Package org.broadinstitute.gatk.utils.haplotype

Examples of org.broadinstitute.gatk.utils.haplotype.Haplotype$Event

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        Assert.assertEquals(haplotypes, Arrays.asList(refHaplotype, altHaplotype));
    }


    private List<Haplotype> assemble(final ReadThreadingAssembler assembler, final byte[] refBases, final GenomeLoc loc, final List<GATKSAMRecord> reads) {
        final Haplotype refHaplotype = new Haplotype(refBases, true);
        final Cigar c = new Cigar();
        c.add(new CigarElement(refHaplotype.getBases().length, CigarOperator.M));
        refHaplotype.setCigar(c);

        final ActiveRegion activeRegion = new ActiveRegion(loc, null, true, genomeLocParser, 0);
        activeRegion.addAll(reads);
//        logger.warn("Assembling " + activeRegion + " with " + engine);
        final AssemblyResultSet assemblyResultSet =  assembler.runLocalAssembly(activeRegion, refHaplotype, refBases, loc, Collections.<VariantContext>emptyList(), null);
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            final String cigar = altBases.length + "M";
            final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, loc.getContig(), loc.getContigIndex(), loc.getStart(), bases, quals, cigar);
            reads.add(read);
        }

        final Haplotype refHaplotype = new Haplotype(refBases, true);
        final Haplotype altHaplotype = new Haplotype(altBases, false);
        final List<Haplotype> haplotypes = assemble(assembler, refBases, loc, reads);
        Assert.assertTrue(haplotypes.size() > 0, "Failed to find ref haplotype");
        Assert.assertEquals(haplotypes.get(0), refHaplotype);

        Assert.assertEquals(haplotypes.size(), 2, "Failed to find single alt haplotype");
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            logger.debug("Bad SW alignment; aborting at " + refContext.getLocus());
            return;
        }

        // order results by start position
        final TreeMap<Integer, VariantContext> source1Map = new TreeMap<Integer, VariantContext>(HaplotypeCallerGenotypingEngine.generateVCsFromAlignment(new Haplotype(source1Haplotype, false, 0, swConsensus1.getCigar()), refContext.getBases(), refContext.getWindow(), source1));
        final TreeMap<Integer, VariantContext> source2Map = new TreeMap<Integer, VariantContext>(HaplotypeCallerGenotypingEngine.generateVCsFromAlignment(new Haplotype(source2Haplotype, false, 0, swConsensus2.getCigar()), refContext.getBases(), refContext.getWindow(), source2));
        if ( source1Map.size() == 0 || source2Map.size() == 0 ) {
            // TODO -- handle errors appropriately
            logger.debug("No source alleles; aborting at " + refContext.getLocus());
            return;
        }
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        final Set<Haplotype> haplotypes = new HashSet<>();
        final Allele ref = Allele.create("A", true);
        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});
        tests.add(new Object[]{new VariantContextBuilder().chr("20").start(1).stop(1).alleles(Arrays.asList(ref, altT)).make(), haplotypes, null});
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        final VariantContext vc2 = new VariantContextBuilder().chr("20").start(2).stop(2).alleles(Arrays.asList(ref, altC)).make();
        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<>();

        // test no phased variants #1
        final Set<Haplotype> haplotypes2 = new HashSet<>();
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        final Civar civar = Civar.fromCharSequence(civarString);
        final List<Civar> unrolledCivars = civar.optionalizeAll().unroll();
        List<Haplotype> result = new ArrayList<>(unrolledCivars.size());
        for (final Civar c : unrolledCivars) {
            final String baseString = c.applyTo(reference);
            final Haplotype haplotype = new Haplotype(baseString.getBytes(),baseString.equals(reference));
            haplotype.setGenomeLocation(genomeLocParser.createGenomeLoc("chr1",1,reference.length()));
            try {
            haplotype.setCigar(c.toCigar(reference.length()));
            } catch (final RuntimeException ex) {
                c.applyTo(reference);
                c.toCigar(reference.length());
                throw new RuntimeException("" + c + " " + ex.getMessage(),ex);
            }
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                  stringRepresentation = cigar.substring(6);
                  result.addAll(expandAllHaplotypeCombinations(cigar.substring(6), reference));
              } else if (cigar.matches("^.*\\d+.*$")) {
                  result.add(cigarToHaplotype(reference, cigar, 0, true));
              } else {
                  final Haplotype h = new Haplotype(cigar.getBytes());
                  h.setGenomeLocation(genomeLocParser.createGenomeLoc("chr1",1,reference.length()));
                  result.add(h);
              }
          }
          haplotypeList = result;
        }
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    private static final Pattern cigarPattern = Pattern.compile("(\\d+)([=A-Z])");


    private Haplotype cigarToHaplotype(final String reference, final String cigar, final int offset, final boolean global) {
        final String sequence = applyCigar(reference,cigar,offset,global);
        final Haplotype haplotype = new Haplotype(sequence.getBytes(),reference.equals(sequence));
        haplotype.setGenomeLocation(genomeLocParser.createGenomeLoc("chr1",1,reference.length()));
        haplotype.setCigar(Civar.fromCharSequence(cigar).toCigar(reference.length()));
        return haplotype;
    }
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            this.expected = expected;
        }
       
        public Map<Integer,VariantContext> calcAlignment() {
            final SWPairwiseAlignment alignment = new SWPairwiseAlignment(ref, hap, new Parameters(3,-1,-4, -1));
            final Haplotype h = new Haplotype(hap, false, alignment.getAlignmentStart2wrt1(), alignment.getCigar());
            return HaplotypeCallerGenotypingEngine.generateVCsFromAlignment(h, ref, genomeLocParser.createGenomeLoc("4", 1, 1 + ref.length), "name");
        }
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            final double[] sortedLikelihoods = new double[sortedHaplotypes.size()];
            unsorted.loadRead(read);
            sorted.loadRead(read);
            final Map<Haplotype,Double> unsortedResults = new HashMap<>(haplotypes.size());
            for (int i = 0; i < sortedHaplotypes.size(); i++) {
                final Haplotype h = sortedHaplotypes.get(i);
                final byte[] haplotypeBases = h.getBases().clone();
                unsorted.loadHaplotypeBases(haplotypeBases);
                double lk = unsorted.calculateLocalLikelihood(0, read.getReadLength(), 0, haplotypeBases.length, false);
                unsortedLikelihoods[i] = lk;
            }
            sorted.calculateLocalLikelihoods(0, read.getReadLength(), haplotypeCollection);
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