Package org.broadinstitute.gatk.utils.haplotype

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

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            final AssemblyResult ar = new AssemblyResult(AssemblyResult.Status.ASSEMBLED_SOME_VARIATION,rtg.convertToSequenceGraph());
            ar.setThreadingGraph(rtg);
            final Object[] haplotypeStrings = (Object[]) THREE_KS_GRAPH_AND_HAPLOTYPES[i][1];
            final Haplotype[] haplotypes = new Haplotype[haplotypeStrings.length];
            for (int j = 0; j < haplotypeStrings.length; j++) {
                haplotypes[j] = new Haplotype(((String)haplotypeStrings[j]).getBytes(),j == 0);
                haplotypes[j].setGenomeLocation(genomeLocParser.createGenomeLoc("chr1",1,haplotypes[j].length() + 1));
            }
            result[i] = new Object[] { Collections.singletonList(ar),Arrays.asList(Arrays.asList(haplotypes))};
            for (int j = 0; j < TEN_KS_GRAPH_AND_HAPLOTYPES.length; j++) {
                final ReadThreadingGraph rtg10 = new ReadThreadingGraph((String) TEN_KS_GRAPH_AND_HAPLOTYPES[j][0]);
                final AssemblyResult ar10 = new AssemblyResult(AssemblyResult.Status.ASSEMBLED_SOME_VARIATION,rtg10.convertToSequenceGraph());
                ar10.setThreadingGraph(rtg10);
                final Object[] haplotypeStrings10 = (Object[]) TEN_KS_GRAPH_AND_HAPLOTYPES[j][1];
                final Haplotype[] haplotype10 = new Haplotype[haplotypeStrings10.length];
                for (int k = 0; k < haplotypeStrings10.length; k++) {
                    haplotype10[k] = new Haplotype(((String)haplotypeStrings10[k]).getBytes(),false);
                    haplotype10[k].setGenomeLocation(genomeLocParser.createGenomeLoc("chr1", 1, haplotype10[k].length() + 1));
                }

                result[THREE_KS_GRAPH_AND_HAPLOTYPES.length + i * TEN_KS_GRAPH_AND_HAPLOTYPES.length + j] = new Object[] { Arrays.asList(ar,ar10),
                        Arrays.asList( Arrays.asList(haplotypes), Arrays.asList(haplotype10)) };
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     * @param refBases the ref bases
     * @param paddedReferenceLoc the location spanning of the refBases -- can be longer than activeRegion.getLocation()
     * @return a reference haplotype
     */
    public static Haplotype createReferenceHaplotype(final ActiveRegion activeRegion, final byte[] refBases, final GenomeLoc paddedReferenceLoc) {
        final Haplotype refHaplotype = new Haplotype(refBases, true);
        final int alignmentStart = activeRegion.getExtendedLoc().getStart() - paddedReferenceLoc.getStart();
        if ( alignmentStart < 0 ) throw new IllegalStateException("Bad alignment start in createReferenceHaplotype " + alignmentStart);
        refHaplotype.setAlignmentStartHapwrtRef(alignmentStart);
        final Cigar c = new Cigar();
        c.add(new CigarElement(refHaplotype.getBases().length, CigarOperator.M));
        refHaplotype.setCigar(c);
        return refHaplotype;
    }
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        if (refHaplotype == null) throw new IllegalStateException();
        if (trimmedActiveRegion == null) throw new NullPointerException();
        final AssemblyResultSet result = new AssemblyResultSet();

        for (final Haplotype trimmed : originalByTrimmedHaplotypes.keySet()) {
            final Haplotype original = originalByTrimmedHaplotypes.get(trimmed);
            if (original == null)
                throw new NullPointerException("all trimmed haplotypes must have an original one");
            final AssemblyResult as = assemblyResultByHaplotype.get(original);
            if (as == null) result.add(trimmed); else result.add(trimmed, as);
        }
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        // trim down the haplotypes
        final Map<Haplotype,Haplotype> originalByTrimmedHaplotypes = new HashMap<>();

        for ( final Haplotype h : haplotypeList ) {
            final Haplotype trimmed = h.trim(trimmedActiveRegion.getExtendedLoc());

            if ( trimmed != null ) {
                if (originalByTrimmedHaplotypes.containsKey(trimmed)) {
                    if (trimmed.isReference()) {
                        originalByTrimmedHaplotypes.remove(trimmed);
                        originalByTrimmedHaplotypes.put(trimmed, h);
                    }
                } else
                    originalByTrimmedHaplotypes.put(trimmed,h);
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            final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, loc.getContig(), loc.getContigIndex(), loc.getStart(), bases, quals, cigar);
            reads.add(read);
        }

        // TODO -- generalize to all assemblers
        final Haplotype refHaplotype = new Haplotype(refBases, true);
        final List<Haplotype> haplotypes = assemble(assembler, refBases, loc, reads);
        Assert.assertEquals(haplotypes, Collections.singletonList(refHaplotype));
    }
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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.assertEquals(haplotypes, Arrays.asList(refHaplotype, altHaplotype));
    }
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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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Related Classes of org.broadinstitute.gatk.utils.haplotype.Haplotype

  • htsjdk.samtools.Cigar
  • htsjdk.samtools.CigarElement
  • htsjdk.variant.variantcontext.Allele
  • org.broadinstitute.gatk.tools.walkers.haplotypecaller.ActiveRegionTestDataSetUnitTest
  • org.broadinstitute.gatk.tools.walkers.haplotypecaller.AssemblyResultSet
  • org.broadinstitute.gatk.tools.walkers.haplotypecaller.AssemblyResultSetUnitTest
  • org.broadinstitute.gatk.tools.walkers.haplotypecaller.GraphBasedLikelihoodCalculationEngineInstance
  • org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs.KBestHaplotype
  • org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller
  • org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngineUnitTest
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