diff BEDTools-Version-2.14.3/src/subtractBed/subtractBed.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/subtractBed/subtractBed.h	Thu Nov 03 10:25:04 2011 -0400
@@ -0,0 +1,53 @@
+/*****************************************************************************
+  subtractBed.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 SUBTRACTBED_H
+#define SUBTRACTBED_H
+
+#include "bedFile.h"
+#include <vector>
+#include <iostream>
+#include <fstream>
+
+using namespace std;
+
+//************************************************
+// Class methods and elements
+//************************************************
+class BedSubtract {
+
+public:
+
+    // constructor
+    BedSubtract(string &bedAFile, string &bedBFile, float overlapFraction, bool sameStrand, bool diffStrand);
+
+    // destructor
+    ~BedSubtract(void);
+
+private:
+
+    // processing variables
+    string _bedAFile;
+    string _bedBFile;
+    float _overlapFraction;
+    bool _sameStrand;
+    bool _diffStrand;
+
+
+    // instances of bed file class.
+    BedFile *_bedA, *_bedB;
+
+    // methods
+    void FindAndSubtractOverlaps(BED &a, vector<BED> &hits);
+    void SubtractBed();
+};
+
+#endif /* SUBTRACTBED_H */