C# Class Illumina.SecondaryAnalysis.CanvasRunner

Run Canvas tools to generate CNV calls:
Mostrar archivo Open project: Illumina/canvas Class Usage Examples

Public Methods

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

Protected Methods

Method 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

Method 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

CallSample() public method

public CallSample ( Canvas.CanvasCallset callset ) : void
callset Canvas.CanvasCallset
return void

CanvasRunner() public method

public CanvasRunner ( ILogger logger, IWorkManager workManager, ICheckpointRunnerAsync checkpointRunner, bool isSomatic, CanvasCoverageMode coverageMode, int countsPerBin, string>.Dictionary customParameters = null ) : System
logger ILogger
workManager IWorkManager
checkpointRunner ICheckpointRunnerAsync
isSomatic bool
coverageMode CanvasCoverageMode
countsPerBin int
customParameters string>.Dictionary
return System

InvokeCanvasBin() protected method

Invoke CanvasBin. Return null if this fails and we need to abort CNV calling for this sample.
protected InvokeCanvasBin ( Canvas.CanvasCallset callset, string canvasReferencePath, string canvasBedPath, string ploidyBedPath ) : IFileLocation
callset Canvas.CanvasCallset
canvasReferencePath string
canvasBedPath string
ploidyBedPath string
return IFileLocation

InvokeCanvasNormalize() protected method

Invoke CanvasNormalize.
protected InvokeCanvasNormalize ( Canvas.CanvasCallset callset, string tumorBinnedPath, string>.Dictionary bamToBinned, string ploidyBedPath, string mode = "weightedaverage" ) : string
callset Canvas.CanvasCallset
tumorBinnedPath string
bamToBinned string>.Dictionary
ploidyBedPath string
mode string
return string

InvokeCanvasSnv() protected method

Invoke CanvasSNV. Return null if this fails and we need to abort CNV calling for this sample.
protected InvokeCanvasSnv ( Canvas.CanvasCallset callset ) : void
callset Canvas.CanvasCallset
return void

RunGermlineCalling() protected method

protected RunGermlineCalling ( IFileLocation partitionedPath, Canvas.CanvasCallset callset, string ploidyBedPath ) : void
partitionedPath IFileLocation
callset Canvas.CanvasCallset
ploidyBedPath string
return void

RunSomaticCalling() protected method

protected RunSomaticCalling ( IFileLocation partitionedPath, Canvas.CanvasCallset callset, string canvasBedPath, string ploidyBedPath, IFileLocation ffpePath ) : void
partitionedPath IFileLocation
callset Canvas.CanvasCallset
canvasBedPath string
ploidyBedPath string
ffpePath IFileLocation
return void