Examples with AllelicCount org.broadinstitute.hellbender.tools.exome.alleliccount.AllelicCount used on opensource projects

Example 56 with AllelicCount

use of org.broadinstitute.hellbender.tools.exome.alleliccount.AllelicCount in project gatk-protected by broadinstitute.

the class CalculatePulldownPhasePosteriors method calculatePhasePosteriors.

@VisibleForTesting
protected static AllelicCountWithPhasePosteriorsCollection calculatePhasePosteriors(final AllelicCountCollection counts, final List<SimpleInterval> segments, final AlleleFractionState state, final AllelicPanelOfNormals allelicPoN) {
    final TargetCollection<SimpleInterval> segmentTargetCollection = new HashedListTargetCollection<>(segments);
    final AllelicCountWithPhasePosteriorsCollection countsWithPhasePosteriors = new AllelicCountWithPhasePosteriorsCollection();
    for (final AllelicCount count : counts.getCounts()) {
        final int segmentIndex = segmentTargetCollection.index(count.getInterval());
        if (segmentIndex < 0) {
            throw new UserException.EmptyIntersection(String.format("The AllelicCount at %s is not located within one of the input segments.", count.getInterval()));
        }
        final AlleleFractionGlobalParameters parameters = state.globalParameters();
        final double minorFraction = state.segmentMinorFraction(segmentIndex);
        final double refMinorLogProb = AlleleFractionLikelihoods.hetLogLikelihood(parameters, minorFraction, count, AlleleFractionIndicator.REF_MINOR, allelicPoN);
        final double altMinorLogProb = AlleleFractionLikelihoods.hetLogLikelihood(parameters, minorFraction, count, AlleleFractionIndicator.ALT_MINOR, allelicPoN);
        final double outlierLogProb = AlleleFractionLikelihoods.hetLogLikelihood(parameters, minorFraction, count, AlleleFractionIndicator.OUTLIER, allelicPoN);
        final AllelicCountWithPhasePosteriors countWithPhasePosteriors = new AllelicCountWithPhasePosteriors(count, refMinorLogProb, altMinorLogProb, outlierLogProb);
        countsWithPhasePosteriors.add(countWithPhasePosteriors);
    }
    return countsWithPhasePosteriors;
}

Example 57 with AllelicCount

use of org.broadinstitute.hellbender.tools.exome.alleliccount.AllelicCount in project gatk by broadinstitute.

the class SNPSegmenterUnitTest method testAllelicFractionBasedSegmentation.

/**
     * Tests that segments are correctly determined using allelic counts from SNP sites.
     * Segment-mean and target-number columns from expected segment file are not checked.
     */
@Test
public void testAllelicFractionBasedSegmentation() {
    final String sampleName = "test";
    final File snpFile = new File(TEST_SUB_DIR, "snps-simplified-for-allelic-fraction-segmentation.tsv");
    final List<AllelicCount> snpCounts = new AllelicCountCollection(snpFile).getCounts();
    final TargetCollection<AllelicCount> snps = new HashedListTargetCollection<>(snpCounts);
    final File resultFile = createTempFile("snp-segmenter-test-result", ".seg");
    SNPSegmenter.writeSegmentFile(snps, sampleName, resultFile);
    final File expectedFile = new File(TEST_SUB_DIR, "snp-segmenter-test-expected.seg");
    Assert.assertTrue(resultFile.exists(), "SNPSegmenterTest output was not written to temp file: " + resultFile);
    final List<SimpleInterval> result = SegmentUtils.readIntervalsFromSegmentFile(resultFile);
    final List<SimpleInterval> expected = SegmentUtils.readIntervalsFromSegmentFile(expectedFile);
    Assert.assertEquals(result, expected);
}

Example 58 with AllelicCount

use of org.broadinstitute.hellbender.tools.exome.alleliccount.AllelicCount in project gatk by broadinstitute.

the class AlleleFractionLikelihoodsUnitTest method testRefMinor.

//ALT_MINOR <--> REF_MINOR is equivalent to f <--> 1 - f
@Test
public void testRefMinor() {
    //pi is just a prefactor so we don't need to test it thoroughly here
    final double pi = 0.01;
    for (final double f : Arrays.asList(0.1, 0.2, 0.3)) {
        for (final double mean : Arrays.asList(0.9, 1.0, 1.1)) {
            for (final double variance : Arrays.asList(0.02, 0.01)) {
                final AlleleFractionGlobalParameters parameters = new AlleleFractionGlobalParameters(mean, variance, pi);
                for (final int a : Arrays.asList(1, 10, 20)) {
                    //alt count
                    for (final int r : Arrays.asList(1, 10, 20)) {
                        //ref count
                        final AllelicCount count = new AllelicCount(DUMMY, r, a);
                        final double altMinorLk = AlleleFractionLikelihoods.hetLogLikelihood(parameters, f, count, AlleleFractionIndicator.ALT_MINOR);
                        final double refMinorLk = AlleleFractionLikelihoods.hetLogLikelihood(parameters, 1 - f, count, AlleleFractionIndicator.REF_MINOR);
                        Assert.assertEquals(altMinorLk, refMinorLk, 1e-10);
                    }
                }
            }
        }
    }
}

Example 59 with AllelicCount

use of org.broadinstitute.hellbender.tools.exome.alleliccount.AllelicCount in project gatk by broadinstitute.

the class AlleleFractionLikelihoodsUnitTest method testHetLogLikelihoodOutlierProbabilityDependence.

@Test
public void testHetLogLikelihoodOutlierProbabilityDependence() {
    final AllelicCount count = new AllelicCount(DUMMY, 11, 37);
    final double f = 0.25;
    final double mean = 1.0;
    final double variance = 0.01;
    final double pi1 = 0.1;
    final double pi2 = 0.2;
    final double pi3 = 0.3;
    final AlleleFractionGlobalParameters parameters1 = new AlleleFractionGlobalParameters(mean, variance, pi1);
    final AlleleFractionGlobalParameters parameters2 = new AlleleFractionGlobalParameters(mean, variance, pi2);
    final AlleleFractionGlobalParameters parameters3 = new AlleleFractionGlobalParameters(mean, variance, pi3);
    final double lk1 = AlleleFractionLikelihoods.hetLogLikelihood(parameters1, f, count, AlleleFractionIndicator.ALT_MINOR);
    final double lk2 = AlleleFractionLikelihoods.hetLogLikelihood(parameters2, f, count, AlleleFractionIndicator.ALT_MINOR);
    final double lk3 = AlleleFractionLikelihoods.hetLogLikelihood(parameters3, f, count, AlleleFractionIndicator.ALT_MINOR);
    Assert.assertEquals(lk2 - lk1, log(1 - pi2) - log(1 - pi1), EPSILON);
    Assert.assertEquals(lk3 - lk2, log(1 - pi3) - log(1 - pi2), EPSILON);
}

Example 60 with AllelicCount

use of org.broadinstitute.hellbender.tools.exome.alleliccount.AllelicCount in project gatk by broadinstitute.

the class AlleleFractionDataUnitTest method testData.

@Test
public void testData() {
    final List<AllelicCount> ac = new ArrayList<>();
    final List<SimpleInterval> segments = new ArrayList<>();
    // segment 0: hets 0-2
    segments.add(new SimpleInterval("chr", 1, 5));
    ac.add(new AllelicCount(new SimpleInterval("chr", 1, 1), 0, 5));
    ac.add(new AllelicCount(new SimpleInterval("chr", 2, 2), 5, 0));
    ac.add(new AllelicCount(new SimpleInterval("chr", 3, 3), 5, 5));
    // segment 1: hets 3-4
    segments.add(new SimpleInterval("chr", 10, 15));
    ac.add(new AllelicCount(new SimpleInterval("chr", 10, 10), 1, 1));
    ac.add(new AllelicCount(new SimpleInterval("chr", 11, 11), 2, 2));
    final Genome genome = new Genome(AlleleFractionSimulatedData.TRIVIAL_TARGETS, ac);
    final SegmentedGenome segmentedGenome = new SegmentedGenome(segments, genome);
    final AlleleFractionData dc = new AlleleFractionData(segmentedGenome);
    Assert.assertEquals(dc.getNumSegments(), 2);
    Assert.assertEquals(dc.getRefCount(0), 0);
    Assert.assertEquals(dc.getAltCount(0), 5);
    Assert.assertEquals(dc.getReadCount(2), 10);
    Assert.assertEquals(dc.getReadCount(3), 2);
    Assert.assertEquals(dc.getRefCount(4), 2);
    Assert.assertEquals(dc.getAltCount(4), 2);
    Assert.assertEquals(dc.getAllelicCount(0).getAltReadCount(), 5);
    Assert.assertEquals(dc.getAllelicCount(1).getAltReadCount(), 0);
    Assert.assertEquals(dc.getAllelicCount(3).getRefReadCount(), 1);
    Assert.assertEquals(dc.getAllelicCount(4).getRefReadCount(), 2);
    Assert.assertEquals(dc.getCountsInSegment(0).get(1).getRefReadCount(), 5);
    Assert.assertEquals(dc.getCountsInSegment(0).get(1).getAltReadCount(), 0);
    final List<Integer> hetsInSegment0 = dc.getHetsInSegment(0);
    Assert.assertEquals(hetsInSegment0.size(), 3);
    Assert.assertEquals((int) hetsInSegment0.get(0), 0);
    Assert.assertEquals((int) hetsInSegment0.get(2), 2);
    final List<Integer> hetsInSegment1 = dc.getHetsInSegment(1);
    Assert.assertEquals(hetsInSegment1.size(), 2);
    Assert.assertEquals((int) hetsInSegment1.get(0), 3);
    Assert.assertEquals((int) hetsInSegment1.get(1), 4);
}