Examples with HomogeneousPloidyModel org.broadinstitute.hellbender.tools.walkers.genotyper.HomogeneousPloidyModel used on opensource projects

Example 6 with HomogeneousPloidyModel

use of org.broadinstitute.hellbender.tools.walkers.genotyper.HomogeneousPloidyModel in project gatk by broadinstitute.

the class ReferenceConfidenceModelUnitTest method testRefConfidencePartialReads.

@Test
public void testRefConfidencePartialReads() {
    final PloidyModel ploidyModel = new HomogeneousPloidyModel(samples, 2);
    final IndependentSampleGenotypesModel genotypingModel = new IndependentSampleGenotypesModel();
    final String ref = "ACGTAACCGGTT";
    for (int readLen = 3; readLen < ref.length(); readLen++) {
        for (int start = 0; start < ref.length() - readLen; start++) {
            final RefConfData data = new RefConfData(ref, 0);
            final List<Haplotype> haplotypes = Arrays.asList(data.getRefHap());
            final List<VariantContext> calls = Collections.emptyList();
            data.getActiveRegion().add(data.makeRead(start, readLen));
            final ReadLikelihoods<Haplotype> likelihoods = createDummyStratifiedReadMap(data.getRefHap(), samples, data.getActiveRegion());
            final List<Integer> expectedDPs = new ArrayList<>(Collections.nCopies(data.getActiveRegion().getSpan().size(), 0));
            for (int i = start; i < readLen + start; i++) expectedDPs.set(i, 1);
            final List<VariantContext> contexts = model.calculateRefConfidence(data.getRefHap(), haplotypes, data.getPaddedRefLoc(), data.getActiveRegion(), likelihoods, ploidyModel, calls);
            checkReferenceModelResult(data, contexts, expectedDPs, calls);
        }
    }
}