public override IEnumerable<string> Process()
{
Progress.SetMessage("filter process started at {0}", DateTime.Now);
var watch = new Stopwatch();
watch.Start();
var tsvfile = _options.OutputFile + ".rtsv";
var roptions = new RProcessorOptions()
{
RExecute = _options.GetRCommand(),
RFile = _options.TargetRFile,
ExpectResultFile = _options.ROutputFile
};
new RProcessor(roptions).Process();
if (!File.Exists(_options.ROutputFile))
{
throw new Exception(string.Format("R command failed, look at the file {0}!\nMake sure that your R and R packages brglm, stringr have been installed.", roptions.RFile + ".log"));
}
else if (!_options.IsValidation)
{
var items = new FilterItemTextFormat().ReadFromFile(_options.ROutputFile);
var unfilteredfile = Path.ChangeExtension(_options.ROutputFile, ".vcf");
new FilterItemVcfWriter(_options).WriteToFile(unfilteredfile, items);
items.RemoveAll(m => !m.Filter.Equals("PASS"));
var vcfFile = Path.ChangeExtension(_options.OutputFile, ".vcf");
new FilterItemVcfWriter(_options).WriteToFile(vcfFile, items);
new FilterItemTextFormat().WriteToFile(_options.OutputFile, items);
}
watch.Stop();
Progress.SetMessage("filter process ended at {0}, cost {1}", DateTime.Now, watch.Elapsed);
return new[] { _options.OutputFile };
}
public RProcessor(RProcessorOptions options)
{
this.options = options;
}
public RProcessor(RProcessorOptions options)
{
this.options = options;
}