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)); }