private PiscesOptionsParser GetParsedApplicationOptions(string arguments)
{
var parsedOptions = new PiscesOptionsParser();
parsedOptions.ParseArgs(arguments.Split(' '), false);
return(parsedOptions);
}
private static void CheckHeader(AlleleReader reader)
{
string piscesCmd = reader.HeaderLines.FirstOrDefault(str => str.Contains("##Pisces_cmdline")).Split("\"\"")[1];
var appOptionParser = new PiscesOptionsParser();
appOptionParser.ParseArgs(piscesCmd.Split(null));
// Check if VCF is diploid
if (appOptionParser.PiscesOptions.VariantCallingParameters.PloidyModel == PloidyModel.DiploidByAdaptiveGT ||
appOptionParser.PiscesOptions.VariantCallingParameters.PloidyModel == PloidyModel.DiploidByThresholding)
{
throw new VariantReaderException("Adaptive Genotyper should be used with VCFs that are called as somatic " +
"VCFs by Pisces. Please check the input VCF file.");
}
// Check if VCF is crushed
else if (appOptionParser.PiscesOptions.VcfWritingParameters.ForceCrush == true)
{
throw new VariantReaderException("Adaptive Genotyper should be used with uncrushed VCFs. Please check the input VCF file.");
}
// Check if GVCF or --minvq 0
else if (!appOptionParser.PiscesOptions.VcfWritingParameters.OutputGvcfFile &&
(appOptionParser.PiscesOptions.VariantCallingParameters.MinimumVariantQScore > 0 ||
appOptionParser.PiscesOptions.VariantCallingParameters.MinimumFrequency > 0.02))
{
throw new VariantReaderException("Adaptive Genotyper should be used with GVCFs or with option -minvq 0. Please" +
" check in the input VCF file.");
}
}