Examples with AmberQC com.hartwig.hmftools.common.amber.qc.AmberQC used on opensource projects

Example 1 with AmberQC

use of com.hartwig.hmftools.common.amber.qc.AmberQC in project hmftools by hartwigmedical.

the class AmberChecker method run.

@NotNull
public BaseResult run(@NotNull final RunContext runContext) throws IOException {
    if (!runContext.isSomaticRun()) {
        return new NoResult(CheckType.AMBER);
    }
    final String amberDirectory = runContext.runDirectory() + File.separator + "amber";
    final AmberQC qcCheck = AmberQCFile.read(AmberQCFile.generateFilename(amberDirectory, runContext.tumorSample()));
    final String meanBaf = String.valueOf(qcCheck.meanBAF());
    final HealthCheck healthCheck = new HealthCheck(runContext.tumorSample(), AmberCheck.MEAN_BAF.toString(), meanBaf);
    return toSingleValueResult(healthCheck);
}