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Public Member Functions | Private Member Functions | Private Attributes

BedWindow Class Reference

Collaboration diagram for BedWindow:
Collaboration graph

List of all members.

Public Member Functions

 BedWindow (string bedAFile, string bedBFile, int leftSlop, int rightSlop, bool anyHit, bool noHit, bool writeCount, bool strandWindows, bool matchOnStrand, bool bamInput, bool bamOutput, bool isUncompressedBam)

Private Member Functions

void AddWindow (const BED &a, CHRPOS &fudgeStart, CHRPOS &fudgeEnd)
bool FindOneOrMoreWindowOverlaps (const BED &a)
void FindWindowOverlaps (const BED &a, vector< BED > &hits)
void WindowIntersectBam (string bamFile)
void WindowIntersectBed ()

Private Attributes

bool _anyHit
bool _bamInput
bool _bamOutput
string _bedAFile
string _bedBFile
bool _isUncompressedBam
int _leftSlop
bool _matchOnStrand
bool _noHit
int _rightSlop
bool _strandWindows
bool _writeCount

Detailed Description

Definition at line 30 of file windowBed.h.

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

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