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Example 1 with CivicAnalyzer

use of com.hartwig.hmftools.patientreporter.civic.CivicAnalyzer 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());
}
Also used : CivicAnalyzer(com.hartwig.hmftools.patientreporter.civic.CivicAnalyzer) StructuralVariantAnalyzer(com.hartwig.hmftools.svannotation.analysis.StructuralVariantAnalyzer) VariantAnalyzer(com.hartwig.hmftools.patientreporter.variants.VariantAnalyzer) StructuralVariantAnalyzer(com.hartwig.hmftools.svannotation.analysis.StructuralVariantAnalyzer) VariantAnnotator(com.hartwig.hmftools.svannotation.VariantAnnotator) NotNull(org.jetbrains.annotations.NotNull)

Aggregations

CivicAnalyzer (com.hartwig.hmftools.patientreporter.civic.CivicAnalyzer)1 VariantAnalyzer (com.hartwig.hmftools.patientreporter.variants.VariantAnalyzer)1 VariantAnnotator (com.hartwig.hmftools.svannotation.VariantAnnotator)1 StructuralVariantAnalyzer (com.hartwig.hmftools.svannotation.analysis.StructuralVariantAnalyzer)1 NotNull (org.jetbrains.annotations.NotNull)1