--- a/BEDTools-Version-2.14.3/src/multiBamCov/multiBamCov.h	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,64 +0,0 @@
-/*****************************************************************************
-  multiBamCov.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 MULTICOVBAM_H
-#define MULTICOVBAM_H
-
-#include "bedFile.h"
-#include "api/BamMultiReader.h"
-using namespace BamTools;
-
-
-#include <vector>
-#include <iostream>
-#include <fstream>
-#include <stdlib.h>
-using namespace std;
-
-
-
-class MultiCovBam {
-
-public:
-
-    // constructor
-    MultiCovBam(const vector<string> &bam_files, const string bed_file, 
-                int minQual, bool properOnly, 
-                bool keepDuplicates, bool keepFailedQC);
-
-    // destructor
-    ~MultiCovBam(void);
-
-    void CollectCoverage();
-
-private:
-
-    //------------------------------------------------
-    // private attributes
-    //------------------------------------------------
-    vector<string> _bam_files;
-    string _bed_file;
-	BedFile *_bed;
-	
-	// attributes to control what is counted
-    int _minQual;
-    bool _properOnly;
-    bool _keepDuplicates;
-    bool _keepFailedQC;
-    
-
-    map<string, int> bamFileMap;
-    
-    void LoadBamFileMap(void);
-    void ReportCounts(const vector<int> &counts);
-};
-
-#endif /* MULTIBAMCOV_H */