private void MoveIntermediateOutput(SampleInfo info, IntermediateOutput output, IFileMover fileMover) { var stub = GetSingleSampleOutputStub(info); // Output: fileMover.Move(output.CnvVcf.VcfFile, SingleSampleCallset.GetVcfOutput(stub)); // Files for visualization: fileMover.Move(output.CoverageBigwig, SingleSampleCallset.GetCoverageBigWig(stub)); var targetBAlleleBedgraph = SingleSampleCallset.GetBAlleleBedGraph(stub); fileMover.Move(output.BAlleleBedgraph.FileLocation, targetBAlleleBedgraph.FileLocation); fileMover.Move(output.BAlleleBedgraph.TabixIndex, targetBAlleleBedgraph.TabixIndex); var targetCopyNumbedBedgraph = SingleSampleCallset.GetCopyNumberBedGraph(stub); fileMover.Move(output.CopyNumberBedgraph.FileLocation, targetCopyNumbedBedgraph.FileLocation); fileMover.Move(output.CopyNumberBedgraph.TabixIndex, targetCopyNumbedBedgraph.TabixIndex); // Deprecated files: #pragma warning disable CS0618 // Type or member is obsolete fileMover.Move(output.CoverageAndVariantFrequencies, SingleSampleCallset.GetCoverageAndVariantFrequencyOutput(stub)); // Used for (non-dynamic) plotting fileMover.Move(output.Partitioned, SingleSampleCallset.GetPartitionedPath(stub)); // used by BSVI fileMover.Move(output.VariantFrequencies, SingleSampleCallset.GetVfSummaryPath(stub)); // used by BSVI fileMover.Move(output.VariantFrequenciesBaf, SingleSampleCallset.GetVfSummaryBafPath(stub)); // used by BSVI #pragma warning restore CS0618 // Type or member is obsolete }
private CanvasSmallPedigreeOutput GetCanvasOutput(SampleSet <CanvasPedigreeSample> pedigreeSamples, IDirectoryLocation sampleSandbox) { var intermediateResults = pedigreeSamples.SelectSamples(sampleInfo => { var sampleId = sampleInfo.Id; var variantFrequencies = SingleSampleCallset.GetVfSummaryPath(sampleSandbox, sampleId); var variantFrequenciesBaf = SingleSampleCallset.GetVfSummaryBafPath(sampleSandbox, sampleId); var partitioned = SingleSampleCallset.GetPartitionedPath(sampleSandbox, sampleId); var coverageAndVariantFrequencies = SingleSampleCallset.GetCoverageAndVariantFrequencyOutput(sampleSandbox, sampleId); var singleSampleVcf = SingleSampleCallset.GetVcfOutput(sampleSandbox, sampleId); var coverageBigwig = SingleSampleCallset.GetCoverageBigWig(sampleSandbox, sampleId); var bAlleleBedgraph = SingleSampleCallset.GetBAlleleBedGraph(sampleSandbox, sampleId); var copyNumberBedgraph = SingleSampleCallset.GetCopyNumberBedGraph(sampleSandbox, sampleId); return(new IntermediateOutput(new Vcf(singleSampleVcf), coverageAndVariantFrequencies, variantFrequencies, variantFrequenciesBaf, partitioned, coverageBigwig, bAlleleBedgraph, copyNumberBedgraph)); }); var cnvVcf = new Vcf(sampleSandbox.GetFileLocation("CNV.vcf.gz")); return(new CanvasSmallPedigreeOutput(cnvVcf, intermediateResults)); }
private CanvasSmallPedigreeOutput Load(CanvasSmallPedigreeInput input) { var intermediateOutputs = input.Samples.SelectData((info, sample) => { var stub = GetSingleSampleOutputStub(info); var coverageAndVariantFrequency = SingleSampleCallset.GetCoverageAndVariantFrequencyOutput(stub); var singleSampleVcf = new Vcf(SingleSampleCallset.GetVcfOutput(stub)); var partitioned = SingleSampleCallset.GetPartitionedPath(stub); var variantFrequencies = SingleSampleCallset.GetVfSummaryPath(stub); var variantFrequenciesBaf = SingleSampleCallset.GetVfSummaryBafPath(stub); var coverageBigwig = SingleSampleCallset.GetCoverageBigWig(stub); var bAlleleBedgraph = SingleSampleCallset.GetBAlleleBedGraph(stub); var copyNumberBedgraph = SingleSampleCallset.GetCopyNumberBedGraph(stub); return(new IntermediateOutput(singleSampleVcf, coverageAndVariantFrequency, variantFrequencies, variantFrequenciesBaf, partitioned, coverageBigwig, bAlleleBedgraph, copyNumberBedgraph)); }); return(new CanvasSmallPedigreeOutput(new Vcf(GetPedigreeVcf()), intermediateOutputs)); }