--- a/BEDTools-Version-2.14.3/src/utils/chromsweep/chromsweep.h	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,89 +0,0 @@
-/*****************************************************************************
-  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 */