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Public Member Functions | Public Attributes | Private Member Functions | Private Attributes

BedFilePE Class Reference

Collaboration diagram for BedFilePE:
Collaboration graph

List of all members.

Public Member Functions

 BedFilePE (string &)
void Close (void)
void FindOverlapsPerBin (int bEnd, string chrom, CHRPOS start, CHRPOS end, string name, string strand, vector< MATE > &hits, float overlapFraction, bool forceStrand, bool enforceDiffNames)
BedLineStatus GetNextBedPE (BEDPE &bedpe, int &lineNum)
void loadBedPEFileIntoMap ()
void Open (void)
void reportBedPENewLine (const BEDPE &a)
void reportBedPETab (const BEDPE &a)
void splitBedPEIntoBeds (const BEDPE &a, const int &lineNum, MATE *bedEntry1, MATE *bedEntry2)

Public Attributes

string bedFile
masterMateMap bedMapEnd1
masterMateMap bedMapEnd2
unsigned int bedType

Private Member Functions

bool parseBedPELine (BEDPE &bed, const vector< string > &lineVector, const int &lineNum)
BedLineStatus parseLine (BEDPE &bedpe, const vector< string > &lineVector, int &lineNum)

Private Attributes

istream * _bedStream

Detailed Description

Definition at line 47 of file bedFilePE.h.

The documentation for this class was generated from the following files:

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