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

Example 11 with FittedRegion

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

the class ExtendDiploidTest method testTooBigTowardsCentromere.

@Test
public void testTooBigTowardsCentromere() {
    final FittedRegion somaticLeft = createValidSomatic(1, 10000, 3.0, 50, SegmentSupport.BND);
    final FittedRegion dubious1 = createDubiousRegion(10001, 11000, 2.0, 21);
    final FittedRegion dubious2 = createDubiousRegion(11001, 12000, 2.0, 21);
    final FittedRegion dubious3 = createDubiousRegion(12001, 20000, 2.0, 21);
    final FittedRegion somaticRight = createValidSomatic(20001, 30000, 3.0, 40, SegmentSupport.CENTROMERE);
    final List<CombinedRegion> result = PURE_VICTIM.extendDiploid(Lists.newArrayList(somaticLeft, dubious1, dubious2, dubious3, somaticRight));
    assertEquals(3, result.size());
    assertRegion(1, 10000, 3, result.get(0));
    assertRegion(10001, 20000, 2, result.get(1));
    assertRegion(20001, 30000, 3, result.get(2));
}

Example 12 with FittedRegion

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

the class ExtendDiploidTest method testMultipleDubiousRegionsGetIncluded.

@Test
public void testMultipleDubiousRegionsGetIncluded() {
    final FittedRegion somaticLeft = createValidSomatic(1, 10000, 3.0, 50, SegmentSupport.BND);
    final FittedRegion dubious1 = createDubiousRegion(10001, 11000, 2.0, 20);
    final FittedRegion dubious2 = createDubiousRegion(11001, 12000, 2.0, 9);
    final FittedRegion dubious3 = createDubiousRegion(12001, 20000, 2.0, 20);
    final FittedRegion somaticRight = createValidSomatic(20001, 30000, 3.0, 40, SegmentSupport.NONE);
    final List<CombinedRegion> result = PURE_VICTIM.extendDiploid(Lists.newArrayList(somaticLeft, dubious1, dubious2, dubious3, somaticRight));
    assertEquals(1, result.size());
    assertRegion(1, 30000, 3, result.get(0));
}

Example 13 with FittedRegion

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

the class FittedPurityFactory method fitPurity.

@NotNull
private FittedPurity fitPurity(final double purity, final double normFactor, final double totalBafCount, @NotNull final Collection<ObservedRegion> observedRegions) {
    ImmutableFittedPurity.Builder builder = ImmutableFittedPurity.builder().purity(purity).normFactor(normFactor);
    double ploidyPenalty = 0;
    double modelDeviation = 0;
    double diploidProportion = 0;
    double averagePloidy = 0;
    for (final ObservedRegion enrichedRegion : observedRegions) {
        final FittedRegion fittedRegion = fittedRegionFactory.fitRegion(purity, normFactor, enrichedRegion);
        ploidyPenalty += enrichedRegion.bafCount() / totalBafCount * fittedRegion.ploidyPenalty();
        modelDeviation += enrichedRegion.bafCount() / totalBafCount * fittedRegion.deviation();
        averagePloidy += fittedRegion.tumorCopyNumber() * fittedRegion.bafCount() / totalBafCount;
        if (fittedRegion.modelPloidy() == 2) {
            diploidProportion += enrichedRegion.bafCount() / totalBafCount;
        }
    }
    return builder.score(ploidyPenalty * modelDeviation).diploidProportion(diploidProportion).ploidy(averagePloidy).build();
}

Example 14 with FittedRegion

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

the class ExtendDiploid method merge.

private boolean merge(@NotNull final List<CombinedRegion> regions, @NotNull final Direction direction, int targetIndex) {
    final CombinedRegion target = regions.get(targetIndex);
    final FittedRegion neighbour = regions.get(direction.moveIndex(targetIndex)).region();
    if (Extend.doNotExtend(target, neighbour)) {
        return false;
    }
    final boolean isNeighbourDubious = isDubious(neighbour);
    if (isNeighbourDubious) {
        int minTumorCount = nextBigBreakIsCentromereOrTelomere(regions, direction, targetIndex) ? minTumorCountAtCentromere : this.minTumorCount;
        if (inTolerance(target.region(), neighbour)) {
            target.extendWithBAFWeightedAverage(neighbour);
            return true;
        } else if (pushThroughDubiousRegion(minTumorCount, regions, direction, targetIndex)) {
            target.extend(neighbour);
            return true;
        } else {
            return false;
        }
    }
    final boolean isNeighbourValid = isValid(neighbour);
    if (!isNeighbourValid) {
        target.extend(neighbour);
        return true;
    } else if (inTolerance(target.region(), neighbour)) {
        target.extendWithBAFWeightedAverage(neighbour);
        return true;
    }
    return false;
}

Example 15 with FittedRegion

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

the class ExtendDiploid method nextIndex.

private static int nextIndex(@NotNull final List<CombinedRegion> regions) {
    int indexOfLargestBaf = -1;
    int indexOfLargestLength = -1;
    int indexOfTumorRatioCount = -1;
    int largestBAFCount = 0;
    long largestBases = 0;
    long largestTumorRatioCount = 0;
    for (int i = 0; i < regions.size(); i++) {
        final CombinedRegion combined = regions.get(i);
        final FittedRegion region = combined.region();
        if (!combined.isProcessed() && region.status().equals(GermlineStatus.DIPLOID)) {
            if (region.bafCount() > largestBAFCount) {
                largestBAFCount = region.bafCount();
                indexOfLargestBaf = i;
            }
            if (region.observedTumorRatioCount() > largestTumorRatioCount) {
                largestTumorRatioCount = region.observedTumorRatioCount();
                indexOfTumorRatioCount = i;
            }
            if (region.bases() > largestBases) {
                largestBases = region.bases();
                indexOfLargestLength = i;
            }
        }
    }
    return indexOfLargestBaf > -1 ? indexOfLargestBaf : (indexOfTumorRatioCount > -1 ? indexOfTumorRatioCount : indexOfLargestLength);
}