--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BEDTools-Version-2.14.3/src/pairToPair/pairToPair.h	Thu Nov 03 10:25:04 2011 -0400
@@ -0,0 +1,76 @@
+/*****************************************************************************
+  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 */