--- a/BEDTools-Version-2.14.3/src/annotateBed/annotateBed.h	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,71 +0,0 @@
-/*****************************************************************************
-  annotateBed.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 ANNOTATEBED_H
-#define ANNOTATEBED_H
-
-#include "bedFile.h"
-#include <vector>
-#include <algorithm>
-#include <iostream>
-#include <iomanip>
-#include <fstream>
-#include <stdlib.h>
-
-using namespace std;
-
-//************************************************
-// Class methods and elements
-//************************************************
-class BedAnnotate {
-
-public:
-
-    // constructor
-    BedAnnotate(const string &mainFile, const vector<string> &annoFileNames,
-                const vector<string> &annoTitles, bool sameStrand, bool diffStrand, bool reportCounts, bool reportBoth);
-
-    // destructor
-    ~BedAnnotate(void);
-
-    // annotate the master file with all of the annotation files.
-    void AnnotateBed();
-
-private:
-
-    // input files.
-    string _mainFile;
-    vector<string> _annoFileNames;
-    vector<string> _annoTitles;
-
-    // instance of a bed file class.
-    BedFile *_bed;
-    vector<BedFile*> _annoFiles;
-
-    // do we care about strandedness when counting coverage?
-    bool _sameStrand;
-    bool _diffStrand;
-    
-    bool _reportCounts;
-    bool _reportBoth;
-
-    // private function for reporting coverage information
-    void ReportAnnotations();
-
-    void OpenAnnoFiles();
-
-    void CloseAnnoFiles();
-
-    void PrintHeader();
-
-    void InitializeMainFile();
-};
-#endif /* ANNOTATEBED_H */