public void Move(IFileLocation fileNameStub, bool includeIntermediateResults, Action <IFileLocation, IFileLocation> move)
{
CanvasOutput.Move(fileNameStub, includeIntermediateResults, move);
CanvasEnrichmentOutput destination = GetFromStub(fileNameStub, includeIntermediateResults);
BinSize.MoveIfNotNull(destination.BinSize, move);
NormalBinned.MoveIfNotNull(destination.NormalBinned, move);
UnsmoothedCnd.MoveIfNotNull(destination.UnsmoothedCnd, move);
}
public static CanvasEnrichmentOutput GetFromStub(IFileLocation stub)
{
var canvasOutput = CanvasOutput.GetFromStub(stub);
IFileLocation binSize = stub.AppendName(".binsize");
IFileLocation normalBinned = stub.AppendName(".binned");
IFileLocation unsmoothedCnd = stub.AppendName(".unsmoothed.cnd");
return(new CanvasEnrichmentOutput(canvasOutput, binSize, normalBinned, unsmoothedCnd));
}
public void Move(IFileLocation fileNameStub, bool includeIntermediateResults, Action <IFileLocation, IFileLocation> move)
{
CanvasOutput destination = GetFromStub(fileNameStub, includeIntermediateResults);
CnvVcf.Move(destination.CnvVcf, move);
move(CoverageAndVariantFrequencies, destination.CoverageAndVariantFrequencies);
VariantFrequencies.MoveIfNotNull(destination.VariantFrequencies, move);
VariantFrequenciesBaf.MoveIfNotNull(destination.VariantFrequenciesBaf, move);
Partitioned.MoveIfNotNull(destination.Partitioned, move);
}
public CanvasEnrichmentOutput(CanvasOutput canvasOutput,
IFileLocation binSize = null,
IFileLocation normalBinned = null,
IFileLocation unsmoothedCnd = null)
{
CanvasOutput = canvasOutput;
BinSize = binSize;
NormalBinned = normalBinned;
UnsmoothedCnd = unsmoothedCnd;
}
public static CanvasEnrichmentOutput GetFromStub(IFileLocation stub, bool includeIntermediateResults)
{
var canvasOutput = CanvasOutput.GetFromStub(stub, includeIntermediateResults);
if (!includeIntermediateResults)
{
return(new CanvasEnrichmentOutput(canvasOutput));
}
IFileLocation binSize = stub.AppendName(".binsize");
IFileLocation normalBinned = stub.AppendName(".binned");
IFileLocation unsmoothedCnd = stub.AppendName(".unsmoothed.cnd");
return(new CanvasEnrichmentOutput(canvasOutput, binSize, normalBinned, unsmoothedCnd));
}
private CanvasEnrichmentOutput GetCanvasOutput(string sampleId, IDirectoryLocation sampleSandbox)
{
var cnvVcf = new Vcf(sampleSandbox.GetFileLocation("CNV.vcf.gz"));
var tempCnvDirectory = sampleSandbox.GetDirectoryLocation($"TempCNV_{sampleId}");
var variantFrequencies = tempCnvDirectory.GetFileLocation($"VFResults{sampleId}.txt.gz");
var variantFrequenciesBaf = tempCnvDirectory.GetFileLocation($"VFResults{sampleId}.txt.gz.baf");
IFileLocation coverageAndVariantFrequencies = sampleSandbox.GetFileLocation("CNV.CoverageAndVariantFrequency.txt");
IFileLocation tempStub = tempCnvDirectory.GetFileLocation($"{sampleId}");
IFileLocation partitioned = tempStub.AppendName(".partitioned");
var canvasOutput = new CanvasOutput(cnvVcf, coverageAndVariantFrequencies, variantFrequencies,
variantFrequenciesBaf, partitioned);
IFileLocation binSize = tempStub.AppendName(".binsize");
IFileLocation normalBinned = tempStub.AppendName(".normal.binned");
IFileLocation unsmoothedCnd = tempStub.AppendName(".ratio.binned.cnd");
if (!binSize.Exists)
{
binSize = null;
}
return(new CanvasEnrichmentOutput(canvasOutput, binSize, normalBinned, unsmoothedCnd));
}
