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

Example 16 with HmfGenomeRegion

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

the class GeneCopyNumberBuilderTest method setup.

@Before
public void setup() {
    HmfGenomeRegion gene = create(1001, 10000);
    victim = new GeneCopyNumberBuilder(gene);
}

Example 17 with HmfGenomeRegion

use of com.hartwig.hmftools.common.region.hmfslicer.HmfGenomeRegion 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;
}