protected override void ProgramExecution() { Logger.WriteToLog("Generating counts file"); string countsFile = Counts.WriteCountsFile(_options.InputVcf, _options.OutputDirectory, _options.LociCount); Logger.WriteToLog("Starting Recalibration"); try { QualityRecalibration.Recalibrate(_options.InputVcf, countsFile, _options.OutputDirectory, _options.BaseQNoise, _options.ZFactor, _options.MaxQScore, _options.FilterQScore, _options.QuotedCommandLineArgumentsString); } catch (Exception e) { Logger.WriteToLog("*** Error encountered: {0}", e); throw e; } Logger.WriteToLog("Work complete."); }
protected override void ProgramExecution() { AdjustOptions(ref _options); Logger.WriteToLog("Generating counts files"); SignatureSorterResultFiles results = SignatureSorter.StrainVcf(_options); Logger.WriteToLog("Starting Recalibration"); try { QualityRecalibration.Recalibrate(results, _options); } catch (Exception e) { Logger.WriteToLog("*** Error encountered: {0}", e); throw e; } Logger.WriteToLog("Work complete."); }
static int Main(string[] arguments) { if (arguments.Length == 0) { ApplicationOptions.PrintUsageInfo(); return(1); } var options = ApplicationOptions.ParseCommandLine(arguments); Init(options); if (options == null) { ApplicationOptions.PrintUsageInfo(); return(1); } try { if (!(options.InputVcf).ToLower().EndsWith(".genome.vcf")) { Logger.WriteToLog(">>> **Warning**: VCF supplied to Recalibration algorithms should be genome VCF. Was this the intent?"); Logger.WriteToLog(">>> continuing..."); } Logger.WriteToLog(">>> generating counts file"); string countsFile = Counts.WriteCountsFile(options.InputVcf, options.OutputDirectory); Logger.WriteToLog(">>> starting Recalibration"); QualityRecalibration.Recalibrate(options.InputVcf, countsFile, options.BaseQNoise, options.ZFactor, options.MaxQScore, options.FilterQScore); } catch (Exception e) { Logger.WriteToLog("*** Error encountered: {0}", e); } Logger.WriteToLog(">>> Work complete."); Logger.TryCloseLog(); return(0); }