C# Класс CanvasBin.CanvasBin

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Открытые методы

Метод	Описание
DeserializeCanvasData ( string inputFile, BitArray>.Dictionary possibleAlignments, HitArray>.Dictionary observedAlignments, Int16[]>.Dictionary fragmentLengths, Object semaphore, CanvasCoverageMode coverageMode ) : void	Deserialize CanvasBin object in multiple threads
Run ( CanvasBinParameters parameters ) : int	Implements the Canvas binning algorithm

Приватные методы

Метод	Описание
BinCounts ( string referenceFile, int binSize, CanvasCoverageMode coverageMode, NexteraManifest manifest, BitArray>.Dictionary possibleAlignments, HitArray>.Dictionary observedAlignments, Int16[]>.Dictionary fragmentLengths, Dictionary predefinedBins, string outFile ) : List	Bin alignments.
BinCountsForChromosome ( BinTaskArguments arguments ) : void	Populate the list of GenomicBin objects for this chromosome.
BinOneGenomicInterval ( CanvasBinParameters parameters, BitArray>.Dictionary possibleAlignments, HitArray>.Dictionary observedAlignments, Int16[]>.Dictionary fragmentLengths ) : int
CalculateNumberOfPossibleAlignmentsPerBin ( int countsPerBin, BitArray>.Dictionary possibleAlignments, HitArray>.Dictionary observedAlignments, NexteraManifest manifest = null ) : int	Calculates how many possible alignments corresponds to the desired number of observed alignments per bin.
ComputeObservedVsExpectedGC ( HitArray>.Dictionary observedAlignments, byte[]>.Dictionary readGCContent, NexteraManifest manifest, bool debugGC, string outFile ) : float[]	Computes fragment-based GC normalization correction factor
CountSetBits ( BitArray bits ) : int	Counts the number of 'on' bits in a BitArray.
CountSetBits ( BitArray bits, List regions ) : int	Counts the number of 'on' bits in a BitArray.
ExcludeTagsOverlappingFilterFile ( string filterFile, BitArray>.IDictionary tags ) : void	Remove possible alignment positions if they intersect a supplied bed file.
InitializeAlignmentArrays ( string fastaFile, string chromosome, CanvasCoverageMode coverageMode, BitArray>.IDictionary possibleAlignments, HitArray>.IDictionary observedAlignments, Int16[]>.IDictionary fragmentLengths ) : void	Sets up two Dictionaries holding BitArrays, one BitArray for each chromosome in a fasta file. One bit for each nucleotide.
LoadObservedAlignmentsBAM ( string bamFile, bool isPairedEnd, string chromosome, CanvasCoverageMode coverageMode, CanvasBin.HitArray observed, Int16 fragmentLengths ) : void	Reads in a bam file and marks within the BitArrays which genomic mers are present.
MeanFragmentSize ( Int16[]>.Dictionary fragmentLengths ) : Int16	Estimate mean fragment length of read pairs.
ScaleIntToByte ( int fragmentLength, int max, int min ) : byte	Scale fragment sizes to a 0 .. 255 byte range
ScreenObservedTags ( HitArray>.IDictionary observedAlignments, BitArray>.IDictionary possibleAlignments ) : void	Remove any observed alignment if it wasn't 'possible'.

Описание методов

DeserializeCanvasData() публичный статический Метод

Deserialize CanvasBin object in multiple threads

public static DeserializeCanvasData ( string inputFile, BitArray>.Dictionary possibleAlignments, HitArray>.Dictionary observedAlignments, Int16[]>.Dictionary fragmentLengths, Object semaphore, CanvasCoverageMode coverageMode ) : void
inputFile	string	inputFile with per-chromosome CanvasBin objects.
possibleAlignments	BitArray>.Dictionary	Stores which alignments are possible (perfect and unique).
observedAlignments	HitArray>.Dictionary	Stores observed alignments from a sample.
fragmentLengths	Int16[]>.Dictionary	Stores fragment length in byte format.
semaphore	Object
coverageMode	CanvasCoverageMode
Результат	void

Run() публичный статический Метод

Implements the Canvas binning algorithm

public static Run ( CanvasBinParameters parameters ) : int
parameters	CanvasBinParameters
Результат	int