--- a/BEDTools-Version-2.14.3/src/maskFastaFromBed/maskFastaFromBed.h	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,56 +0,0 @@
-/*****************************************************************************
-  maskFastaFromBed.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 MASKFASTAFROMBED_H
-#define MASKFASTAFROMBED_H
-
-#include "bedFile.h"
-#include "sequenceUtils.h"
-#include <vector>
-#include <iostream>
-#include <fstream>
-#include <cctype>   /* for tolower */
-
-using namespace std;
-
-//************************************************
-// Class methods and elements
-//************************************************
-class MaskFastaFromBed {
-
-public:
-
-    // constructor
-    MaskFastaFromBed(const string &fastaInFile,  const string &bedFile, 
-                     const string &fastaOutFile, bool softMask, char maskChar);
-
-    // destructor
-    ~MaskFastaFromBed(void);
-
-
-private:
-
-    bool _softMask;
-
-    string _fastaInFile;
-    string _bedFile;
-    string _fastaOutFile;
-    char   _maskChar;     // typically "N", but user's can choose something else, e.g., "X"
-
-    // instance of a bed file class.
-    BedFile *_bed;
-
-    void MaskFasta();
-
-    void PrettyPrintChrom(ofstream &out, string chrom, const string &sequence, int width);
-
-};
-
-#endif /* MASKFASTAFROMBED */