--- a/BEDTools-Version-2.14.3/src/utils/genomeFile/genomeFile.h	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,62 +0,0 @@
-/*****************************************************************************
-  genomeFile.h
-
-  (c) 2009 - Aaron Quinlan
-  Hall Laboratory
-  Department of Biochemistry and Molecular Genetics
-  University of Virginia
-  aaronquinlan@gmail.com
-
-  Licensed under the GNU General Public License 2.0 license.
-******************************************************************************/
-#ifndef GENOMEFILE_H
-#define GENOMEFILE_H
-
-#include <map>
-#include <string>
-#include <iostream>
-#include <sstream>
-#include <fstream>
-#include <cstring>
-#include <cstdio>
-#include "api/BamReader.h"
-#include "api/BamAux.h"
-using namespace BamTools;
-
-using namespace std;
-
-
-// typedef for mapping b/w chrom name and it's size in b.p.
-typedef map<string, int, std::less<string> > chromToSizes;
-
-
-class GenomeFile {
-
-public:
-
-    // Constructor using a file
-    GenomeFile(const string &genomeFile);
-    
-    // Constructor using a vector of BamTools RefVector
-    GenomeFile(const RefVector &genome);
-
-    // Destructor
-    ~GenomeFile(void);
-
-    // load a GENOME file into a map keyed by chrom. value is size of chrom.
-    void loadGenomeFileIntoMap();
-
-    int getChromSize(const string &chrom);  // return the size of a chromosome
-    vector<string> getChromList();          // return a list of chrom names
-    int getNumberOfChroms();                // return the number of chroms
-    string getGenomeFileName();             // return the name of the genome file
-
-
-
-private:
-    string  _genomeFile;
-    chromToSizes _chromSizes;
-    vector<string> _chromList;
-};
-
-#endif /* GENOMEFILE_H */