Examples with Alteration com.hartwig.hmftools.patientreporter.report.data.Alteration used on opensource projects

Example 6 with Alteration

use of com.hartwig.hmftools.patientreporter.report.data.Alteration in project hmftools by hartwigmedical.

the class CivicAnalyzer method civicFusionAlterations.

@NotNull
private static List<Alteration> civicFusionAlterations(@NotNull final List<GeneFusionData> fusions, @NotNull final Set<String> relevantDoids) {
    LOGGER.info("  Fetching civic fusion alterations...");
    final List<Alteration> alterations = Lists.newArrayList();
    for (final GeneFusionData fusion : fusions) {
        alterations.addAll(queryCivicAlteration(fusion.geneStartEntrezIds(), variantList -> Alteration.from(fusion, variantList, relevantDoids), "  Failed to get civic variants for fusion: " + fusion.geneStart() + " - " + fusion.geneEnd()));
        alterations.addAll(queryCivicAlteration(fusion.geneEndEntrezIds(), variantList -> Alteration.from(fusion, variantList, relevantDoids), "  Failed to get civic variants for fusion: " + fusion.geneStart() + " - " + fusion.geneEnd()));
    }
    return alterations;
}

Example 7 with Alteration

use of com.hartwig.hmftools.patientreporter.report.data.Alteration in project hmftools by hartwigmedical.

the class CivicAnalyzer method queryCivicAlteration.

@NotNull
private static List<Alteration> queryCivicAlteration(@NotNull final List<Integer> entrezIds, io.reactivex.functions.Function<List<CivicVariantWithEvidence>, Alteration> alterationBuilder, @NotNull final String error) {
    final CivicApiWrapper civicApi = new CivicApiWrapper();
    final List<Alteration> result = Lists.newArrayList();
    try {
        result.addAll(Observable.fromIterable(entrezIds).flatMap(civicApi::getVariantsForGene).toList().map(alterationBuilder).filter(alteration -> !alteration.getMatches().isEmpty()).toObservable().toList().blockingGet());
    } catch (final Throwable throwable) {
        LOGGER.error("{}. Error message: {}", error, throwable.getMessage());
    }
    civicApi.releaseResources();
    return result;
}