Examples with AllelicPanelOfNormalsCreator org.broadinstitute.hellbender.tools.pon.allelic.AllelicPanelOfNormalsCreator used on opensource projects

Example 1 with AllelicPanelOfNormalsCreator

use of org.broadinstitute.hellbender.tools.pon.allelic.AllelicPanelOfNormalsCreator in project gatk by broadinstitute.

the class CreateAllelicPanelOfNormals method doWork.

@Override
protected Object doWork() {
    validateArguments();
    if (!new HDF5Library().load(null)) {
        //Note: passing null means using the default temp dir.
        throw new UserException.HardwareFeatureException("Cannot load the required HDF5 library. " + "HDF5 is currently supported on x86-64 architecture and Linux or OSX systems.");
    }
    logger.info("Starting allelic panel of normals creation...");
    final AllelicPanelOfNormals allelicPoN = new AllelicPanelOfNormalsCreator(inputFiles).create(siteFrequencyThreshold);
    logger.info("Allelic panel of normals created.");
    logger.info("Writing allelic panel of normals to output HDF5 file...");
    allelicPoN.write(outputFile, HDF5File.OpenMode.CREATE);
    logger.info("Allelic panel of normals written to " + outputFile + ".");
    if (outputTSVFile != null) {
        allelicPoN.write(outputTSVFile);
        logger.info("Allelic panel of normals written as tab-separated values to " + outputTSVFile + ".");
    }
    return "SUCCESS";
}

Example 2 with AllelicPanelOfNormalsCreator

use of org.broadinstitute.hellbender.tools.pon.allelic.AllelicPanelOfNormalsCreator in project gatk-protected by broadinstitute.

the class CreateAllelicPanelOfNormals method doWork.

@Override
protected Object doWork() {
    validateArguments();
    if (!new HDF5Library().load(null)) {
        //Note: passing null means using the default temp dir.
        throw new UserException.HardwareFeatureException("Cannot load the required HDF5 library. " + "HDF5 is currently supported on x86-64 architecture and Linux or OSX systems.");
    }
    logger.info("Starting allelic panel of normals creation...");
    final AllelicPanelOfNormals allelicPoN = new AllelicPanelOfNormalsCreator(inputFiles).create(siteFrequencyThreshold);
    logger.info("Allelic panel of normals created.");
    logger.info("Writing allelic panel of normals to output HDF5 file...");
    allelicPoN.write(outputFile, HDF5File.OpenMode.CREATE);
    logger.info("Allelic panel of normals written to " + outputFile + ".");
    if (outputTSVFile != null) {
        allelicPoN.write(outputTSVFile);
        logger.info("Allelic panel of normals written as tab-separated values to " + outputTSVFile + ".");
    }
    return "SUCCESS";
}