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#pragma warning disable CS0618 // Type or member is obsolete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#pragma warning restore CS0618 // Type or member is obsolete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 void MoveIntermediateOutput(SampleInfo info, IntermediateOutput output, IFileMover fileMover)
{
var stub = GetStub(info.Id);
fileMover.Move(output.CoverageAndVariantFrequencies, SingleSampleCallset.GetCoverageAndVariantFrequencyOutput(stub));
if (_canvasWorkerFactory.IncludeIntermediateResults())
{
fileMover.Move(output.Partitioned, SingleSampleCallset.GetPartitionedPath(stub));
fileMover.Move(output.VariantFrequencies, SingleSampleCallset.GetVfSummaryPath(stub));
fileMover.Move(output.VariantFrequenciesBaf, SingleSampleCallset.GetVfSummaryPath(stub));
}
}
private CanvasSmallPedigreeOutput GetCanvasOutput(SampleSet <Bam> pedigreeBams, IDirectoryLocation sampleSandbox)
{
var readGroupSamples = pedigreeBams.SelectData(GetReadGroupSample);
var intermediateResults = readGroupSamples.SelectData(readGroupSample =>
{
var variantFrequencies = SingleSampleCallset.GetVfSummaryPath(sampleSandbox, readGroupSample);
var variantFrequenciesBaf = SingleSampleCallset.GetVfSummaryBafPath(sampleSandbox, readGroupSample);
var partitioned = SingleSampleCallset.GetPartitionedPath(sampleSandbox, readGroupSample);
var coverageAndVariantFrequencies = SingleSampleCallset.GetCoverageAndVariantFrequencyOutput(sampleSandbox, readGroupSample);
return(new IntermediateOutput(coverageAndVariantFrequencies, variantFrequencies, variantFrequenciesBaf, partitioned));
});
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 = GetStub(info.Id);
var coverageAndVariantFrequency = SingleSampleCallset.GetCoverageAndVariantFrequencyOutput(stub);
if (!_canvasWorkerFactory.IncludeIntermediateResults())
{
return(new IntermediateOutput(coverageAndVariantFrequency, null, null, null));
}
var partitioned = SingleSampleCallset.GetPartitionedPath(stub);
var variantFrequencies = SingleSampleCallset.GetVfSummaryPath(stub);
var variantFrequenciesBaf = SingleSampleCallset.GetVfSummaryPath(stub);
return(new IntermediateOutput(coverageAndVariantFrequency, variantFrequencies, variantFrequenciesBaf, partitioned));
});
return(new CanvasSmallPedigreeOutput(new Vcf(GetCnvVcf()), intermediateOutputs));
}
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));
}