public SampleSet <CanvasEnrichmentOutput> Run(SampleSet <CanvasEnrichmentInput> inputs, IDirectoryLocation sandbox)
{
var targetedDbSnpVcfs = _enrichmentInputCreator.CreateDbSnpVcfForManifests(inputs, sandbox, _annotationFileProvider);
var manifests = _enrichmentInputCreator.WriteManifests(inputs, sandbox);
var outputs = new SampleSet <CanvasEnrichmentOutput>();
foreach (var input in inputs)
{
IDirectoryLocation sampleSandbox = sandbox.CreateSubdirectory(input.Key.Id);
var dbSnpVcf = targetedDbSnpVcfs[input.Value.NexteraManifest];
var manifest = manifests[input.Value.NexteraManifest];
outputs.Add(input.Key, RunSingleSample(input.Key.Id, input.Value, dbSnpVcf, manifest, sampleSandbox));
}
return(outputs);
}
public SampleSet <CanvasOutput> Run(SampleSet <CanvasTumorNormalEnrichmentInput> inputs, IDirectoryLocation sandbox)
{
var bAlleleVcfs = GetBAlleleVcfs(inputs, sandbox);
var manifests = _enrichmentInputCreator.WriteManifests(inputs, sandbox);
var outputs = new SampleSet <CanvasOutput>();
foreach (var input in inputs)
{
IDirectoryLocation sampleSandbox = sandbox.CreateSubdirectory(input.Key.Id);
var bAlleleVcf = bAlleleVcfs[input.Key].Item1;
var isDbSnpVcf = bAlleleVcfs[input.Key].Item2;
var manifest = manifests[input.Value.NexteraManifest];
outputs.Add(input.Key, RunSingleSample(input.Key.Id, input.Value, bAlleleVcf, isDbSnpVcf, manifest, sampleSandbox));
}
return(outputs);
}