Examples with SexGenotypeData org.broadinstitute.hellbender.tools.exome.sexgenotyper.SexGenotypeData used on opensource projects

Example 6 with SexGenotypeData

use of org.broadinstitute.hellbender.tools.exome.sexgenotyper.SexGenotypeData in project gatk-protected by broadinstitute.

the class CoverageModelEMWorkspace method getViterbiAsNDArray.

/**
     * Fetches the Viterbi copy ratio (or copy number) states as a target-sample matrix
     *
     * @return an {@link INDArray}
     */
protected INDArray getViterbiAsNDArray(final List<List<HiddenStateSegmentRecord<STATE, Target>>> segments) {
    final INDArray res = Nd4j.create(numSamples, numTargets);
    final TargetCollection<Target> targetCollection = new HashedListTargetCollection<>(processedTargetList);
    for (int si = 0; si < numSamples; si++) {
        final SexGenotypeData sampleSexGenotype = processedSampleSexGenotypeData.get(si);
        /* start with all ref */
        final double[] calls = IntStream.range(0, numTargets).mapToDouble(ti -> referenceStateFactory.apply(sampleSexGenotype, processedTargetList.get(ti)).getScalar()).toArray();
        /* go through segments and mutate ref calls as necessary */
        segments.get(si).forEach(seg -> {
            final IndexRange range = targetCollection.indexRange(seg.getSegment());
            final double copyRatio = seg.getSegment().getCall().getScalar();
            for (int ti = range.from; ti < range.to; ti++) {
                calls[ti] = copyRatio;
            }
        });
        res.get(NDArrayIndex.point(si), NDArrayIndex.all()).assign(Nd4j.create(calls, new int[] { 1, numTargets }));
    }
    return res.transpose();
}