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);
}
