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); }