--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BEDTools-Version-2.14.3/src/coverageBed/coverageBed.h	Thu Nov 03 10:25:04 2011 -0400
@@ -0,0 +1,83 @@
+/*****************************************************************************
+  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 */