Examples with GenomeRegionSelector com.hartwig.hmftools.common.region.GenomeRegionSelector used on opensource projects

Example 1 with GenomeRegionSelector

use of com.hartwig.hmftools.common.region.GenomeRegionSelector in project hmftools by hartwigmedical.

the class StructuralVariantLegPloidyFactory method create.

@VisibleForTesting
@NotNull
Optional<ModifiableStructuralVariantLegPloidy> create(@NotNull StructuralVariantLeg leg, @NotNull final GenomeRegionSelector<T> selector) {
    final GenomePosition svPositionLeft = GenomePositions.create(leg.chromosome(), leg.position() - 1);
    final Optional<Double> left = selector.select(svPositionLeft).flatMap(x -> Optional.ofNullable(copyNumberExtractor.apply(x))).filter(Doubles::positive);
    final Optional<Double> right = selector.select(leg).flatMap(x -> Optional.ofNullable(copyNumberExtractor.apply(x))).filter(Doubles::positive);
    final Optional<Double> correct;
    final Optional<Double> alternate;
    if (leg.orientation() == 1) {
        correct = left;
        alternate = right;
    } else {
        correct = right;
        alternate = left;
    }
    if (!correct.isPresent() && !alternate.isPresent()) {
        return Optional.empty();
    }
    final double vaf = leg.alleleFrequency();
    final double ploidy;
    final double weight;
    if (correct.isPresent()) {
        double copyNumber = correct.get();
        ploidy = purityAdjustedPloidy(leg.chromosome(), vaf, copyNumber);
        weight = 1;
    } else {
        double copyNumber = alternate.get();
        double reciprocalVAF = vaf / (1 - vaf);
        if (!Double.isFinite(reciprocalVAF)) {
            return Optional.empty();
        }
        ploidy = purityAdjustedPloidy(leg.chromosome(), reciprocalVAF, copyNumber);
        weight = 1 / (1 + Math.pow(Math.max(copyNumber, 2) / Math.min(Math.max(copyNumber, 0.01), 2), 2));
    }
    return Optional.of(ModifiableStructuralVariantLegPloidy.create().from(leg).setVaf(vaf).setOrientation(leg.orientation()).setUnweightedImpliedPloidy(ploidy).setLeftCopyNumber(left).setRightCopyNumber(right).setWeight(weight));
}