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 <Tuple <IFileLocation, bool> > GetBAlleleVcfs(SampleSet <CanvasTumorNormalEnrichmentInput> inputs, IDirectoryLocation sandbox)
{
var inputsUsingDbSnpVcf = inputs.WhereData(input => _annotationFileProvider.CustomDbSnpVcf(input.GenomeMetadata));
var targetedDbSnpVcfs = _enrichmentInputCreator.CreateDbSnpVcfForManifests(inputsUsingDbSnpVcf, sandbox, _annotationFileProvider);
var bAlleleVcfs = new SampleSet <Tuple <IFileLocation, bool> >();
foreach (var input in inputs)
{
IFileLocation bAlleleVcf;
bool isDbSnpVcf = true;
if (!targetedDbSnpVcfs.TryGetValue(input.Value.NexteraManifest, out bAlleleVcf))
{
bAlleleVcf = input.Value.NormalVcf.VcfFile;
isDbSnpVcf = false;
}
bAlleleVcfs[input.Key] = Tuple.Create(bAlleleVcf, isDbSnpVcf);
}
return(bAlleleVcfs);
}
