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Public Member Functions | Private Member Functions | Private Attributes

BedIntersect Class Reference

Collaboration diagram for BedIntersect:
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List of all members.

Public Member Functions

 BedIntersect (string bedAFile, string bedBFile, bool anyHit, bool writeA, bool writeB, bool writeOverlap, bool writeAllOverlap, float overlapFraction, bool noHit, bool writeCount, bool forceStrand, bool reciprocal, bool obeySplits, bool bamInput, bool bamOutput)
 BedIntersect (string bedAFile, string bedBFile, bool anyHit, bool writeA, bool writeB, bool writeOverlap, bool writeAllOverlap, float overlapFraction, bool noHit, bool writeCount, bool forceStrand, bool reciprocal, bool obeySplits, bool bamInput, bool bamOutput, bool isUncompressedBam)

Private Member Functions

void AddHits (BED *x, const BED &y)
void ChromSwitch (const string &chrom)
bool FindOneOrMoreOverlap (const BED &a)
bool FindOneOrMoreOverlap (const BED &a)
bool FindOverlaps (const BED &a, vector< BED > &hits)
bool FindOverlaps (const BED &a, vector< BED > &hits)
void FlushOutputBuffer (bool final=false)
vector< BED * > * GetWindow (const string &chrom, bool isA)
void IntersectBam (string bamFile)
void IntersectBam (string bamFile)
void IntersectBed (istream &bedInput)
void IntersectBed ()
void IntersectBed (istream &bedInput)
void IntersectBed ()
bool processHits (const BED &a, const vector< BED > &hits, bool printable)
bool processHits (BED &a, vector< BED > &hits)
void ReportHits (set< BED > &A, set< BED > &B)
void ReportOverlapDetail (const int &overlapBases, const BED &a, const BED &b, const CHRPOS &s, const CHRPOS &e)
void ReportOverlapDetail (const int &overlapBases, const BED &a, const BED &b, const CHRPOS &s, const CHRPOS &e)
void ReportOverlapSummary (const BED &a, const int &numOverlapsFound)
void ReportOverlapSummary (const BED &a, const int &numOverlapsFound)
void Scan (BED *x, vector< BED * > *windowX, BedLineStatus xStatus, const BED &y, vector< BED * > *windowY, BedLineStatus yStatus)

Private Attributes

bool _anyHit
bool _bamInput
bool _bamOutput
BedFile_bedA
string _bedAFile
BedFile_bedB
string _bedBFile
bool _forceStrand
bool _isUncompressedBam
bool _lastPick
bool _noHit
bool _obeySplits
queue< BED * > _outputBuffer
float _overlapFraction
bool _printable
bool _reciprocal
map< string, vector< BED * > > _windowA
map< string, vector< BED * > > _windowB
bool _writeA
bool _writeAllOverlap
bool _writeB
bool _writeCount
bool _writeOverlap

Detailed Description

Definition at line 32 of file fjoin.h.


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

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