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

Example 16 with FittedRegion

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

the class ExtendGermline method reduce.

@NotNull
private static CombinedRegion reduce(@NotNull final CombinedRegion parent, long start, long end) {
    assert (start >= parent.start());
    assert (end <= parent.end());
    int bafCount = 0;
    int observedTumorRatioCount = 0;
    for (FittedRegion fittedRegion : parent.regions()) {
        if (fittedRegion.start() >= start && fittedRegion.end() <= end) {
            bafCount += fittedRegion.bafCount();
            observedTumorRatioCount += fittedRegion.observedTumorRatioCount();
        }
    }
    final ModifiableFittedRegion smallerRegion = ModifiableFittedRegion.create().from(parent.region()).setStart(start).setEnd(end).setBafCount(bafCount).setObservedTumorRatioCount(observedTumorRatioCount);
    CombinedRegion result = new CombinedRegion(parent.isBafWeighted(), smallerRegion);
    result.setCopyNumberMethod(parent.copyNumberMethod());
    for (FittedRegion fittedRegion : parent.regions()) {
        if (fittedRegion.start() >= start && fittedRegion.end() <= end) {
            result.extend(fittedRegion);
        }
    }
    return result;
}

Example 17 with FittedRegion

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

the class ExtendGermline method extractChildren.

@NotNull
private List<CombinedRegion> extractChildren(@NotNull final EnumSet<GermlineStatus> eligibleStatus, @NotNull final CombinedRegion parent, @Nullable final CombinedRegion neighbour) {
    final List<CombinedRegion> children = Lists.newArrayList();
    double baf = parent.tumorBAF();
    double copyNumber = parent.tumorCopyNumber();
    for (int i = 0; i < parent.regions().size(); i++) {
        final FittedRegion child = parent.regions().get(i);
        final FittedRegion next = i + 1 == parent.regions().size() ? (neighbour == null ? null : neighbour.regions().get(0)) : parent.regions().get(i + 1);
        if (eligibleStatus.contains(child.status())) {
            if (child.status().equals(GermlineStatus.AMPLIFICATION)) {
                final double lowerBound = lowerBound(child);
                if (isValidAmplification(copyNumber, lowerBound, child, next)) {
                    children.add(createChild(child, lowerBound, baf));
                }
            }
            if (child.status().equals(GermlineStatus.HET_DELETION)) {
                final double upperBound = upperBound(child);
                if (Doubles.lessThan(upperBound, Math.min(0.5, copyNumber))) {
                    children.add(createChild(child, upperBound, baf));
                }
            }
            if (child.status().equals(GermlineStatus.HOM_DELETION)) {
                children.add(createChild(child, child.refNormalisedCopyNumber(), baf));
            }
        }
    }
    return extendRight(children);
}

Example 18 with FittedRegion

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

the class ExtendDiploid method pushThroughDubiousRegion.

private boolean pushThroughDubiousRegion(int minTumorCount, @NotNull final List<CombinedRegion> regions, @NotNull final Direction direction, int targetIndex) {
    int dubiousCount = 0;
    final CombinedRegion target = regions.get(targetIndex);
    for (int i = direction.moveIndex(targetIndex); i >= 0 && i < regions.size(); i = direction.moveIndex(i)) {
        final FittedRegion neighbour = regions.get(i).region();
        // JOBA: Coming from left to right, EXCLUDE neighbour from decision on break.
        if (neighbour.start() > target.start()) {
            if (neighbour.support() == SegmentSupport.CENTROMERE) {
                return dubiousCount < minTumorCount;
            }
            if (neighbour.support().isSV()) {
                return false;
            }
        }
        if (isDubious(neighbour)) {
            dubiousCount += neighbour.observedTumorRatioCount();
            if (dubiousCount >= minTumorCount) {
                return false;
            }
        }
        if (isValid(neighbour)) {
            return inTolerance(target.region(), neighbour);
        }
        // JOBA: Coming from right to left, INCLUDE neighbour from decision on break.
        if (neighbour.start() < target.start()) {
            if (neighbour.support() == SegmentSupport.CENTROMERE) {
                return dubiousCount < minTumorCount;
            }
            if (neighbour.support().isSV()) {
                return false;
            }
        }
    }
    return dubiousCount < minTumorCount;
}

Example 19 with FittedRegion

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

the class ExtendDiploid method extendDiploid.

@NotNull
List<CombinedRegion> extendDiploid(@NotNull final Collection<FittedRegion> fittedRegions) {
    final boolean bafWeighted = fittedRegions.stream().anyMatch(x -> x.bafCount() >= MIN_BAF_COUNT_TO_WEIGH_WITH_BAF);
    final List<CombinedRegion> regions = Lists.newLinkedList();
    for (FittedRegion fittedRegion : fittedRegions) {
        regions.add(new CombinedRegion(bafWeighted, fittedRegion));
    }
    int highestConfidenceIndex = nextIndex(regions);
    while (highestConfidenceIndex > -1) {
        final CombinedRegion highestConfidence = regions.get(highestConfidenceIndex);
        highestConfidence.setCopyNumberMethod(CopyNumberMethod.BAF_WEIGHTED);
        LOGGER.debug("Selected region {}", toString(highestConfidence.region()));
        extendRight(regions, highestConfidenceIndex);
        extendLeft(regions, highestConfidenceIndex);
        LOGGER.debug("Completed region {}", toString(highestConfidence.region()));
        highestConfidenceIndex = nextIndex(regions);
    }
    return regions;
}

Example 20 with FittedRegion

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

the class StructuralVariantImpliedTest method copyNumber.

@NotNull
private static CombinedRegion copyNumber(long start, long end, double copyNumber, SegmentSupport support) {
    final FittedRegion region = PurpleDatamodelTest.createDefaultFittedRegion(CHROMOSOME, start, end).tumorCopyNumber(copyNumber).tumorBAF(0.5).support(support).build();
    final CombinedRegion result = new CombinedRegion(true, region);
    if (Doubles.positive(copyNumber)) {
        result.setCopyNumberMethod(CopyNumberMethod.BAF_WEIGHTED);
    }
    return result;
}