--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BEDTools-Version-2.14.3/src/utils/chromsweep/chromsweep.h	Thu Nov 03 10:25:04 2011 -0400
@@ -0,0 +1,89 @@
+/*****************************************************************************
+  chromsweepBed.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 CHROMSWEEP_H
+#define CHROMSWEEP_H
+
+#include "bedFile.h"
+#include <vector>
+#include <queue>
+#include <iostream>
+#include <fstream>
+#include <stdlib.h>
+using namespace std;
+
+
+
+class ChromSweep {
+
+// public interface.
+public:
+
+    // A is the query and B is the database
+    
+    // constructor using existing BedFile pointers
+    ChromSweep(BedFile *bedA, BedFile *bedB, bool sameStrand = false, bool diffStrand = false);
+    
+    // constructor using filenames
+    ChromSweep(string &bedAFile, string &bedBFile);
+    
+    // destructor
+    ~ChromSweep(void);
+    
+    // loads next (a pair) with the current query and it's overlaps
+    //   next.first is the current query interval
+    //   next.second is a vector of the current query's hits.
+    // returns true if overlap
+    bool Next(pair<BED, vector<BED> > &next);
+    
+    // Usage:
+    //     ChromSweep sweep = ChromSweep(_bedA, _bedB);
+    //     pair<BED, vector<BED> > hit_set;
+    //     while (sweep.Next(hit_set)) 
+    //     {
+    //        // magic happens here!
+    //        processHits(hit_set.first, hit_set.second);
+    //     }
+    
+// private variables.
+private:
+
+    // instances of a bed file class.
+    BedFile *_bedA, *_bedB;
+    // do we care about strandedness.
+    bool _sameStrand, _diffStrand;
+    // a cache of still active features from the database file
+    vector<BED> _cache;
+    // the set of hits in the database for the current query
+    vector<BED> _hits;
+    // a queue from which we retrieve overlap results.  used by Next()
+    queue< pair<BED, vector<BED> > > _results;
+    BED _nullBed;
+    // an empty BED vector for returning no hits for a given query
+    vector<BED> _no_hits;
+    // the current query and db features.
+    BED _curr_qy, _curr_db;
+    // a cache of the current chrom from the query. used to handle chrom changes.
+    string _curr_chrom;
+    // the current line status in the database and query files
+    BedLineStatus _qy_status, _db_status;
+    // the current line numbers in the database and query files
+    int _qy_lineNum, _db_lineNum;
+
+// private methods.
+private:
+    
+    void ScanCache();
+    bool ChromChange();
+    bool IsValidHit(const BED &query, const BED &db);
+};
+
+#endif /* CHROMSWEEP_H */