Examples with GenomePosition com.hartwig.hmftools.common.position.GenomePosition used on opensource projects

Example 6 with GenomePosition

use of com.hartwig.hmftools.common.position.GenomePosition in project hmftools by hartwigmedical.

the class GenomeRegionSelectorImpl method select.

@Override
public void select(@NotNull final GenomeRegion region, @NotNull final Consumer<R> handler) {
    final GenomePosition start = GenomePositions.create(region.chromosome(), region.start());
    final GenomePosition end = GenomePositions.create(region.chromosome(), region.end());
    if (lastPosition != null && start.compareTo(lastPosition) < 0) {
        throw new IllegalArgumentException("Selector only goes forward, never backwards!");
    }
    while (next != null && compare(start, next) > 0) {
        next = regions.hasNext() ? this.regions.next() : null;
    }
    while (next != null && compare(start, next) <= 0 && compare(end, next) >= 0) {
        handler.accept(next);
        next = regions.hasNext() ? this.regions.next() : null;
    }
    lastPosition = end;
}

Example 7 with GenomePosition

use of com.hartwig.hmftools.common.position.GenomePosition in project hmftools by hartwigmedical.

the class BachelorEligibility method processStructuralVariant.

private Collection<EligibilityReport> processStructuralVariant(final String patient, final GenomePosition position, final GenomePosition other, final StructuralVariantType svType) {
    final List<EligibilityReport> results = Lists.newArrayList();
    // TODO: can we do better than this performance wise? new map?
    for (final HmfGenomeRegion region : allGenesByChromosomeMap.get(position.chromosome())) {
        if (!region.contains(position)) {
            continue;
        }
        // skip non-inversion intronic variants
        if (region.contains(other) && svType != StructuralVariantType.INV) {
            final int intronStart = intron(region.exome(), position);
            final int intronEnd = intron(region.exome(), other);
            // the variant is intronic in a gene -- we will filter it
            if (intronStart >= 0 && intronStart == intronEnd) {
                continue;
            }
        }
        programs.stream().filter(p -> p.disruptionProcessor().test(region)).map(p -> ImmutableEligibilityReport.builder().patient(patient).source(SOMATIC_DISRUPTION).program(p.name()).id("").genes(region.gene()).chrom(region.chromosome()).pos(position.position()).ref("").alts("").effects("").build()).forEach(results::add);
    }
    return results;
}