Examples with SomaticVariant com.hartwig.hmftools.common.variant.SomaticVariant used on opensource projects

Example 6 with SomaticVariant

use of com.hartwig.hmftools.common.variant.SomaticVariant in project hmftools by hartwigmedical.

the class GeneCopyNumberFactory method geneCopyNumbers.

@NotNull
public static List<GeneCopyNumber> geneCopyNumbers(@NotNull final List<HmfGenomeRegion> genes, @NotNull final List<PurpleCopyNumber> somaticCopyNumbers, @NotNull final List<PurpleCopyNumber> germlineDeletions, @NotNull final List<PurityAdjustedSomaticVariant> enrichedSomatics) {
    final ListMultimap<String, PurityAdjustedSomaticVariant> variantMap = Multimaps.index(enrichedSomatics, SomaticVariant::gene);
    final List<GeneCopyNumber> result = Lists.newArrayList();
    for (HmfGenomeRegion gene : genes) {
        final List<PurityAdjustedSomaticVariant> variants = variantMap.containsKey(gene.gene()) ? variantMap.get(gene.gene()) : Collections.EMPTY_LIST;
        final GeneCopyNumberBuilder builder = new GeneCopyNumberBuilder(gene);
        RegionZipper.zip(somaticCopyNumbers, gene.exome(), builder);
        RegionZipper.zip(germlineDeletions, gene.exome(), builder);
        variants.forEach(builder::somatic);
        GeneCopyNumber geneCopyNumber = builder.build();
        if (geneCopyNumber.totalRegions() > 0) {
            result.add(geneCopyNumber);
        }
    }
    return result;
}