public static int Run(CanvasNormalizeParameters parameters)
{
NexteraManifest manifest = string.IsNullOrEmpty(parameters.manifestPath) ? null : new NexteraManifest(parameters.manifestPath, null, Console.WriteLine);
switch (parameters.normalizationMode)
{
case CanvasNormalizeMode.BestLR2:
GetBestLR2BinCount(parameters.tumorBedPath, parameters.normalBedPaths, parameters.weightedAverageNormalBedPath,
manifest: manifest);
break;
case CanvasNormalizeMode.WeightedAverage:
GetWeightedAverageBinCount(parameters.normalBedPaths, parameters.weightedAverageNormalBedPath, manifest: manifest);
break;
default:
throw new Exception(string.Format("Invalid CanvasNormalize mode '{0}'", parameters.normalizationMode));
}
GetBinRatio(parameters.tumorBedPath, parameters.weightedAverageNormalBedPath, parameters.outBedPath,
parameters.ploidyBedPath, manifest: manifest);
return 0;
}