--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BEDTools-Version-2.14.3/src/intersectBed/intersectBed.h	Thu Nov 03 10:25:04 2011 -0400
@@ -0,0 +1,98 @@
+/*****************************************************************************
+  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 */