/**
* Project all of the normals used to create the PoN into the reduced panel.
*
* @param pon Not {@code null}.
* @param ctx Spark context, {@code null} indicates no spark context available, which is
* supported.
* @return never {@code null}. Result will contain multiple columns in each of the
* ReadCountCollection attributes.
*/
public static TangentNormalizationResult tangentNormalizeNormalsInPoN(
final PoN pon, final JavaSparkContext ctx) {
// Get the list of sample names in a modifiable List
final List<String> sampleNamesCopy = new ArrayList<>(pon.getSampleNames());
logger.info("Loading normalized counts...");
final ReadCountCollection coverageProfile =
new ReadCountCollection(
SetUniqueList.setUniqueList(pon.getTargets()),
SetUniqueList.setUniqueList(sampleNamesCopy),
pon.getNormalizedCounts());
logger.info("Tangent normalizing the normals (normalized by target factors) ...");
// For each sample in the PoN, tangent normalize against the qc reduced PoN.
return TangentNormalizer.tangentNormalize(pon, coverageProfile, ctx);
}
