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

Example 1 with AllelicCountWithPhasePosteriors

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

the class CalculatePulldownPhasePosteriorsIntegrationTest method testCalculatePhasePosteriors.

/**
     * Uses {@link AlleleFractionSimulatedData} to test recovery of phase indicators.  Phase with highest posterior
     * probability is compared to the true phase; we require that
     * {@link CalculatePulldownPhasePosteriorsIntegrationTest#FRACTION_OF_INDICATORS_CORRECT_THRESHOLD} of the
     * indicators are recovered correctly.
     */
@Test
public void testCalculatePhasePosteriors() {
    final double averageHetsPerSegment = 100;
    final int numSegments = 100;
    final int averageDepth = 100;
    final double biasMean = 1.1;
    final double biasVariance = 0.01;
    final double outlierProbability = 0.02;
    final AlleleFractionSimulatedData simulatedData = new AlleleFractionSimulatedData(averageHetsPerSegment, numSegments, averageDepth, biasMean, biasVariance, outlierProbability);
    final SegmentedGenome segmentedGenome = simulatedData.getSegmentedGenome();
    final AlleleFractionState trueState = simulatedData.getTrueState();
    final AlleleFractionSimulatedData.PhaseIndicators truePhases = simulatedData.getTruePhases();
    final AllelicCountCollection counts = new AllelicCountCollection();
    //note that chromosomes are in lexicographical order
    segmentedGenome.getGenome().getSNPs().targets().stream().forEach(counts::add);
    final AllelicCountWithPhasePosteriorsCollection countsWithPhasePosteriors = CalculatePulldownPhasePosteriors.calculatePhasePosteriors(counts, segmentedGenome.getSegments(), trueState, AllelicPanelOfNormals.EMPTY_PON);
    int numIndicatorsCorrect = 0;
    //order is ALT_MINOR, REF_MINOR, OUTLIER
    final Iterator<AlleleFractionIndicator> phaseIterator = truePhases.iterator();
    final Iterator<AllelicCountWithPhasePosteriors> countWithPhasePosteriorsIterator = countsWithPhasePosteriors.getCounts().iterator();
    while (phaseIterator.hasNext() && countWithPhasePosteriorsIterator.hasNext()) {
        final AlleleFractionIndicator truePhase = phaseIterator.next();
        final AllelicCountWithPhasePosteriors countWithPhasePosteriors = countWithPhasePosteriorsIterator.next();
        final List<Double> phaseProbabilities = Arrays.asList(countWithPhasePosteriors.getAltMinorProb(), countWithPhasePosteriors.getRefMinorProb(), countWithPhasePosteriors.getOutlierProb());
        final int indexOfMaxProbPhase = phaseProbabilities.indexOf(Collections.max(phaseProbabilities));
        final AlleleFractionIndicator maxProbPhase = AlleleFractionIndicator.values()[indexOfMaxProbPhase];
        if (maxProbPhase.equals(truePhase)) {
            numIndicatorsCorrect++;
        }
    }
    final double fractionOfIndicatorsCorrect = (double) numIndicatorsCorrect / countsWithPhasePosteriors.getCounts().size();
    Assert.assertTrue(fractionOfIndicatorsCorrect >= FRACTION_OF_INDICATORS_CORRECT_THRESHOLD);
}

Example 2 with AllelicCountWithPhasePosteriors

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

the class CalculatePulldownPhasePosteriorsIntegrationTest method testCalculatePhasePosteriors.

/**
     * Uses {@link AlleleFractionSimulatedData} to test recovery of phase indicators.  Phase with highest posterior
     * probability is compared to the true phase; we require that
     * {@link CalculatePulldownPhasePosteriorsIntegrationTest#FRACTION_OF_INDICATORS_CORRECT_THRESHOLD} of the
     * indicators are recovered correctly.
     */
@Test
public void testCalculatePhasePosteriors() {
    final double averageHetsPerSegment = 100;
    final int numSegments = 100;
    final int averageDepth = 100;
    final double biasMean = 1.1;
    final double biasVariance = 0.01;
    final double outlierProbability = 0.02;
    final AlleleFractionSimulatedData simulatedData = new AlleleFractionSimulatedData(averageHetsPerSegment, numSegments, averageDepth, biasMean, biasVariance, outlierProbability);
    final SegmentedGenome segmentedGenome = simulatedData.getSegmentedGenome();
    final AlleleFractionState trueState = simulatedData.getTrueState();
    final AlleleFractionSimulatedData.PhaseIndicators truePhases = simulatedData.getTruePhases();
    final AllelicCountCollection counts = new AllelicCountCollection();
    //note that chromosomes are in lexicographical order
    segmentedGenome.getGenome().getSNPs().targets().stream().forEach(counts::add);
    final AllelicCountWithPhasePosteriorsCollection countsWithPhasePosteriors = CalculatePulldownPhasePosteriors.calculatePhasePosteriors(counts, segmentedGenome.getSegments(), trueState, AllelicPanelOfNormals.EMPTY_PON);
    int numIndicatorsCorrect = 0;
    //order is ALT_MINOR, REF_MINOR, OUTLIER
    final Iterator<AlleleFractionIndicator> phaseIterator = truePhases.iterator();
    final Iterator<AllelicCountWithPhasePosteriors> countWithPhasePosteriorsIterator = countsWithPhasePosteriors.getCounts().iterator();
    while (phaseIterator.hasNext() && countWithPhasePosteriorsIterator.hasNext()) {
        final AlleleFractionIndicator truePhase = phaseIterator.next();
        final AllelicCountWithPhasePosteriors countWithPhasePosteriors = countWithPhasePosteriorsIterator.next();
        final List<Double> phaseProbabilities = Arrays.asList(countWithPhasePosteriors.getAltMinorProb(), countWithPhasePosteriors.getRefMinorProb(), countWithPhasePosteriors.getOutlierProb());
        final int indexOfMaxProbPhase = phaseProbabilities.indexOf(Collections.max(phaseProbabilities));
        final AlleleFractionIndicator maxProbPhase = AlleleFractionIndicator.values()[indexOfMaxProbPhase];
        if (maxProbPhase.equals(truePhase)) {
            numIndicatorsCorrect++;
        }
    }
    final double fractionOfIndicatorsCorrect = (double) numIndicatorsCorrect / countsWithPhasePosteriors.getCounts().size();
    Assert.assertTrue(fractionOfIndicatorsCorrect >= FRACTION_OF_INDICATORS_CORRECT_THRESHOLD);
}

Example 3 with AllelicCountWithPhasePosteriors

use of org.broadinstitute.hellbender.tools.exome.alleliccount.AllelicCountWithPhasePosteriors in project gatk 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 4 with AllelicCountWithPhasePosteriors

use of org.broadinstitute.hellbender.tools.exome.alleliccount.AllelicCountWithPhasePosteriors 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;
}