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

Example 1 with PloidyModel

use of org.broadinstitute.hellbender.tools.walkers.genotyper.PloidyModel in project gatk-protected 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);
        }
    }
}

Example 2 with PloidyModel

use of org.broadinstitute.hellbender.tools.walkers.genotyper.PloidyModel in project gatk-protected by broadinstitute.

the class ReferenceConfidenceModelUnitTest method testRefConfidenceBasic.

@Test(dataProvider = "RefConfidenceData")
public void testRefConfidenceBasic(final int nReads, final int extension) {
    final RefConfData data = new RefConfData("ACGTAACCGGTT", extension);
    final List<Haplotype> haplotypes = Arrays.asList(data.getRefHap());
    final List<VariantContext> calls = Collections.emptyList();
    for (int i = 0; i < nReads; i++) {
        data.getActiveRegion().add(data.makeRead(0, data.getRefLength()));
    }
    final ReadLikelihoods<Haplotype> likelihoods = createDummyStratifiedReadMap(data.getRefHap(), samples, data.getActiveRegion());
    final PloidyModel ploidyModel = new HomogeneousPloidyModel(samples, 2);
    final IndependentSampleGenotypesModel genotypingModel = new IndependentSampleGenotypesModel();
    final List<Integer> expectedDPs = Collections.nCopies(data.getActiveRegion().getSpan().size(), nReads);
    final List<VariantContext> contexts = model.calculateRefConfidence(data.getRefHap(), haplotypes, data.getPaddedRefLoc(), data.getActiveRegion(), likelihoods, ploidyModel, calls);
    checkReferenceModelResult(data, contexts, expectedDPs, calls);
}

Example 3 with PloidyModel

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

the class ReferenceConfidenceModelUnitTest method testRefConfidenceWithCalls.

@Test
public void testRefConfidenceWithCalls() {
    final RefConfData xxxdata = new RefConfData("ACGTAACCGGTT", 0);
    final int start = xxxdata.getStart();
    final int stop = xxxdata.getEnd();
    final PloidyModel ploidyModel = new HomogeneousPloidyModel(samples, 2);
    final IndependentSampleGenotypesModel genotypingModel = new IndependentSampleGenotypesModel();
    for (int nReads = 0; nReads < 2; nReads++) {
        final VariantContext vcStart = GATKVariantContextUtils.makeFromAlleles("test", "chr1", start, Arrays.asList("A", "C"));
        final VariantContext vcEnd = GATKVariantContextUtils.makeFromAlleles("test", "chr1", stop, Arrays.asList("A", "C"));
        final VariantContext vcMiddle = GATKVariantContextUtils.makeFromAlleles("test", "chr1", start + 2, Arrays.asList("A", "C"));
        final VariantContext vcDel = GATKVariantContextUtils.makeFromAlleles("test", "chr1", start + 4, Arrays.asList("AAC", "A"));
        final VariantContext vcIns = GATKVariantContextUtils.makeFromAlleles("test", "chr1", start + 8, Arrays.asList("G", "GCG"));
        final List<VariantContext> allCalls = Arrays.asList(vcStart, vcEnd, vcMiddle, vcDel, vcIns);
        for (int n = 1; n <= allCalls.size(); n++) {
            for (final List<VariantContext> calls : Utils.makePermutations(allCalls, n, false)) {
                final RefConfData data = new RefConfData("ACGTAACCGGTT", 0);
                final List<Haplotype> haplotypes = Arrays.asList(data.getRefHap());
                for (int i = 0; i < nReads; i++) {
                    data.getActiveRegion().add(data.makeRead(0, data.getRefLength()));
                }
                final ReadLikelihoods<Haplotype> likelihoods = createDummyStratifiedReadMap(data.getRefHap(), samples, data.getActiveRegion());
                final List<Integer> expectedDPs = Collections.nCopies(data.getActiveRegion().getSpan().size(), nReads);
                final List<VariantContext> contexts = model.calculateRefConfidence(data.getRefHap(), haplotypes, data.getPaddedRefLoc(), data.getActiveRegion(), likelihoods, ploidyModel, calls);
                checkReferenceModelResult(data, contexts, expectedDPs, calls);
            }
        }
    }
}

Example 4 with PloidyModel

use of org.broadinstitute.hellbender.tools.walkers.genotyper.PloidyModel in project gatk-protected by broadinstitute.

the class ReferenceConfidenceModelUnitTest method testRefConfidenceWithCalls.

@Test
public void testRefConfidenceWithCalls() {
    final RefConfData xxxdata = new RefConfData("ACGTAACCGGTT", 0);
    final int start = xxxdata.getStart();
    final int stop = xxxdata.getEnd();
    final PloidyModel ploidyModel = new HomogeneousPloidyModel(samples, 2);
    final IndependentSampleGenotypesModel genotypingModel = new IndependentSampleGenotypesModel();
    for (int nReads = 0; nReads < 2; nReads++) {
        final VariantContext vcStart = GATKVariantContextUtils.makeFromAlleles("test", "chr1", start, Arrays.asList("A", "C"));
        final VariantContext vcEnd = GATKVariantContextUtils.makeFromAlleles("test", "chr1", stop, Arrays.asList("A", "C"));
        final VariantContext vcMiddle = GATKVariantContextUtils.makeFromAlleles("test", "chr1", start + 2, Arrays.asList("A", "C"));
        final VariantContext vcDel = GATKVariantContextUtils.makeFromAlleles("test", "chr1", start + 4, Arrays.asList("AAC", "A"));
        final VariantContext vcIns = GATKVariantContextUtils.makeFromAlleles("test", "chr1", start + 8, Arrays.asList("G", "GCG"));
        final List<VariantContext> allCalls = Arrays.asList(vcStart, vcEnd, vcMiddle, vcDel, vcIns);
        for (int n = 1; n <= allCalls.size(); n++) {
            for (final List<VariantContext> calls : Utils.makePermutations(allCalls, n, false)) {
                final RefConfData data = new RefConfData("ACGTAACCGGTT", 0);
                final List<Haplotype> haplotypes = Arrays.asList(data.getRefHap());
                for (int i = 0; i < nReads; i++) {
                    data.getActiveRegion().add(data.makeRead(0, data.getRefLength()));
                }
                final ReadLikelihoods<Haplotype> likelihoods = createDummyStratifiedReadMap(data.getRefHap(), samples, data.getActiveRegion());
                final List<Integer> expectedDPs = Collections.nCopies(data.getActiveRegion().getSpan().size(), nReads);
                final List<VariantContext> contexts = model.calculateRefConfidence(data.getRefHap(), haplotypes, data.getPaddedRefLoc(), data.getActiveRegion(), likelihoods, ploidyModel, calls);
                checkReferenceModelResult(data, contexts, expectedDPs, calls);
            }
        }
    }
}

Example 5 with PloidyModel

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

the class ReferenceConfidenceModelUnitTest method testRefConfidenceBasic.

@Test(dataProvider = "RefConfidenceData")
public void testRefConfidenceBasic(final int nReads, final int extension) {
    final RefConfData data = new RefConfData("ACGTAACCGGTT", extension);
    final List<Haplotype> haplotypes = Arrays.asList(data.getRefHap());
    final List<VariantContext> calls = Collections.emptyList();
    for (int i = 0; i < nReads; i++) {
        data.getActiveRegion().add(data.makeRead(0, data.getRefLength()));
    }
    final ReadLikelihoods<Haplotype> likelihoods = createDummyStratifiedReadMap(data.getRefHap(), samples, data.getActiveRegion());
    final PloidyModel ploidyModel = new HomogeneousPloidyModel(samples, 2);
    final IndependentSampleGenotypesModel genotypingModel = new IndependentSampleGenotypesModel();
    final List<Integer> expectedDPs = Collections.nCopies(data.getActiveRegion().getSpan().size(), nReads);
    final List<VariantContext> contexts = model.calculateRefConfidence(data.getRefHap(), haplotypes, data.getPaddedRefLoc(), data.getActiveRegion(), likelihoods, ploidyModel, calls);
    checkReferenceModelResult(data, contexts, expectedDPs, calls);
}