--- a/BEDTools-Version-2.14.3/src/shuffleBed/shuffleBed.h	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,76 +0,0 @@
-/*****************************************************************************
-  shuffleBed.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.
-******************************************************************************/
-#include "bedFile.h"
-#include "genomeFile.h"
-
-#include <vector>
-#include <iostream>
-#include <fstream>
-#include <map>
-#include <cstdlib>
-#include <ctime>
-#include <sys/time.h>
-#include <unistd.h>
-#include <sys/types.h>
-using namespace std;
-
-const int MAX_TRIES = 1000000;
-
-//************************************************
-// Class methods and elements
-//************************************************
-class BedShuffle {
-
-public:
-
-    // constructor
-    BedShuffle(string &bedFile, string &genomeFile, string &excludeFile, string &includeFile, 
-                           bool haveSeed, bool haveExclude, bool haveInclude, bool sameChrom, 
-                           float overlapFraction, int seed);
-
-    // destructor
-    ~BedShuffle(void);
-
-private:
-
-    string _bedFile;
-    string _genomeFile;
-    string _excludeFile;
-    string _includeFile;
-    float  _overlapFraction;
-    int _seed;
-    bool _sameChrom;
-    bool _haveExclude;
-    bool _haveInclude;
-    bool _haveSeed;
-
-
-    // The BED file from which to compute coverage.
-    BedFile *_bed;
-    BedFile *_exclude;
-    BedFile *_include;
-
-    GenomeFile *_genome;
-
-    vector<string> _chroms;
-    int _numChroms;
-    vector<string> _includeChroms;
-    int _numIncludeChroms;
-
-    // methods
-    void Shuffle();
-    void ShuffleWithExclusions();
-    void ShuffleWithInclusions();
-
-    void ChooseLocus(BED &);
-    void ChooseLocusFromInclusionFile(BED &);
-};