrays.asList(ref, altT)).make();
        final VariantContext vc4 = new VariantContextBuilder().chr("20").start(4).stop(4).alleles(Arrays.asList(ref, altC)).make();
        final List<VariantContext> calls = Arrays.asList(vc2, vc3, vc4);

        final Haplotype pos1 = new Haplotype("CAAAA".getBytes());
        pos1.setEventMap(new EventMap(Arrays.asList(vc1)));
        pos1.getEventMap().put(1, vc1);
        final Haplotype pos2 = new Haplotype("ACAAA".getBytes());
        pos2.setEventMap(new EventMap(Arrays.asList(vc2)));
        pos2.getEventMap().put(2, vc2);
        final Haplotype pos3 = new Haplotype("AACAA".getBytes());
        pos3.setEventMap(new EventMap(Arrays.asList(vc3)));
        pos3.getEventMap().put(3, vc3);
        final Haplotype pos4 = new Haplotype("AAACA".getBytes());
        pos4.setEventMap(new EventMap(Arrays.asList(vc4)));
        pos4.getEventMap().put(4, vc4);
        final Haplotype pos24 = new Haplotype("ACACA".getBytes());
        pos24.setEventMap(new EventMap(Arrays.asList(vc2, vc4)));
        pos24.getEventMap().put(2, vc2);
        pos24.getEventMap().put(4, vc4);
        final Haplotype pos34 = new Haplotype("AACCA".getBytes());
        pos34.setEventMap(new EventMap(Arrays.asList(vc3, vc4)));
        pos34.getEventMap().put(3, vc3);
        pos34.getEventMap().put(4, vc4);
        final Haplotype pos234 = new Haplotype("ACCCA".getBytes());
        pos234.setEventMap(new EventMap(Arrays.asList(vc2, vc3, vc4)));
        pos234.getEventMap().put(2, vc2);
        pos234.getEventMap().put(3, vc3);
        pos234.getEventMap().put(4, vc4);

        final Map<VariantContext, Set<Haplotype>> haplotypeMap = new HashMap<>();
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        // the overlapping events to merge into a common reference view
        final List<VariantContext> eventsAtThisLoc = new ArrayList<>();

        if( activeAllelesToGenotype.isEmpty() ) {
            for( final Haplotype h : haplotypes ) {
                final EventMap eventMap = h.getEventMap();
                final VariantContext vc = eventMap.get(loc);
                if( vc != null && !containsVCWithMatchingAlleles(eventsAtThisLoc, vc) ) {
                    eventsAtThisLoc.add(vc);
                }
            }
        } else { // we are in GGA mode!
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        return eventMapper;
    }

    @Deprecated
    protected static Map<Integer,VariantContext> generateVCsFromAlignment( final Haplotype haplotype, final byte[] ref, final GenomeLoc refLoc, final String sourceNameToAdd ) {
        return new EventMap(haplotype, ref, refLoc, sourceNameToAdd);
    }
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Related Classes of org.broadinstitute.gatk.utils.haplotype.EventMap

  • htsjdk.samtools.Cigar
  • htsjdk.samtools.CigarElement
  • htsjdk.variant.variantcontext.Allele
  • htsjdk.variant.variantcontext.VariantContext
  • htsjdk.variant.variantcontext.VariantContextBuilder
  • org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine
  • org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngineUnitTest
  • org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException
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