--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BEDTools-Version-2.14.3/src/fjoin/fjoin.h	Thu Nov 03 10:25:04 2011 -0400
@@ -0,0 +1,114 @@
+/*****************************************************************************
+  intersectBed.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 INTERSECTBED_H
+#define INTERSECTBED_H
+
+#include "bedFile.h"
+// #include "BamReader.h"
+// #include "BamWriter.h"
+// #include "BamAncillary.h"
+// #include "BamAux.h"
+// using namespace BamTools;
+
+
+#include <vector>
+#include <queue>
+#include <iostream>
+#include <fstream>
+#include <stdlib.h>
+using namespace std;
+
+
+
+class BedIntersect {
+
+public:
+
+    // constructor
+    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);
+
+    // destructor
+    ~BedIntersect(void);
+
+private:
+
+    //------------------------------------------------
+    // private attributes
+    //------------------------------------------------
+    string _bedAFile;
+    string _bedBFile;
+
+    bool  _writeA;            // should the original A feature be reported?
+    bool  _writeB;            // should the original B feature be reported?
+    bool  _writeOverlap;
+    bool  _writeAllOverlap;
+
+    bool  _forceStrand;
+    bool  _reciprocal;
+    float _overlapFraction;
+
+    bool  _anyHit;
+    bool  _noHit;
+    bool  _writeCount;        // do we want a count of the number of overlaps in B?
+    bool  _obeySplits;
+    bool  _bamInput;
+    bool  _bamOutput;
+
+    bool _printable;
+
+    queue<BED*> _outputBuffer;
+    bool  _lastPick;
+
+    map<string, vector<BED*> > _windowA;
+    map<string, vector<BED*> > _windowB;
+
+    // instance of a bed file class.
+    BedFile *_bedA, *_bedB;
+
+    //------------------------------------------------
+    // private methods
+    //------------------------------------------------
+    void IntersectBed(istream &bedInput);
+
+    void Scan(BED *x, vector<BED *> *windowX, BedLineStatus xStatus,
+        const BED &y, vector<BED *> *windowY, BedLineStatus yStatus);
+
+    void AddHits(BED *x, const BED &y);
+
+    void FlushOutputBuffer(bool final = false);
+
+    vector<BED*>* GetWindow(const string &chrom, bool isA);
+
+    void ChromSwitch(const string &chrom);
+
+    void IntersectBed();
+
+    void IntersectBam(string bamFile);
+
+    bool processHits(BED &a, vector<BED> &hits);
+
+    bool FindOverlaps(const BED &a, vector<BED> &hits);
+
+    bool FindOneOrMoreOverlap(const BED &a);
+
+    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 ReportHits(set<BED> &A, set<BED> &B);
+
+};
+
+#endif /* INTERSECTBED_H */