Examples with TestingReadThreadingGraph org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.TestingReadThreadingGraph used on opensource projects

Example 1 with TestingReadThreadingGraph

use of org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.TestingReadThreadingGraph in project gatk by broadinstitute.

the class AssemblyResultSetUnitTest method assemblyResults.

@DataProvider(name = "assemblyResults")
public 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 TestingReadThreadingGraph((String) THREE_KS_GRAPH_AND_HAPLOTYPES[i][0]);
        final AssemblyResult ar = new AssemblyResult(AssemblyResult.Status.ASSEMBLED_SOME_VARIATION, rtg.toSequenceGraph(), 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("1", 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 TestingReadThreadingGraph((String) TEN_KS_GRAPH_AND_HAPLOTYPES[j][0]);
            final AssemblyResult ar10 = new AssemblyResult(AssemblyResult.Status.ASSEMBLED_SOME_VARIATION, rtg10.toSequenceGraph(), 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("1", 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)) };
        }
    }
    return Arrays.asList(result).iterator();
}

Example 2 with TestingReadThreadingGraph

use of org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.TestingReadThreadingGraph in project gatk-protected by broadinstitute.

the class AssemblyResultSetUnitTest method assemblyResults.

@DataProvider(name = "assemblyResults")
public 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 TestingReadThreadingGraph((String) THREE_KS_GRAPH_AND_HAPLOTYPES[i][0]);
        final AssemblyResult ar = new AssemblyResult(AssemblyResult.Status.ASSEMBLED_SOME_VARIATION, rtg.toSequenceGraph(), 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("1", 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 TestingReadThreadingGraph((String) TEN_KS_GRAPH_AND_HAPLOTYPES[j][0]);
            final AssemblyResult ar10 = new AssemblyResult(AssemblyResult.Status.ASSEMBLED_SOME_VARIATION, rtg10.toSequenceGraph(), 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("1", 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)) };
        }
    }
    return Arrays.asList(result).iterator();
}