// 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 [MinMapQ]");
return(1);
}
string chromosome = arguments[0];
string vcfPath = arguments[1];
string bamPath = arguments[2];
string outputPath = arguments[3];
int minMapQ = 0; // only use reads with MAPQ greater than this number
if (arguments.Length > 4)
{
minMapQ = int.Parse(arguments[4]);
}
// 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(chromosome, vcfPath, bamPath, outputPath, minMapQ);
return(processor.Run());
}
static int Main(string[] args)
{
CanvasCommon.Utilities.LogCommandLine(args);
string chromosome = null;
string vcfPath = null;
string bamPath = null;
string outputPath = null;
string sampleName = null;
bool isSomatic = false;
bool isDbSnpVcf = false; // assume vcf file comes from a small variant caller (Strelka)
int minMapQ = 0; // only use reads with MAPQ greater than this number
bool needHelp = false;
var p = new OptionSet()
{
{ "c|chromosome=", "chromosome namne", v => chromosome = v },
{ "v|vcfPath=", "file containing small variants", v => vcfPath = v },
{ "b|bamPath=", "bam file", v => bamPath = v },
{ "o|outputPath=", "name of output directory", v => outputPath = v },
{ "n|sampleName=", "sample name for output VCF header (optional)", v => sampleName = v },
{ "i|isDbSnpVcf=", "flag to specify if vcf file contains dbSNP variants (optional)", v => isDbSnpVcf = v != null },
{ "q|minMapQ=", "mapQ threshold for vcf file (optional)", v => minMapQ = int.Parse(v) },
{ "s|isSomatic", "flag to specify if Canvas workflow is somatic (optional)", v => isSomatic = v != null },
{ "h|help", "show this message and exit", v => needHelp = v != null },
};
var extraArgs = p.Parse(args);
if (extraArgs.Count > 0)
{
Console.WriteLine("* Error: I don't understand the argument '{0}'", extraArgs[0]);
needHelp = true;
}
if (needHelp)
{
ShowHelp(p);
return(0);
}
if (string.IsNullOrEmpty(chromosome) || string.IsNullOrEmpty(outputPath))
{
ShowHelp(p);
return(0);
}
if (!File.Exists(vcfPath))
{
Console.WriteLine($"CanvasSNV.exe: File {vcfPath} does not exist! Exiting.");
return(1);
}
if (!File.Exists(bamPath))
{
Console.WriteLine($"CanvasSNV.exe: File {bamPath} does not exist! Exiting.");
return(1);
}
// 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(chromosome, vcfPath, bamPath, outputPath, sampleName, isDbSnpVcf, minMapQ, isSomatic);
return(processor.Run());
}
