// Arguments: chromosome, NormalVCFPath, TumorBamPath, OutputPath
static int Main(string[] arguments)
{
CanvasCommon.Utilities.LogCommandLine(arguments);
if (arguments.Length < 4)
{
Console.WriteLine("Usage: Chromosome NormalVCFPath TumorBAMPath OutputPath");
return 1;
}
string chromosome = arguments[0];
string vcfPath = arguments[1];
string bamPath = arguments[2];
string outputPath = arguments[3];
// Handle some special cases, if the "chromosome" is a special string:
switch (chromosome.ToLowerInvariant())
{
case "histogram":
return BuildEmpiricalHistograms(vcfPath, bamPath, outputPath);
case "regionhistogram":
return BuildRegionHistograms(vcfPath, bamPath, outputPath);
default:
// Ordinary chromosome name.
break;
}
// Standard logic: Process one chromosome, write output to the specified file path:
SNVReviewer processor = new SNVReviewer();
processor.Chromosome = chromosome;
return processor.Main(vcfPath, bamPath, outputPath);
}
