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comparison 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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1 /*****************************************************************************
2 subtractBed.h
3
4 (c) 2009 - Aaron Quinlan
5 Hall Laboratory
6 Department of Biochemistry and Molecular Genetics
7 University of Virginia
8 aaronquinlan@gmail.com
9
10 Licenced under the GNU General Public License 2.0 license.
11 ******************************************************************************/
12 #ifndef SUBTRACTBED_H
13 #define SUBTRACTBED_H
14
15 #include "bedFile.h"
16 #include <vector>
17 #include <iostream>
18 #include <fstream>
19
20 using namespace std;
21
22 //************************************************
23 // Class methods and elements
24 //************************************************
25 class BedSubtract {
26
27 public:
28
29 // constructor
30 BedSubtract(string &bedAFile, string &bedBFile, float overlapFraction, bool sameStrand, bool diffStrand);
31
32 // destructor
33 ~BedSubtract(void);
34
35 private:
36
37 // processing variables
38 string _bedAFile;
39 string _bedBFile;
40 float _overlapFraction;
41 bool _sameStrand;
42 bool _diffStrand;
43
44
45 // instances of bed file class.
46 BedFile *_bedA, *_bedB;
47
48 // methods
49 void FindAndSubtractOverlaps(BED &a, vector<BED> &hits);
50 void SubtractBed();
51 };
52
53 #endif /* SUBTRACTBED_H */