--- a/BEDTools-Version-2.14.3/src/fjoin/fjoin.h	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,114 +0,0 @@
-/*****************************************************************************
-  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 */