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• CanvasRunner

C# Class Illumina.SecondaryAnalysis.CanvasRunner

Afficher le fichier Open project: Illumina/canvas Class Usage Examples

Méthodes publiques

Méthode	Description
CallSample ( Canvas.CanvasCallset callset ) : void
CanvasRunner ( ILogger logger, IWorkManager workManager, ICheckpointRunnerAsync checkpointRunner, bool isSomatic, CanvasCoverageMode coverageMode, int countsPerBin, string>.Dictionary customParameters = null ) : System

Méthodes protégées

Méthode	Description
InvokeCanvasBin ( Canvas.CanvasCallset callset, string canvasReferencePath, string canvasBedPath, string ploidyBedPath ) : IFileLocation	Invoke CanvasBin. Return null if this fails and we need to abort CNV calling for this sample.
InvokeCanvasNormalize ( Canvas.CanvasCallset callset, string tumorBinnedPath, string>.Dictionary bamToBinned, string ploidyBedPath, string mode = "weightedaverage" ) : string	Invoke CanvasNormalize.
InvokeCanvasSnv ( Canvas.CanvasCallset callset ) : void	Invoke CanvasSNV. Return null if this fails and we need to abort CNV calling for this sample.
RunGermlineCalling ( IFileLocation partitionedPath, Canvas.CanvasCallset callset, string ploidyBedPath ) : void
RunSomaticCalling ( IFileLocation partitionedPath, Canvas.CanvasCallset callset, string canvasBedPath, string ploidyBedPath, IFileLocation ffpePath ) : void

Private Methods

Méthode	Description
CallSampleInternal ( Canvas.CanvasCallset callset ) : Task	Germline workflow: - Run CanvasBin, CanvasClean, CanvasPartition, CanvasDiploidCaller Somatic workflow: - Run CanvasBin, CanvasClean, CanvasPartition, CanvasSNV, CanvasSomaticCaller
GetBinSize ( Canvas.CanvasCallset callset, string bamPath, List intermediateDataPaths, string canvasReferencePath, string canvasBedPath ) : int
IntersectBinsWithTargetedRegions ( Canvas.CanvasCallset callset, IFileLocation partitionedPath ) : IFileLocation	Intersect bins with the targeted regions defined in callset.Manifest. Assumes that the targeted regions don't intersect, the bins are sorted by genomic location and the bins don't intersect.
InvokeCanvasClean ( Canvas.CanvasCallset callset, IFileLocation binnedPath ) : CanvasCleanOutput
InvokeCanvasPartition ( Canvas.CanvasCallset callset, IFileLocation cleanedPath, string canvasBedPath ) : IFileLocation
SmallestFile ( List paths ) : string

Method Details