private CanvasCleanOutput InvokeCanvasClean(CanvasCallset callset, IFileLocation binnedPath)
{
StringBuilder commandLine = new StringBuilder();
commandLine.Length = 0;
string executablePath = Path.Combine(_canvasFolder, "CanvasClean.exe");
if (CrossPlatform.IsThisMono())
{
commandLine.AppendFormat("{0} ", executablePath);
executablePath = Utilities.GetMonoPath();
}
commandLine.AppendFormat("-i \"{0}\" ", binnedPath);
string cleanedPath = Path.Combine(callset.TempFolder, string.Format("{0}.cleaned", callset.Id));
commandLine.AppendFormat("-o \"{0}\" ", cleanedPath);
commandLine.AppendFormat("-g");
string ffpePath = null;
// TruSight Cancer has 1,737 targeted regions. The cut-off 2000 is somewhat arbitrary.
// TruSight One has 62,309 targeted regions.
// Nextera Rapid Capture v1.1 has 411,513 targeted regions.
if (!callset.IsEnrichment || callset.Manifest.Regions.Count > 2000)
{
ffpePath = Path.Combine(callset.TempFolder, "FilterRegions.txt");
commandLine.AppendFormat(" -s -r -f \"{0}\"", ffpePath);
}
if (callset.IsEnrichment) // manifest
{
if (!File.Exists(callset.TempManifestPath))
{
NexteraManifestUtils.WriteNexteraManifests(callset.Manifest, callset.TempManifestPath);
}
commandLine.AppendFormat(" -t \"{0}\"", callset.TempManifestPath);
}
UnitOfWork cleanJob = new UnitOfWork()
{
ExecutablePath = executablePath,
LoggingFolder = _workManager.LoggingFolder.FullName,
LoggingStub = Path.GetFileName(cleanedPath),
CommandLine = commandLine.ToString()
};
if (_customParameters.ContainsKey("CanvasClean"))
{
cleanJob.CommandLine = Utilities.MergeCommandLineOptions(cleanJob.CommandLine, _customParameters["CanvasClean"], true);
}
_workManager.DoWorkSingleThread(cleanJob);
var canvasCleanOutput = new CanvasCleanOutput(new FileLocation(cleanedPath), new FileLocation(ffpePath));
return(canvasCleanOutput);
}
private CanvasCleanOutput InvokeCanvasClean(CanvasCallset callset, IFileLocation binnedPath)
{
StringBuilder commandLine = new StringBuilder();
commandLine.Length = 0;
string executablePath = Path.Combine(_canvasFolder, "CanvasClean.exe");
if (CrossPlatform.IsThisMono())
{
commandLine.AppendFormat("{0} ", executablePath);
executablePath = Utilities.GetMonoPath();
}
commandLine.AppendFormat("-i \"{0}\" ", binnedPath);
string cleanedPath = Path.Combine(callset.TempFolder, string.Format("{0}.cleaned", callset.Id));
commandLine.AppendFormat("-o \"{0}\" ", cleanedPath);
commandLine.AppendFormat("-g");
string ffpePath = null;
// TruSight Cancer has 1,737 targeted regions. The cut-off 2000 is somewhat arbitrary.
// TruSight One has 62,309 targeted regions.
// Nextera Rapid Capture v1.1 has 411,513 targeted regions.
if (!callset.IsEnrichment || callset.Manifest.Regions.Count > 2000)
{
ffpePath = Path.Combine(callset.TempFolder, "FilterRegions.txt");
commandLine.AppendFormat(" -s -r -f \"{0}\"", ffpePath);
}
if (callset.IsEnrichment) // manifest
{
if (!File.Exists(callset.TempManifestPath))
{
NexteraManifestUtils.WriteNexteraManifests(callset.Manifest, callset.TempManifestPath);
}
commandLine.AppendFormat(" -t \"{0}\"", callset.TempManifestPath);
}
UnitOfWork cleanJob = new UnitOfWork()
{
ExecutablePath = executablePath,
LoggingFolder = _workManager.LoggingFolder.FullName,
LoggingStub = Path.GetFileName(cleanedPath),
CommandLine = commandLine.ToString()
};
if (_customParameters.ContainsKey("CanvasClean"))
{
cleanJob.CommandLine = Utilities.MergeCommandLineOptions(cleanJob.CommandLine, _customParameters["CanvasClean"], true);
}
_workManager.DoWorkSingleThread(cleanJob);
var canvasCleanOutput = new CanvasCleanOutput(new FileLocation(cleanedPath), new FileLocation(ffpePath));
return canvasCleanOutput;
}
