Examples with StandardCovariateList org.broadinstitute.hellbender.utils.recalibration.covariates.StandardCovariateList used on opensource projects

Example 6 with StandardCovariateList

use of org.broadinstitute.hellbender.utils.recalibration.covariates.StandardCovariateList in project gatk by broadinstitute.

the class BaseRecalibratorEngineSparkWrapper method saveTextualReport.

// saves to output
public static void saveTextualReport(String output, SAMFileHeader header, RecalibrationTables rt, RecalibrationArgumentCollection recalArgs, AuthHolder auth) throws IOException {
    OutputStream oStream = BucketUtils.createFile(output);
    QuantizationInfo qi = new QuantizationInfo(rt, recalArgs.QUANTIZING_LEVELS);
    if (recalArgs.FORCE_PLATFORM != null) {
        recalArgs.DEFAULT_PLATFORM = recalArgs.FORCE_PLATFORM;
    }
    StandardCovariateList covariates = new StandardCovariateList(recalArgs, header);
    try (PrintStream reportStream = new PrintStream(oStream)) {
        RecalUtils.outputRecalibrationReport(reportStream, recalArgs, qi, rt, covariates);
    }
}