private CanvasOutput 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"); return(new CanvasOutput(cnvVcf, coverageAndVariantFrequencies, variantFrequencies, variantFrequenciesBaf, partitioned)); }
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)); }
public static IDirectoryLocation GetSampleOutputFolder(IDirectoryLocation analysisOutputFolder, string sampleName) { return(analysisOutputFolder.GetDirectoryLocation($"TempCNV_{sampleName}")); }