LoadStructuralVariants.java 文件源码

@NotNull
private static List<EnrichedStructuralVariant> enrichStructuralVariants(@NotNull List<StructuralVariant> variants,
        @NotNull DatabaseAccess dbAccess, @NotNull String tumorSample) {
    final PurityContext purityContext = dbAccess.readPurityContext(tumorSample);

    if (purityContext == null) {
        LOGGER.warn("Unable to retrieve purple data. Enrichment may be incomplete.");
    }

    final PurityAdjuster purityAdjuster = purityContext == null
            ? new PurityAdjuster(Gender.FEMALE, 1, 1)
            : new PurityAdjuster(purityContext.gender(), purityContext.bestFit().purity(), purityContext.bestFit().normFactor());

    final List<PurpleCopyNumber> copyNumberList = dbAccess.readCopynumbers(tumorSample);
    final Multimap<String, PurpleCopyNumber> copyNumbers = Multimaps.index(copyNumberList, PurpleCopyNumber::chromosome);
    return EnrichedStructuralVariantFactory.enrich(variants, purityAdjuster, copyNumbers);
}