Examples with VariantAnnotator com.hartwig.hmftools.svannotation.VariantAnnotator used on opensource projects

Example 1 with VariantAnnotator

use of com.hartwig.hmftools.svannotation.VariantAnnotator 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());
}