static int Main(string[] args)
{
CanvasCommon.Utilities.LogCommandLine(args);
string inFile = null;
string outFile = null;
string variantFrequencyFile = null;
string referenceFolder = null;
string name = "SAMPLE";
string truthDataPath = null;
string somaticVCFPath = null;
bool needHelp = false;
string bedPath = null;
string ploidyBedPath = null;
string ffpeOutliersPath = null;
bool isEnrichment = false;
bool isDbsnpVcf = false;
double? localSDmetric = null;
double minimumCallSize;
int qualityFilterThreshold = 0;
// Parameters, for parameter-sweep, somatic model training:
bool isTrainMode = false;
float? userPurity = null;
float? userPloidy = null;
CanvasCommon.CanvasSomaticClusteringMode somaticClusteringMode = CanvasCommon.CanvasSomaticClusteringMode.Density;
string parameterconfigPath = Path.Combine(Isas.Shared.Utilities.GetAssemblyFolder(typeof(Program)), "SomaticCallerParameters.json");
OptionSet 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=", "folder that contains both genome.fa and GenomeSize.xml", v => referenceFolder = v },
{ "n|name=", "sample name for output VCF header (optional)", v => name = v },
{ "t|truth=", "path to vcf/bed with CNV truth data (optional)", v => truthDataPath = v },
{ "h|help", "show this message and exit", v => needHelp = v != null },
{ "e|enrichment", "flag indicating this is enrichment data", v => isEnrichment = v != null },
{ "s|somaticvcf=", "somatic vcf file - optionally used for purity estimation", v => somaticVCFPath = v },
{ "b|bedfile=", "bed file containing regions to exclude from calling", v => bedPath = v},
{ "p|ploidyBedFile=", "bed file specifying reference ploidy (e.g. for sex chromosomes) (optional)", v => ploidyBedPath = v},
{ "f|localSDFile=", "text file with localSD metric (calculate within CanvasClean) (optional)", v => ffpeOutliersPath = v},
{ "d|dbsnpvcf", "flag indicating a dbSNP VCF file is used to generate the variant frequency file", v => isDbsnpVcf = v != null },
{ "M|minimumcall=", "INTERNAL: minimum call size", v => minimumCallSize = int.Parse(v) },
{ "q|qualitythreshold=", $"quality filter threshold (default {qualityFilterThreshold})", v => qualityFilterThreshold = int.Parse(v) },
{ "c|parameterconfig=", $"parameter configuration path (default {parameterconfigPath})", v => parameterconfigPath = v },
{ "u|definedpurity=", "INTERNAL: user pre-defined purity", v => userPurity = float.Parse(v) },
{ "l|definedploidy=", "INTERNAL: user pre-defined ploidy", v => userPloidy = float.Parse(v) },
{ "a|trainmodel=", "INTERNAL: user pre-defined ploidy", v => isTrainMode = v != null }
};
List<string> extraArgs = p.Parse(args);
if (extraArgs.Count > 0)
{
Console.WriteLine("Error: Argument '{0}' not understood", extraArgs[0]);
needHelp = true;
}
if (needHelp)
{
ShowHelp(p);
return 0;
}
if (inFile == null || outFile == null || referenceFolder == null)
{
ShowHelp(p);
return 0;
}
if (!File.Exists(inFile))
{
Console.WriteLine("Canvas error: File {0} does not exist! Exiting.", inFile);
return 1;
}
if (!File.Exists(variantFrequencyFile))
{
Console.WriteLine("Canvas error: File {0} does not exist! Exiting.", variantFrequencyFile);
return 1;
}
if (!File.Exists(Path.Combine(referenceFolder, "GenomeSize.xml")))
{
Console.WriteLine("Canvas error: File {0} does not exist! Exiting.", Path.Combine(referenceFolder, "GenomeSize.xml"));
return 1;
}
if (qualityFilterThreshold < 0)
throw new ArgumentException($"Quality filter threshold must be greater than or equal to zero. Value was {qualityFilterThreshold}");
if (!File.Exists(parameterconfigPath))
{
Console.WriteLine("Canvas error: File {0} does not exist! Exiting.", parameterconfigPath);
return 1;
}
DataContractJsonSerializer js = new DataContractJsonSerializer(typeof(SomaticCallerParameters));
string parameterconfigFile = File.ReadAllText(parameterconfigPath);
MemoryStream ms = new MemoryStream(Encoding.ASCII.GetBytes(parameterconfigFile));
SomaticCallerParameters somaticCallerParametersJSON = (SomaticCallerParameters)js.ReadObject(ms);
SomaticCaller caller = new SomaticCaller();
caller.somaticCallerParameters = somaticCallerParametersJSON;
caller.TruthDataPath = truthDataPath;
caller.SomaticVCFPath = somaticVCFPath;
caller.IsEnrichment = isEnrichment;
caller.IsDbsnpVcf = isDbsnpVcf;
caller.userPurity = userPurity;
caller.userPloidy = userPloidy;
caller.IsTrainingMode = isTrainMode;
caller.QualityFilterThreshold = qualityFilterThreshold;
// Set parameters:
if (!string.IsNullOrEmpty(ploidyBedPath))
{
caller.LoadReferencePloidy(ploidyBedPath);
}
if (!string.IsNullOrEmpty(ffpeOutliersPath))
{
localSDmetric = CanvasCommon.CanvasIO.ReadLocalSDFromTextFile(ffpeOutliersPath);
}
caller.LoadBedFile(bedPath);
return caller.CallVariants(inFile, variantFrequencyFile, outFile, referenceFolder, name, localSDmetric, somaticClusteringMode);
}
static int Main(string[] args)
{
CanvasCommon.Utilities.LogCommandLine(args);
string inFile = null;
string outFile = null;
string variantFrequencyFile = null;
string referenceFolder = null;
string name = "SAMPLE";
string truthDataPath = null;
string somaticVCFPath = null;
bool needHelp = false;
string bedPath = null;
string ploidyBedPath = null;
string ffpeOutliersPath = null;
bool isEnrichment = false;
bool isDbsnpVcf = false;
double? localSDmetric = null;
// Parameters, for parameter-sweep:
float deviationFactor = SomaticCaller.DefaultDeviationFactor;
double coverageWeighting = SomaticCaller.DefaultCoverageWeighting;
int minimumCallSize = SomaticCaller.DefaultMinimumCallSize;
double precisionWeightingFactor = SomaticCaller.DefaultPrecisionWeightingFactor;
float? userPurity = null;
float? userPloidy = null;
OptionSet 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=", "folder that contains both genome.fa and GenomeSize.xml", v => referenceFolder = v },
{ "n|name=", "sample name for output VCF header (optional)", v => name = v },
{ "t|truth=", "path to vcf/bed with CNV truth data (optional)", v => truthDataPath = v },
{ "h|help", "show this message and exit", v => needHelp = v != null },
{ "e|enrichment", "flag indicating this is enrichment data", v => isEnrichment = v != null },
{ "s|somaticvcf=", "somatic vcf file - optionally used for purity estimation", v => somaticVCFPath = v },
{ "b|bedfile=", "bed file containing regions to exclude from calling", v => bedPath = v},
{ "p|ploidyBedFile=", "bed file specifying reference ploidy (e.g. for sex chromosomes) (optional)", v => ploidyBedPath = v},
{ "f|localSDFile=", "text file with localSD metric (calculate within CanvasClean) (optional)", v => ffpeOutliersPath = v},
{ "d|dbsnpvcf", "flag indicating a dbSNP VCF file is used to generate the variant frequency file", v => isDbsnpVcf = v != null },
{ "D|deviation=", "INTERNAL: best deviation parameter", v => deviationFactor = float.Parse(v) },
{ "C|coverageweight=", "INTERNAL: coverage weighting", v => coverageWeighting = float.Parse(v) },
{ "M|minimumcall=", "INTERNAL: minimum call size", v => minimumCallSize = int.Parse(v) },
{ "P|precisionweight=", "INTERNAL: precision weighting factor", v => precisionWeightingFactor = double.Parse(v) },
{ "u|definedpurity=", "INTERNAL: user pre-defined purity", v => userPurity = float.Parse(v) },
{ "l|definedploidy=", "INTERNAL: user pre-defined ploidy", v => userPloidy = float.Parse(v) },
};
List<string> extraArgs = p.Parse(args);
if (extraArgs.Count > 0)
{
Console.WriteLine("Error: Argument '{0}' not understood", extraArgs[0]);
needHelp = true;
}
if (needHelp)
{
ShowHelp(p);
return 0;
}
if (inFile == null || outFile == null || referenceFolder == null)
{
ShowHelp(p);
return 0;
}
if (!File.Exists(inFile))
{
Console.WriteLine("Canvas error: 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("Canvas error: File {0} does not exist! Exiting.", Path.Combine(referenceFolder, "GenomeSize.xml"));
return 1;
}
if (userPurity == null && userPloidy != null || userPurity != null && userPloidy == null)
{
Console.WriteLine("Canvas error: both definedpurity and definedploidy should be specified");
return 1;
}
SomaticCaller caller = new SomaticCaller();
// Set parameters:
caller.TruthDataPath = truthDataPath;
caller.SomaticVCFPath = somaticVCFPath;
caller.IsEnrichment = isEnrichment;
caller.IsDbsnpVcf = isDbsnpVcf;
caller.DeviationFactor = deviationFactor;
caller.MinimumCallSize = minimumCallSize;
caller.CoverageWeighting = coverageWeighting;
caller.userPurity = userPurity;
caller.userPloidy = userPloidy;
caller.PrecisionWeightingFactor = precisionWeightingFactor;
if (!string.IsNullOrEmpty(ploidyBedPath))
{
caller.LoadReferencePloidy(ploidyBedPath);
}
if (!string.IsNullOrEmpty(ffpeOutliersPath))
{
localSDmetric = CanvasCommon.CanvasIO.ReadLocalSDFromTextFile(ffpeOutliersPath);
}
caller.LoadBedFile(bedPath);
return caller.CallVariants(inFile, variantFrequencyFile, outFile, referenceFolder, name, localSDmetric);
}