private static int MainHelper(string[] args)
{
EvaluateCnvOptionsParser optionsParser = new EvaluateCnvOptionsParser();
if (args.Length < 4)
{
ShowHelp(optionsParser, Console.Error);
return(1);
}
var parsingResult = optionsParser.Parse(args.Skip(4));
if (!parsingResult.Success)
{
Console.Error.WriteLine(parsingResult.ErrorMessage);
ShowHelp(optionsParser, Console.Error);
return(1);
}
var options = parsingResult.Result;
if (options.Help)
{
ShowHelp(optionsParser, Console.Out);
return(0);
}
CNVChecker.Evaluate(args[0], args[1], args[2], args[3], options);
return(0);
}
public static void ShowHelp(EvaluateCnvOptionsParser optionsParser, System.IO.TextWriter writer)
{
writer.WriteLine("EvaluateCNV {0}",
System.Reflection.Assembly.GetEntryAssembly().GetName().Version);
writer.WriteLine("For more info see: http://confluence.illumina.com/display/BIOINFO/EvaluateCNV");
writer.WriteLine();
writer.WriteLine("Usage info:");
writer.WriteLine("EvaluateCNV $TruthSetPath $CNV.vcf $ExcludedRegionsBed $OutputDir [OPTIONS]+ [$RegionOfInterestBed]");
writer.WriteLine("Options:");
optionsParser.ShowHelp(writer.WriteLine);
}