Examples with VariantAnalyzer com.hartwig.hmftools.patientreporter.variants.VariantAnalyzer used on opensource projects

Example 1 with VariantAnalyzer

use of com.hartwig.hmftools.patientreporter.variants.VariantAnalyzer in project hmftools by hartwigmedical.

the class PatientReporterTest method canRunOnRunDirectory.

@Test
public void canRunOnRunDirectory() throws IOException {
    final GeneModel geneModel = new GeneModel(HmfGenePanelSupplier.hmfPanelGeneMap());
    final BaseReporterData baseReporterData = testBaseReporterData();
    final HmfReporterData reporterData = testHmfReporterData();
    final VariantAnalyzer variantAnalyzer = VariantAnalyzer.of(geneModel, reporterData.microsatelliteAnalyzer());
    final StructuralVariantAnalyzer svAnalyzer = new StructuralVariantAnalyzer(new TestAnnotator(), geneModel.regions(), CosmicFusions.readFromCSV(FUSIONS_CSV));
    final PatientReporter algo = ImmutablePatientReporter.of(baseReporterData, reporterData, variantAnalyzer, svAnalyzer, mockedCivicAnalyzer());
    assertNotNull(algo.run(RUN_DIRECTORY, null));
}

Example 2 with VariantAnalyzer

use of com.hartwig.hmftools.patientreporter.variants.VariantAnalyzer in project hmftools by hartwigmedical.

the class PatientReporter method analyseGenomeData.

@NotNull
private GenomeAnalysis analyseGenomeData(@NotNull final String sample, @NotNull final String runDirectory) throws IOException {
    LOGGER.info(" Loading somatic snv and indels...");
    final List<SomaticVariant> variants = PatientReporterHelper.loadPassedSomaticVariants(sample, runDirectory);
    LOGGER.info("  " + variants.size() + " somatic passed snps, mnps and indels loaded for sample " + sample);
    LOGGER.info(" Analyzing somatic snp/mnp and indels....");
    final VariantAnalysis variantAnalysis = variantAnalyzer().run(variants);
    LOGGER.info(" Loading purity numbers...");
    final PurityContext context = PatientReporterHelper.loadPurity(runDirectory, sample);
    if (context.status().equals(FittedPurityStatus.NO_TUMOR)) {
        LOGGER.warn("PURPLE DID NOT DETECT A TUMOR. Proceed with utmost caution!");
    }
    final FittedPurity purity = context.bestFit();
    final FittedPurityScore purityScore = context.score();
    final List<PurpleCopyNumber> purpleCopyNumbers = PatientReporterHelper.loadPurpleCopyNumbers(runDirectory, sample);
    final List<GeneCopyNumber> panelGeneCopyNumbers = PatientReporterHelper.loadPurpleGeneCopyNumbers(runDirectory, sample).stream().filter(x -> reporterData().panelGeneModel().panel().contains(x.gene())).collect(Collectors.toList());
    LOGGER.info("  " + purpleCopyNumbers.size() + " purple copy number regions loaded for sample " + sample);
    LOGGER.info(" Analyzing purple somatic copy numbers...");
    final PurpleAnalysis purpleAnalysis = ImmutablePurpleAnalysis.builder().gender(context.gender()).status(context.status()).fittedPurity(purity).fittedScorePurity(purityScore).copyNumbers(purpleCopyNumbers).panelGeneCopyNumbers(panelGeneCopyNumbers).build();
    final Path structuralVariantVCF = PatientReporterHelper.findStructuralVariantVCF(runDirectory);
    LOGGER.info(" Loading structural variants...");
    final List<StructuralVariant> structuralVariants = StructuralVariantFileLoader.fromFile(structuralVariantVCF.toString(), true);
    LOGGER.info(" Enriching structural variants with purple data.");
    final List<EnrichedStructuralVariant> enrichedStructuralVariants = purpleAnalysis.enrichStructuralVariants(structuralVariants);
    LOGGER.info(" Analysing structural variants...");
    final StructuralVariantAnalysis structuralVariantAnalysis = structuralVariantAnalyzer().run(enrichedStructuralVariants, false);
    return ImmutableGenomeAnalysis.of(sample, variantAnalysis, purpleAnalysis, structuralVariantAnalysis);
}

Example 3 with VariantAnalyzer

use of com.hartwig.hmftools.patientreporter.variants.VariantAnalyzer in project hmftools by hartwigmedical.

the class PatientReporterApplication method buildReporter.

@NotNull
private static PatientReporter buildReporter(@NotNull final CommandLine cmd, @NotNull final HmfReporterData reporterData) throws IOException, SQLException {
    final VariantAnalyzer variantAnalyzer = VariantAnalyzer.of(reporterData.panelGeneModel(), reporterData.microsatelliteAnalyzer());
    final VariantAnnotator annotator;
    if (cmd.hasOption(ENSEMBL_DB)) {
        final String url = "jdbc:" + cmd.getOptionValue(ENSEMBL_DB);
        LOGGER.info("connecting to: {}", url);
        annotator = MySQLAnnotator.make(url);
    } else {
        annotator = NullAnnotator.make();
    }
    final StructuralVariantAnalyzer svAnalyzer = new StructuralVariantAnalyzer(annotator, reporterData.panelGeneModel().regions(), reporterData.cosmicFusionModel());
    return ImmutablePatientReporter.of(buildBaseReporterData(cmd), reporterData, variantAnalyzer, svAnalyzer, new CivicAnalyzer());
}