diff BEDTools-Version-2.14.3/src/slopBed/slopBed.h @ 0:dfcd8b6c1bda

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author aaronquinlan
date Thu, 03 Nov 2011 10:25:04 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BEDTools-Version-2.14.3/src/slopBed/slopBed.h	Thu Nov 03 10:25:04 2011 -0400
@@ -0,0 +1,59 @@
+/*****************************************************************************
+  slopBed.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 <vector>
+#include <iostream>
+#include <fstream>
+#include <map>
+#include <cstdlib>
+#include <ctime>
+using namespace std;
+
+
+//************************************************
+// Class methods and elements
+//************************************************
+class BedSlop {
+
+public:
+
+    // constructor
+    BedSlop(string &bedFile, string &genomeFile, bool forceStrand, float leftSlop, float rightSlop, bool fractional);
+
+    // destructor
+    ~BedSlop(void);
+
+
+
+private:
+
+    string _bedFile;
+    string _genomeFile;
+
+    bool   _forceStrand;
+    float  _leftSlop;
+    float  _rightSlop;
+    bool   _fractional;
+
+    BedFile *_bed;
+    GenomeFile *_genome;
+
+    // methods
+
+    void SlopBed();
+
+    // method to add requested "slop" to a single BED entry
+    void AddSlop(BED &bed, int leftSlop, int rightSlop);
+};