--- a/BEDTools-Version-2.14.3/src/pairToPair/pairToPair.h	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,76 +0,0 @@
-/*****************************************************************************
-  pairToPair.h
-
-  (c) 2009 - Aaron Quinlan
-  Hall Laboratory
-  Department of Biochemistry and Molecular Genetics
-  University of Virginia
-  aaronquinlan@gmail.com
-
-  Licenced under the GNU General Public License 2.0 license.
-******************************************************************************/
-#ifndef PAIRTOPAIR_H
-#define PAIRTOPAIR_H
-
-#include "bedFile.h"
-#include "bedFilePE.h"
-#include <vector>
-#include <iostream>
-#include <fstream>
-
-using namespace std;
-
-
-
-//************************************************
-// Class methods and elements
-//************************************************
-class PairToPair {
-
-public:
-
-    // constructor
-    PairToPair(string &bedAFilePE, string &bedBFilePE, float &overlapFraction,
-        string searchType, bool ignoreStrand, bool reqDiffNames, int slop, bool strandedSlop);
-
-    // destructor
-    ~PairToPair(void);
-
-    void IntersectPairs();
-
-
-private:
-
-    string _bedAFilePE;
-    string _bedBFilePE;
-
-    float _overlapFraction;
-    string _searchType;
-    bool _ignoreStrand;
-    bool _reqDiffNames;
-    int _slop;
-    bool _strandedSlop;
-
-    // instance of a paired-end bed file class.
-    BedFilePE *_bedA;
-
-    // instance of a bed file class.
-    BedFilePE *_bedB;
-
-    // methods
-    // void FindOverlaps(const BEDPE &a, vector<MATE> &hitsA1B1, vector<MATE> &hitsA1B2,
-    //  vector<MATE> &hitsA2B1, vector<MATE> &hitsA2B2);
-    void FindOverlaps(const BEDPE &a);
-
-    void FindQualityHitsBetweenEnds(CHRPOS start, CHRPOS end,
-        const vector<MATE> &hits, vector<MATE> &qualityHits, int &numOverlaps);
-
-    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);
-
-};
-
-#endif /* PAIRTOPAIR_H */