--- a/BEDTools-Version-2.14.3/src/nucBed/nucBed.h	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,55 +0,0 @@
-/*****************************************************************************
-  nucBed.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 NUCBED_H
-#define NUCBED_H
-
-#include "bedFile.h"
-#include "sequenceUtils.h"
-#include "Fasta.h"
-#include <vector>
-#include <iostream>
-#include <fstream>
-
-using namespace std;
-
-//************************************************
-// Class methods and elements
-//************************************************
-class NucBed {
-
-public:
-
-    // constructor
-    NucBed(string &dbFile, string &bedFile, bool printSeq, 
-           bool hasPattern, const string &pattern,
-           bool forceStrand);
-    // destructor
-    ~NucBed(void);
-
-    void ProfileDNA();
-
-
-private:
-    string _dbFile;
-    string _bedFile;
-    bool   _printSeq;
-    bool   _hasPattern;
-    string _pattern;
-    bool _forceStrand;
-
-    // instance of a bed file class.
-    BedFile  *_bed;
-    void PrintHeader(void);
-    void ReportDnaProfile(const BED& bed, const string &sequence, int seqLength);
-};
-
-#endif