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comparison BEDTools-Version-2.14.3/src/flankBed/flankBed.h @ 0:dfcd8b6c1bda

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author aaronquinlan
date Thu, 03 Nov 2011 10:25:04 -0400
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1 /*****************************************************************************
2 flankBed.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
13 #include "bedFile.h"
14 #include "genomeFile.h"
15
16 #include <vector>
17 #include <iostream>
18 #include <fstream>
19 #include <map>
20 #include <cstdlib>
21 #include <ctime>
22 using namespace std;
23
24
25 //************************************************
26 // Class methods and elements
27 //************************************************
28 class BedFlank {
29
30 public:
31
32 // constructor
33 BedFlank(string &bedFile, string &genomeFile, bool forceStrand, float leftSlop, float rightSlop, bool fractional);
34
35 // destructor
36 ~BedFlank(void);
37
38
39
40 private:
41
42 string _bedFile;
43 string _genomeFile;
44
45 bool _forceStrand;
46 float _leftFlank;
47 float _rightFlank;
48 bool _fractional;
49
50 BedFile *_bed;
51 GenomeFile *_genome;
52
53 // methods
54
55 void FlankBed();
56
57 // method to grab requested flank w.r.t. a single BED entry
58 void AddFlank(BED &bed, int leftSlop, int rightSlop);
59
60 // method to grab requested flank w.r.t. a single BED entry,
61 // while choosing flanks based on strand
62 void AddStrandedFlank(BED &bed, int leftSlop, int rightSlop);
63 };