--- a/BEDTools-Version-2.14.3/src/intersectBed/intersectBed.h	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,98 +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 "chromsweep.h"
-#include "api/BamReader.h"
-#include "api/BamWriter.h"
-#include "api/BamAux.h"
-#include "BamAncillary.h"
-using namespace BamTools;
-
-
-#include <vector>
-#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 sameStrand, bool diffStrand,
-                               bool reciprocal, bool obeySplits, bool bamInput, bool bamOutput, bool isUncompressedBam,
-                               bool sortedInput);
-
-    // 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  _sameStrand;
-    bool  _diffStrand;
-    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  _isUncompressedBam;
-    bool  _sortedInput;
-    bool  _printable;
-    
-    // instance of a bed file class.
-    BedFile *_bedA, *_bedB;
-
-    //------------------------------------------------
-    // private methods
-    //------------------------------------------------
-    void IntersectBed(istream &bedInput);
-
-    void IntersectBed();
-
-    void IntersectBam(string bamFile);
-
-    bool processHits(const BED &a, const vector<BED> &hits);
-
-    bool FindOverlaps(const BED &a, vector<BED> &hits);
-
-    bool FindOneOrMoreOverlap(const BED &a);
-
-    void ReportOverlapDetail(int overlapBases, const BED &a, const BED &b, CHRPOS s, CHRPOS e);
-    
-    void ReportOverlapSummary(const BED &a, const int &numOverlapsFound);
-
-};
-
-#endif /* INTERSECTBED_H */