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 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 = 10; // Default quality filter threshold = 10, overridable via -q command-line argument
// 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.Framework.Utilities.Utilities.GetAssemblyFolder(typeof(Program)),
"SomaticCallerParameters.json");
string qualityScoreConfigPath = Path.Combine(Isas.Framework.Utilities.Utilities.GetAssemblyFolder(typeof(Program)),
"QualityScoreParameters.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
},
{
"g|qscoreconfig=", $"parameter configuration path (default {qualityScoreConfigPath})",
v => qualityScoreConfigPath = 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);
}
FileLocation parameterconfigFile = new FileLocation(parameterconfigPath);
SomaticCallerParameters somaticCallerParametersJSON = Deserialize <SomaticCallerParameters>(parameterconfigFile);
FileLocation qscoreConfigFile = new FileLocation(qualityScoreConfigPath);
CanvasCommon.QualityScoreParameters qscoreParametersJSON = Deserialize <CanvasCommon.QualityScoreParameters>(qscoreConfigFile);
SomaticCaller caller = new SomaticCaller();
caller.somaticCallerParameters = somaticCallerParametersJSON;
caller.somaticCallerQscoreParameters = qscoreParametersJSON;
caller.TruthDataPath = truthDataPath;
caller.SomaticVCFPath = somaticVCFPath;
caller.IsEnrichment = isEnrichment;
caller.IsDbsnpVcf = isDbsnpVcf;
caller.userPurity = userPurity;
caller.userPloidy = userPloidy;
caller.IsTrainingMode = truthDataPath != null || isTrainMode;
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));
}
