--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BEDTools-Version-2.14.3/src/shuffleBed/shuffleBed.h	Thu Nov 03 10:25:04 2011 -0400
@@ -0,0 +1,76 @@
+/*****************************************************************************
+  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 &);
+};