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";
}
}
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";
}
}
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