--- a/BEDTools-Version-2.14.3/src/coverageBed/coverageBed.h	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,83 +0,0 @@
-/*****************************************************************************
-  coverageBed.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 COVERAGEBED_H
-#define COVERAGEBED_H
-
-#include "bedFile.h"
-
-#include "api/BamReader.h"
-#include "api/BamAux.h"
-#include "BamAncillary.h"
-using namespace BamTools;
-
-#include <vector>
-#include <algorithm>
-#include <iostream>
-#include <iomanip>
-#include <fstream>
-#include <stdlib.h>
-
-using namespace std;
-
-//************************************************
-// Class methods and elements
-//************************************************
-class BedCoverage {
-
-public:
-
-    // constructor
-    BedCoverage(string &bedAFile, string &bedBFile, bool sameStrand, bool diffStrand, bool writeHistogram,
-                bool bamInput, bool obeySplits, bool eachBase, bool countsOnly);
-
-    // destructor
-    ~BedCoverage(void);
-
-private:
-
-    // input files.
-    string _bedAFile;
-    string _bedBFile;
-
-    // instance of a bed file class.
-    BedFile *_bedA, *_bedB;
-
-    // do we care about same or opposite strandedness when counting coverage?
-    bool _sameStrand;
-    bool _diffStrand;
-
-    // should we write a histogram for each feature in B?
-    bool _writeHistogram;
-
-    // are we dealing with BAM input for "A"?
-    bool _bamInput;
-
-    // should we split BED/BAM into discrete blocks?
-    bool _obeySplits;
-
-    // should discrete coverage be reported for each base in each feature?
-    bool _eachBase;
-    
-    // should we just count overlaps and not try to describe the breadth?
-    bool _countsOnly;
-
-    // private function for reporting coverage information
-    void ReportCoverage();
-    
-    // private function for reporting overlap counts
-    void ReportCounts();
-
-    void CollectCoverageBed();
-
-    void CollectCoverageBam(string bamFile);
-};
-#endif /* COVERAGEBED_H */