private CanvasOutput RunSingleSample(string sampleId, CanvasTumorNormalEnrichmentInput input, IFileLocation bAlleleVcf, bool isDbSnpVcf, IFileLocation manifest, IDirectoryLocation sampleSandbox)
{
if (!_annotationFileProvider.IsSupported(input.GenomeMetadata))
{
_logger.Info($"Skipping Canvas for sample {sampleId}: unsupported reference genome '{input.GenomeMetadata.Name}'");
return(null);
}
StringBuilder commandLine = new StringBuilder("Tumor-normal-enrichment");
commandLine.Append(_singleSampleInputCommandLineBuilder.GetSingleSampleCommandLine(sampleId, input.TumorBam, input.GenomeMetadata, sampleSandbox));
commandLine.Append($" --normal-bam \"{input.NormalBam.BamFile}\"");
commandLine.Append($" --manifest \"{manifest}\"");
var bAlleleVcfOptionName = isDbSnpVcf ?
SingleSampleCommonOptionsParser.PopulationBAlleleVcfOptionName :
SingleSampleCommonOptionsParser.SampleBAlleleVcfOptionName;
commandLine.Append($" --{bAlleleVcfOptionName} {bAlleleVcf.WrapWithShellQuote()}");
commandLine.Append($" --somatic-vcf \"{input.SomaticVcf.VcfFile}\"");
AddPloidyVcf(commandLine, SingleSampleCommonOptionsParser.PloidyVcfOptionName, input, sampleId, sampleSandbox);
commandLine.Append(_singleSampleInputCommandLineBuilder.GetCustomParameters());
commandLine = _singleSampleInputCommandLineBuilder.MergeCustomCanvasParameters(commandLine);
var job = new JobInfo(_runtimeExecutable.FullName, _canvasExe + " " + commandLine, "Canvas_" + sampleId);
return(_workDoer.DoWork(WorkResourceRequest.CreateExact(1, 8), job, GetCanvasOutput(sampleId, sampleSandbox)).Await());
}
private CanvasOutput RunSingleSample(string sampleId, CanvasTumorNormalEnrichmentInput input, IFileLocation bAlleleVcf, bool isDbSnpVcf, IFileLocation manifest, IDirectoryLocation sampleSandbox)
{
if (!_annotationFileProvider.IsSupported(input.GenomeMetadata))
{
_logger.Info($"Skipping Canvas for sample {sampleId}: unsupported reference genome '{input.GenomeMetadata.Name}'");
return(null);
}
StringBuilder commandLine = new StringBuilder("Tumor-normal-enrichment");
commandLine.Append(_singleSampleInputCommandLineBuilder.GetSingleSampleCommandLine(sampleId, input.TumorBam, input.GenomeMetadata, sampleSandbox));
commandLine.Append($" --normal-bam \"{input.NormalBam.BamFile}\"");
commandLine.Append($" --manifest \"{manifest}\"");
var bAlleleVcfOptionName = isDbSnpVcf ?
SingleSampleCommonOptionsParser.PopulationBAlleleVcfOptionName :
SingleSampleCommonOptionsParser.SampleBAlleleVcfOptionName;
commandLine.Append($" --{bAlleleVcfOptionName} {bAlleleVcf.WrapWithShellQuote()}");
commandLine.Append($" --somatic-vcf \"{input.SomaticVcf.VcfFile}\"");
IFileLocation ploidyBed = _canvasPloidyBedCreator.CreatePloidyBed(input.NormalVcf, input.GenomeMetadata, sampleSandbox);
if (ploidyBed != null)
{
commandLine.Append($" --{SingleSampleCommonOptionsParser.PloidyBedOptionName} \"{ploidyBed}\"");
}
commandLine.Append(_singleSampleInputCommandLineBuilder.GetCustomParameters());
commandLine = _singleSampleInputCommandLineBuilder.MergeCustomCanvasParameters(commandLine);
UnitOfWork singleSampleJob = new UnitOfWork
{
ExecutablePath = CrossPlatform.IsThisLinux() ? _runtimeExecutable.FullName : _canvasExe.FullName,
CommandLine = CrossPlatform.IsThisLinux() ? _canvasExe + " " + commandLine : commandLine.ToString(),
LoggingFolder = _workManager.LoggingFolder.FullName,
LoggingStub = "Canvas_" + sampleId,
};
_workManager.DoWorkSingleThread(singleSampleJob);
return(GetCanvasOutput(sampleId, sampleSandbox));
}