public static ExitCodes Run(string command, string[] commandArgs)
{
var creator = new GnomadSnvMain();
var ops = new OptionSet
{
{
"ref|r=",
"compressed reference sequence file",
v => _compressedReference = v
},
{
"genome|g=",
"input directory containing VCF (and .version) files with genomic frequencies",
v => _genomeDirectory = v
},
{
"exome|e=",
"input directory containing VCF (and .version) files with exomic frequencies",
v => _exomeDirectory = v
},
{
"temp|t=",
"output temp directory for intermediate (per chrom) NSA files",
v => _tempDirectory = v
},
{
"out|o=",
"output directory for NSA file",
v => _outputDirectory = v
}
};
var commandLineExample = $"{command} [options]";
var exitCode = new ConsoleAppBuilder(commandArgs, ops)
.Parse()
.CheckInputFilenameExists(_compressedReference, "compressed reference sequence file name", "--ref")
.CheckDirectoryExists(_genomeDirectory, "input directory containing genome vcf files", "--genome")
.CheckDirectoryExists(_outputDirectory, "output Supplementary directory", "--out")
.SkipBanner()
.ShowHelpMenu("Reads provided supplementary data files and populates tsv files", commandLineExample)
.ShowErrors()
.Execute(ProgramExecution);
return(exitCode);
}
public static ExitCodes Run(string command, string[] commandArgs)
{
var creator = new GnomadSnvMain();
var ops = new OptionSet
{
{
"ref|r=",
"compressed reference sequence file",
v => _referenceSequencePath = v
},
{
"in|i=",
"input file path (along with a .version file)",
v => _inputFile = v
},
{
"out|o=",
"output directory for NSI file",
v => _outputDirectory = v
}
};
var commandLineExample = $"{command} [options]";
var exitCode = new ConsoleAppBuilder(commandArgs, ops)
.Parse()
.CheckInputFilenameExists(_referenceSequencePath, "compressed reference sequence file name", "--ref")
.CheckInputFilenameExists(_inputFile, "input file with LCR regions", "--ref")
.CheckDirectoryExists(_outputDirectory, "output Supplementary directory", "--out")
.SkipBanner()
.ShowHelpMenu("Reads provided supplementary data files and populates tsv files", commandLineExample)
.ShowErrors()
.Execute(ProgramExecution);
return(exitCode);
}
