--- a/BEDTools-Version-2.14.3/src/genomeCoverageBed/genomeCoverageBed.h	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,104 +0,0 @@
-/*****************************************************************************
-genomeCoverage.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.
-******************************************************************************/
-#include "bedFile.h"
-#include "genomeFile.h"
-
-#include "BamAncillary.h"
-#include "api/BamReader.h"
-#include "api/BamAux.h"
-using namespace BamTools;
-
-#include <vector>
-#include <set>
-#include <iostream>
-#include <fstream>
-using namespace std;
-
-
-//***********************************************
-// Typedefs
-//***********************************************
-typedef map<int, DEPTH, less<int> > depthMap;
-typedef map<string, depthMap, less<string> > chromDepthMap;
-
-typedef map<int, unsigned int, less<int> > histMap;
-typedef map<string, histMap, less<string> > chromHistMap;
-
-//************************************************
-// Class methods and elements
-//************************************************
-class BedGenomeCoverage {
-
-public:
-
-    // constructor
-    BedGenomeCoverage(string bedFile, string genomeFile, 
-                      bool eachBase, bool startSites,
-                      bool bedGraph, bool bedGraphAll, 
-                      int max, float scale, 
-                      bool bamInput, bool obeySplits,
-                      bool filterByStrand, string requestedStrand,
-                      bool only_5p_end, bool only_3p_end,
-                      bool eachBaseZeroBased,
-                      bool add_gb_track_line, string gb_track_line_opts);
-
-    // destructor
-    ~BedGenomeCoverage(void);
-
-private:
-
-    // data (parms)
-    string _bedFile;
-    string _genomeFile;
-    bool _bamInput;
-    bool _eachBase;
-    bool _eachBaseZeroBased;
-    bool _startSites;
-    bool _bedGraph;
-    bool _bedGraphAll;
-    int _max;
-    float _scale;
-    bool _obeySplits;
-    bool _filterByStrand;
-    bool _only_5p_end;
-    bool _only_3p_end;
-    bool _add_gb_track_line;
-    string _gb_track_line_opts;
-    string _requestedStrand;
-
-    BedFile *_bed;
-    GenomeFile *_genome;
-
-    // data for internal processing
-    chromDepthMap _chromCov;
-    string _currChromName ;
-    vector<DEPTH> _currChromCoverage;
-    chromHistMap _currChromDepthHist;
-    int _currChromSize ;
-    set<string> _visitedChromosomes;
-
-
-    // methods
-    void CoverageBed();
-    void CoverageBam(string bamFile);
-    void LoadBamHeaderIntoGenomeFile(const string &bamFile);
-    void ReportChromCoverage(const vector<DEPTH> &, const int &chromSize, const string &chrom, chromHistMap&);
-    void ReportGenomeCoverage(chromHistMap &chromDepthHist);
-    void ReportChromCoverageBedGraph(const vector<DEPTH> &chromCov, const int &chromSize, const string &chrom);
-    void ResetChromCoverage();
-    void StartNewChrom (const string& chrom);
-    void AddCoverage (int start, int end);
-    void AddBlockedCoverage(const vector<BED> &bedBlocks);
-    void PrintFinalCoverage();
-    void PrintTrackDefinitionLine();
-};
-