Examples of ReadThreadingGraph

Examples of org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.ReadThreadingGraph

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        final List<Haplotype> haplotypes = actd.haplotypeList();
        for (final Haplotype h : haplotypes)
            h.setGenomeLocation(activeRegion.getExtendedLoc());

        final ReadThreadingGraph rtg = new ReadThreadingGraph(10);
        for (final Haplotype h : haplotypes)
            rtg.addSequence("seq-" + Math.abs(h.hashCode()), h.getBases(), h.isReference());
        final SeqGraph seqGraph = rtg.convertToSequenceGraph();
        final AssemblyResult ar = new AssemblyResult(AssemblyResult.Status.ASSEMBLED_SOME_VARIATION,seqGraph);
        ar.setThreadingGraph(rtg);
        final Map<Haplotype,AssemblyResult> result =
                new HashMap<>();
        for (final Haplotype h : haplotypes)
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Examples of org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.ReadThreadingGraph

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    public java.util.Iterator<Object[]> assemblyResults() {
        final int size = THREE_KS_GRAPH_AND_HAPLOTYPES.length * (1 + TEN_KS_GRAPH_AND_HAPLOTYPES.length);
        final Object[][] result = new Object[size][];

        for (int i = 0; i < THREE_KS_GRAPH_AND_HAPLOTYPES.length; i++) {
            final ReadThreadingGraph rtg = new ReadThreadingGraph((String) THREE_KS_GRAPH_AND_HAPLOTYPES[i][0]);
            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);
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Examples of org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.ReadThreadingGraph

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        else return stringRepresentation;
    }

    public AssemblyResultSet assemblyResultSet() {
        if (assemblyResultSet == null) {
            final ReadThreadingGraph rtg = new ReadThreadingGraph(kmerSize);
            rtg.addSequence("anonymous", this.getReference().getBytes(), true);
            for (final String haplotype : this.haplotypesStrings()) {
                rtg.addSequence("anonymous", haplotype.getBytes(), false);
            }
            rtg.buildGraphIfNecessary();
            if (rtg.hasCycles())
                throw new RuntimeException("there is cycles in the reference with kmer size " + kmerSize + ". Don't use this size for the benchmark or change the reference");

            List<Haplotype> haplotypeList = this.haplotypeList();

            assemblyResultSet = new AssemblyResultSet();
            final AssemblyResult ar = new AssemblyResult((haplotypeList.size() > 1 ?
                    AssemblyResult.Status.ASSEMBLED_SOME_VARIATION : AssemblyResult.Status.JUST_ASSEMBLED_REFERENCE),rtg.convertToSequenceGraph());
            ar.setThreadingGraph(rtg);

            for (final Haplotype h : haplotypeList)
                assemblyResultSet.add(h, ar);
        }
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