--- a/BEDTools-Version-2.14.3/src/windowBed/windowBed.h	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,69 +0,0 @@
-/*****************************************************************************
-  windowBed.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 WINDOWBED_H
-#define WINDOWBED_H
-
-#include "api/BamReader.h"
-#include "api/BamWriter.h"
-#include "api/BamAux.h"
-using namespace BamTools;
-
-#include "bedFile.h"
-#include <vector>
-#include <iostream>
-#include <fstream>
-
-using namespace std;
-
-//************************************************
-// Class methods and elements
-//************************************************
-class BedWindow {
-
-public:
-
-    // constructor
-    BedWindow(string bedAFile, string bedBFile, int leftSlop, int rightSlop,
-              bool anyHit, bool noHit, bool writeCount, bool strandWindows,
-              bool matchOnSameStrand, bool matchOnDiffStrand, bool bamInput, bool bamOutput, bool isUncompressedBam);
-
-    // destructor
-    ~BedWindow(void);
-
-private:
-
-    string _bedAFile;
-    string _bedBFile;
-    bool _anyHit;
-    bool _writeCount;
-    int _leftSlop;
-    int _rightSlop;
-    bool _noHit;
-    bool _strandWindows;
-    bool _matchOnSameStrand;
-    bool _matchOnDiffStrand;
-    bool _bamInput;
-    bool _bamOutput;
-    bool  _isUncompressedBam;
-
-    // instance of a bed file class.
-    BedFile *_bedA, *_bedB;
-
-    // methods
-    void WindowIntersectBed();
-    void WindowIntersectBam(string bamFile);
-    void FindWindowOverlaps(const BED &a, vector<BED> &hits);
-    bool FindOneOrMoreWindowOverlaps(const BED &a);
-    void AddWindow(const BED &a, CHRPOS &fudgeStart, CHRPOS &fudgeEnd);
-
-};
-#endif /* WINDOWBED_H */