| public CallVariants ( string variantFrequencyFile, string inFile, string outFile, string ploidyBedPath, string referenceFolder, string sampleName, string truthDataPath ) : int | ||
| variantFrequencyFile | string | |
| inFile | string | |
| outFile | string | |
| ploidyBedPath | string | |
| referenceFolder | string | |
| sampleName | string | |
| truthDataPath | string | |
| Результат | int | |
static int Main(string[] args)
{
CanvasCommon.Utilities.LogCommandLine(args);
string inFile = null;
string outFile = null;
string variantFrequencyFile = null;
string ploidyBedPath = null;
string referenceFolder = null;
string sampleName = "SAMPLE";
bool needHelp = false;
string truthDataPath = null;
string qualityScoreConfigPath = Path.Combine(Utilities.GetAssemblyFolder(typeof(Program)), "QualityScoreParameters.json");
var p = new OptionSet()
{
{ "i|infile=", "file containing bins, their counts, and assigned segments (obtained from CanvasPartition.exe)", v => inFile = v },
{ "v|varfile=", "file containing variant frequencies (obtained from CanvasSNV.exe)", v => variantFrequencyFile = v },
{ "o|outfile=", "file name prefix to ouput copy number calls to outfile.vcf", v => outFile = v },
{ "r|reference=", "reference genome folder that contains GenomeSize.xml", v => referenceFolder = v },
{ "n|sampleName=", "sample name for output VCF header (optional)", v => sampleName = v },
{ "p|ploidyBed=", "bed file specifying reference ploidy (e.g. for sex chromosomes) (optional)", v => ploidyBedPath = v },
{ "d|dbsnpvcf", "flag indicating a dbSNP VCF file is used to generate the variant frequency file (Obsolete)", v => { } },
{ "h|help", "show this message and exit", v => needHelp = v != null },
{ "s|qscoreconfig=", $"parameter configuration path (default {qualityScoreConfigPath})", v => qualityScoreConfigPath = v },
{ "t|truth=", "path to vcf/bed with CNV truth data (optional)", v => truthDataPath = v },
};
List <string> 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 (inFile == null || outFile == null || string.IsNullOrEmpty(variantFrequencyFile) || string.IsNullOrEmpty(referenceFolder))
{
ShowHelp(p);
return(0);
}
if (!File.Exists(inFile))
{
Console.WriteLine("CanvasDiploidCaller.exe: File {0} does not exist! Exiting.", inFile);
return(1);
}
if (!File.Exists(variantFrequencyFile))
{
Console.WriteLine("Canvas error: File {0} does not exist! Exiting.", variantFrequencyFile);
return(1);
}
if (!File.Exists(Path.Combine(referenceFolder, "GenomeSize.xml")))
{
Console.WriteLine("CanvasDiploidCaller.exe: File {0} does not exist! Exiting.", Path.Combine(referenceFolder, "GenomeSize.xml"));
return(1);
}
FileLocation qscoreConfigFile = new FileLocation(qualityScoreConfigPath);
CanvasCommon.QualityScoreParameters qscoreParametersJson = Deserialize <CanvasCommon.QualityScoreParameters>(qscoreConfigFile);
// Set parameters:
var logger = new Logger(new[] { Console.Out }, new[] { Console.Error });
CanvasDiploidCaller caller = new CanvasDiploidCaller(logger, qscoreParametersJson);
return(caller.CallVariants(variantFrequencyFile, inFile, outFile, ploidyBedPath, referenceFolder, sampleName, truthDataPath));
}
static int Main(string[] args)
{
CanvasCommon.Utilities.LogCommandLine(args);
string inFile = null;
string outFile = null;
string variantFrequencyFile = null;
string ploidyBedPath = null;
string referenceFolder = null;
string sampleName = "SAMPLE";
bool isDbsnpVcf = false;
bool needHelp = false;
string truthDataPath = null;
var p = new OptionSet()
{
{ "i|infile=", "file containing bins, their counts, and assigned segments (obtained from CanvasPartition.exe)", v => inFile = v },
{ "v|varfile=", "file containing variant frequencies (obtained from CanvasSNV.exe)", v => variantFrequencyFile = v },
{ "o|outfile=", "file name prefix to ouput copy number calls to outfile.vcf", v => outFile = v },
{ "r|reference=", "reference genome folder that contains GenomeSize.xml", v => referenceFolder = v },
{ "n|sampleName=", "sample name for output VCF header (optional)", v => sampleName = v },
{ "p|ploidyBed=", "bed file specifying reference ploidy (e.g. for sex chromosomes) (optional)", v => ploidyBedPath = v },
{ "d|dbsnpvcf", "flag indicating a dbSNP VCF file is used to generate the variant frequency file", v => isDbsnpVcf = v != null },
{ "h|help", "show this message and exit", v => needHelp = v != null },
{ "t|truth=", "path to vcf/bed with CNV truth data (optional)", v => truthDataPath = v },
};
List<string> 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 (inFile == null || outFile == null || string.IsNullOrEmpty(variantFrequencyFile) || string.IsNullOrEmpty(referenceFolder))
{
ShowHelp(p);
return 0;
}
if (!File.Exists(inFile))
{
Console.WriteLine("CanvasDiploidCaller.exe: File {0} does not exist! Exiting.", inFile);
return 1;
}
if (!File.Exists(variantFrequencyFile))
{
Console.WriteLine("Canvas error: File {0} does not exist! Exiting.", variantFrequencyFile);
return 1;
}
if (!File.Exists(Path.Combine(referenceFolder, "GenomeSize.xml")))
{
Console.WriteLine("CanvasDiploidCaller.exe: File {0} does not exist! Exiting.", Path.Combine(referenceFolder, "GenomeSize.xml"));
return 1;
}
CanvasDiploidCaller caller = new CanvasDiploidCaller();
// Set parameters:
caller.IsDbsnpVcf = isDbsnpVcf;
return caller.CallVariants(variantFrequencyFile, inFile, outFile, ploidyBedPath, referenceFolder, sampleName, truthDataPath);
}
