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#pragma warning disable CS0618 // Type or member is obsolete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#pragma warning restore CS0618 // Type or member is obsolete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));
}
}
