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Example 1 with PCATangentNormalizationResult

use of org.broadinstitute.hellbender.tools.pon.coverage.pca.PCATangentNormalizationResult in project gatk by broadinstitute.

the class NormalizeSomaticReadCounts method doWork.

@Override
protected Object doWork() {
    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.");
    }
    IOUtils.canReadFile(ponFile);
    try (final HDF5File hdf5PoNFile = new HDF5File(ponFile)) {
        final PCACoveragePoN pon = new HDF5PCACoveragePoN(hdf5PoNFile, logger);
        final TargetCollection<Target> targetCollection = readTargetCollection(targetFile);
        final ReadCountCollection proportionalCoverageProfile = readInputReadCounts(readCountsFile, targetCollection);
        final PCATangentNormalizationResult tangentNormalizationResult = pon.normalize(proportionalCoverageProfile);
        ;
        tangentNormalizationResult.write(getCommandLine(), tangentNormalizationOutFile, preTangentNormalizationOutFile, betaHatsOutFile, fntOutFile);
        return "SUCCESS";
    }
}
Also used : HDF5PCACoveragePoN(org.broadinstitute.hellbender.tools.pon.coverage.pca.HDF5PCACoveragePoN) HDF5Library(org.broadinstitute.hdf5.HDF5Library) HDF5PCACoveragePoN(org.broadinstitute.hellbender.tools.pon.coverage.pca.HDF5PCACoveragePoN) PCACoveragePoN(org.broadinstitute.hellbender.tools.pon.coverage.pca.PCACoveragePoN) PCATangentNormalizationResult(org.broadinstitute.hellbender.tools.pon.coverage.pca.PCATangentNormalizationResult) HDF5File(org.broadinstitute.hdf5.HDF5File)

Example 2 with PCATangentNormalizationResult

use of org.broadinstitute.hellbender.tools.pon.coverage.pca.PCATangentNormalizationResult in project gatk-protected by broadinstitute.

the class NormalizeSomaticReadCounts method doWork.

@Override
protected Object doWork() {
    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.");
    }
    IOUtils.canReadFile(ponFile);
    try (final HDF5File hdf5PoNFile = new HDF5File(ponFile)) {
        final PCACoveragePoN pon = new HDF5PCACoveragePoN(hdf5PoNFile, logger);
        final TargetCollection<Target> targetCollection = readTargetCollection(targetFile);
        final ReadCountCollection proportionalCoverageProfile = readInputReadCounts(readCountsFile, targetCollection);
        final PCATangentNormalizationResult tangentNormalizationResult = pon.normalize(proportionalCoverageProfile);
        ;
        tangentNormalizationResult.write(getCommandLine(), tangentNormalizationOutFile, preTangentNormalizationOutFile, betaHatsOutFile, fntOutFile);
        return "SUCCESS";
    }
}
Also used : HDF5PCACoveragePoN(org.broadinstitute.hellbender.tools.pon.coverage.pca.HDF5PCACoveragePoN) HDF5Library(org.broadinstitute.hdf5.HDF5Library) HDF5PCACoveragePoN(org.broadinstitute.hellbender.tools.pon.coverage.pca.HDF5PCACoveragePoN) PCACoveragePoN(org.broadinstitute.hellbender.tools.pon.coverage.pca.PCACoveragePoN) PCATangentNormalizationResult(org.broadinstitute.hellbender.tools.pon.coverage.pca.PCATangentNormalizationResult) HDF5File(org.broadinstitute.hdf5.HDF5File)

Aggregations

HDF5File (org.broadinstitute.hdf5.HDF5File)2 HDF5Library (org.broadinstitute.hdf5.HDF5Library)2 HDF5PCACoveragePoN (org.broadinstitute.hellbender.tools.pon.coverage.pca.HDF5PCACoveragePoN)2 PCACoveragePoN (org.broadinstitute.hellbender.tools.pon.coverage.pca.PCACoveragePoN)2 PCATangentNormalizationResult (org.broadinstitute.hellbender.tools.pon.coverage.pca.PCATangentNormalizationResult)2