Examples with StructuralVariantLegPloidy com.hartwig.hmftools.common.purple.copynumber.sv.StructuralVariantLegPloidy used on opensource projects

Example 1 with StructuralVariantLegPloidy

use of com.hartwig.hmftools.common.purple.copynumber.sv.StructuralVariantLegPloidy in project hmftools by hartwigmedical.

the class StructuralVariantImpliedTest method testImpliedCopyNumber.

@Test
public void testImpliedCopyNumber() {
    final StructuralVariantLegPloidy left = create(1, Optional.of(4d), Optional.empty());
    final StructuralVariantLegPloidy right = create(-1, Optional.empty(), Optional.of(5d));
    final double bothKnown = StructuralVariantImplied.inferCopyNumberFromStructuralVariants(Optional.of(left), Optional.of(right));
    assertEquals(3.5, bothKnown, EPSILON);
    final double leftKnown = StructuralVariantImplied.inferCopyNumberFromStructuralVariants(Optional.of(left), Optional.empty());
    assertEquals(3, leftKnown, EPSILON);
    final double rightKnown = StructuralVariantImplied.inferCopyNumberFromStructuralVariants(Optional.empty(), Optional.of(right));
    assertEquals(4, rightKnown, EPSILON);
}

Example 2 with StructuralVariantLegPloidy

use of com.hartwig.hmftools.common.purple.copynumber.sv.StructuralVariantLegPloidy in project hmftools by hartwigmedical.

the class StructuralVariantImplied method svImpliedCopyNumber.

@NotNull
ListMultimap<String, CombinedRegion> svImpliedCopyNumber(final List<StructuralVariant> structuralVariants, @NotNull final ListMultimap<String, CombinedRegion> copyNumbers) {
    long previousMissingCopyNumbers = copyNumbers.size();
    long currentMissingCopyNumbers = missingCopyNumberCount(copyNumbers);
    while (currentMissingCopyNumbers < previousMissingCopyNumbers && currentMissingCopyNumbers > 0) {
        final GenomePositionSelector<StructuralVariantLegPloidy> selector = GenomePositionSelectorFactory.create(createPloidies(structuralVariants, copyNumbers));
        for (Chromosome chromosome : HumanChromosome.values()) {
            final String chromosomeName = chromosome.toString();
            final List<CombinedRegion> chromosomeCopyNumbers = copyNumbers.get(chromosomeName);
            boolean svInferred = false;
            for (final CombinedRegion copyNumber : chromosomeCopyNumbers) {
                if (implyCopyNumberFromSV(copyNumber)) {
                    final Optional<StructuralVariantLegPloidy> optionalStart = selector.select(GenomePositions.create(chromosomeName, copyNumber.start()));
                    final Optional<StructuralVariantLegPloidy> optionalEnd = selector.select(GenomePositions.create(chromosomeName, copyNumber.end() + 1));
                    if (optionalStart.isPresent() || optionalEnd.isPresent()) {
                        svInferred = true;
                        inferCopyNumberFromStructuralVariants(copyNumber, optionalStart, optionalEnd);
                    }
                }
            }
            // JOBA: Extend structural variant segments
            if (svInferred) {
                ExtendStructuralVariant.extendStructuralVariants(chromosomeCopyNumbers);
            }
        }
        previousMissingCopyNumbers = currentMissingCopyNumbers;
        currentMissingCopyNumbers = missingCopyNumberCount(copyNumbers);
    }
    return copyNumbers;
}

Example 3 with StructuralVariantLegPloidy

use of com.hartwig.hmftools.common.purple.copynumber.sv.StructuralVariantLegPloidy in project hmftools by hartwigmedical.

the class EnrichedStructuralVariantFactory method enrich.

@NotNull
public static List<EnrichedStructuralVariant> enrich(@NotNull final List<StructuralVariant> variants, @NotNull final PurityAdjuster purityAdjuster, @NotNull final Multimap<String, PurpleCopyNumber> copyNumbers) {
    final StructuralVariantLegPloidyFactory<PurpleCopyNumber> ploidyFactory = new StructuralVariantLegPloidyFactory<>(purityAdjuster, PurpleCopyNumber::averageTumorCopyNumber);
    final List<EnrichedStructuralVariant> result = Lists.newArrayList();
    for (final StructuralVariant variant : variants) {
        final ImmutableEnrichedStructuralVariant.Builder builder = ImmutableEnrichedStructuralVariant.builder().from(variant);
        final ImmutableEnrichedStructuralVariantLeg.Builder startBuilder = ImmutableEnrichedStructuralVariantLeg.builder().from(variant.start());
        final ImmutableEnrichedStructuralVariantLeg.Builder endBuilder = ImmutableEnrichedStructuralVariantLeg.builder().from(variant.end());
        final List<StructuralVariantLegPloidy> ploidies = ploidyFactory.create(variant, copyNumbers);
        if (!ploidies.isEmpty()) {
            Double roundedPloidy = round(ploidies.get(0).averageImpliedPloidy());
            builder.ploidy(roundedPloidy);
        }
        if (ploidies.size() == 2) {
            final StructuralVariantLegPloidy start = ploidies.get(0);
            final StructuralVariantLegPloidy end = ploidies.get(1);
            startBuilder.adjustedAlleleFrequency(round(adjustedVAF(purityAdjuster, start)));
            startBuilder.adjustedCopyNumber(round(adjustedCopyNumber(start)));
            startBuilder.adjustedCopyNumberChange(round(adjustedCopyNumberChange(start)));
            endBuilder.adjustedAlleleFrequency(round(adjustedVAF(purityAdjuster, end)));
            endBuilder.adjustedCopyNumber(round(adjustedCopyNumber(end)));
            endBuilder.adjustedCopyNumberChange(round(adjustedCopyNumberChange(end)));
        }
        result.add(builder.start(startBuilder.build()).end(endBuilder.build()).build());
    }
    return result;
}