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

Example 6 with AllelicCountWithPhasePosteriorsCollection

use of org.broadinstitute.hellbender.tools.exome.alleliccount.AllelicCountWithPhasePosteriorsCollection 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 7 with AllelicCountWithPhasePosteriorsCollection

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

the class CalculatePulldownPhasePosteriorsIntegrationTest method testRun.

private void testRun(final String[] arguments, final String outputFileName) {
    runCommandLine(arguments);
    //only check that file is created and can be read as an AllelicCountWithPhasePosteriorsCollection,
    //do not check for correctness of results (which is tested by testCalculatePhasePosteriors)
    final File outputFile = new File(outputFileName);
    Assert.assertTrue(outputFile.isFile(), outputFile.getAbsolutePath() + " is not a file.");
    Assert.assertTrue(outputFile.length() > 0);
    try {
        //check that file has:
        //  - at least two lines and all either start with "#" or contain at least one "\t"
        //  - at least two lines with tab (column names + 1 SNP)
        final List<String> outputLines = FileUtils.readLines(outputFile);
        Assert.assertTrue(outputLines.size() >= 2);
        Assert.assertEquals(outputLines.stream().filter(l -> l.contains("\t") || l.startsWith("#")).count(), outputLines.size());
        Assert.assertTrue(outputLines.stream().filter(l -> l.split("\t").length > 2 && !l.startsWith("#")).count() > 2, "File: " + outputFile + " does not seem to have at least one SNP and a header.");
        final AllelicCountWithPhasePosteriorsCollection counts = new AllelicCountWithPhasePosteriorsCollection(outputFile);
    } catch (final Exception e) {
        Assert.fail("Could not create AllelicCountWithPhasePosteriorsCollection from file: " + outputFile, e);
    }
}

Example 8 with AllelicCountWithPhasePosteriorsCollection

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