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Public Member Functions | Private Member Functions | Private Attributes

PairToPair Class Reference

Collaboration diagram for PairToPair:
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List of all members.

Public Member Functions

void IntersectPairs ()
 PairToPair (string &bedAFilePE, string &bedBFilePE, float &overlapFraction, string searchType, bool ignoreStrand, bool reqDiffNames, int slop, bool strandedSlop)

Private Member Functions

bool FindHitsOnBothEnds (const BEDPE &a, const vector< MATE > &qualityHitsEnd1, const vector< MATE > &qualityHitsEnd2)
void FindHitsOnEitherEnd (const BEDPE &a, const vector< MATE > &qualityHitsEnd1, const vector< MATE > &qualityHitsEnd2)
void FindOverlaps (const BEDPE &a)
void FindQualityHitsBetweenEnds (CHRPOS start, CHRPOS end, const vector< MATE > &hits, vector< MATE > &qualityHits, int &numOverlaps)

Private Attributes

BedFilePE_bedA
string _bedAFilePE
BedFilePE_bedB
string _bedBFilePE
bool _ignoreStrand
float _overlapFraction
bool _reqDiffNames
string _searchType
int _slop
bool _strandedSlop

Detailed Description

Definition at line 28 of file pairToPair.h.


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

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