C# Class CanvasBin.FragmentBinner.BinTask

Mostra file Open project: Illumina/canvas Class Usage Examples

Public Methods

Method	Description
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?

Private Methods

Method	Description
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.

Method Details

BinOneAlignment() public static method

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
return	void

BinTask() public method

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
return	System

DoIt() public method

Performs fragment binning for the chromosome.

public DoIt ( ) : void
return	void

FindBestBin() public static method

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
return	int

IsDuplicateFailedQCLowQuality() public static method

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
return	bool

IsRightMostInPair() public static method

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

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