C# Класс CanvasBin.FragmentBinner.BinTask

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Открытые методы

Метод	Описание
BinOneAlignment ( BamAlignment alignment, uint qualityThreshold, int>.Dictionary readNameToBinIndex, HashSet samePositionReadNames, long &usableFragmentCount, List bins, int &binIndexStart ) : void	Bins the fragment identified by alignment. Increases bin count if the first read of a pair passes all the filters. Decreases bin count if the second read of a pair does not pass all the filters.
BinTask ( string fastaFile, string chrom, string bamFile, List bins ) : System
DoIt ( ) : void	Performs fragment binning for the chromosome.
FindBestBin ( List bins, int binIndexStart, int fragmentStart, int fragmentStop ) : int	Starting from the bin at binIndexStart, increments the bin index and searches for the bin that overlaps the fragment the most. In case of a tie, the bin encountered first is returned.
IsDuplicateFailedQCLowQuality ( BamAlignment alignment, uint qualityThreshold ) : bool	Checks if any of the conditions is true: 1. The read is a duplicate, 2. The read failed QC, 3. The read is of low mapping quality.
IsRightMostInPair ( BamAlignment alignment ) : bool	Is the read the right-most one (by genomic position) in a pair?

Приватные методы

Метод	Описание
InitializeBins ( ) : void	Sets bin counts to 0.
binFragments ( ) : void	Bins fragments.
isBinGCAvailable ( ) : bool	Is %GC available for all bins?
populateBinGC ( ) : void	Calculates %GC for bins on the chromosome.

Описание методов

BinOneAlignment() публичный статический Метод

Bins the fragment identified by alignment. Increases bin count if the first read of a pair passes all the filters. Decreases bin count if the second read of a pair does not pass all the filters.

public static BinOneAlignment ( BamAlignment alignment, uint qualityThreshold, int>.Dictionary readNameToBinIndex, HashSet samePositionReadNames, long &usableFragmentCount, List bins, int &binIndexStart ) : void
alignment	BamAlignment
qualityThreshold	uint	minimum mapping quality
readNameToBinIndex	int>.Dictionary	Dictionary of read name to bin index
samePositionReadNames	HashSet
usableFragmentCount	long	number of usable fragments
bins	List	predefined bins
binIndexStart	int	bin index from which to start searching for the best bin
Результат	void

BinTask() публичный Метод

public BinTask ( string fastaFile, string chrom, string bamFile, List bins ) : System
fastaFile	string
chrom	string	chromosome
bamFile	string	path to BAM
bins	List	predefined bins
Результат	System

DoIt() публичный Метод

Performs fragment binning for the chromosome.

public DoIt ( ) : void
Результат	void

FindBestBin() публичный статический Метод

Starting from the bin at binIndexStart, increments the bin index and searches for the bin that overlaps the fragment the most. In case of a tie, the bin encountered first is returned.

public static FindBestBin ( List bins, int binIndexStart, int fragmentStart, int fragmentStop ) : int
bins	List
binIndexStart	int
fragmentStart	int
fragmentStop	int
Результат	int

IsDuplicateFailedQCLowQuality() публичный статический Метод

Checks if any of the conditions is true: 1. The read is a duplicate, 2. The read failed QC, 3. The read is of low mapping quality.

public static IsDuplicateFailedQCLowQuality ( BamAlignment alignment, uint qualityThreshold ) : bool
alignment	BamAlignment
qualityThreshold	uint
Результат	bool

IsRightMostInPair() публичный статический Метод

Is the read the right-most one (by genomic position) in a pair?

public static IsRightMostInPair ( BamAlignment alignment ) : bool
alignment	BamAlignment
Результат	bool