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

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author aaronquinlan
date Thu, 03 Nov 2011 10:25:04 -0400
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1 /*****************************************************************************
2 closestBed.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 CLOSESTBED_H
13 #define CLOSESTBED_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 BedClosest {
26
27 public:
28
29 // constructor
30 BedClosest(string &bedAFile, string &bedBFile,
31 bool sameStrand, bool diffStrand, string &tieMode,
32 bool reportDistance, bool signDistance, string &strandedDistMode,
33 bool ignoreOverlaps);
34
35 // destructor
36 ~BedClosest(void);
37
38 // find the closest feature in B to A
39 void FindClosestBed();
40
41 private:
42
43 // data
44 string _bedAFile;
45 string _bedBFile;
46 string _tieMode;
47 bool _sameStrand;
48 bool _diffStrand;
49 bool _reportDistance;
50 bool _signDistance;
51 string _strandedDistMode;
52 bool _ignoreOverlaps;
53
54 BedFile *_bedA, *_bedB;
55
56 // methods
57 void reportNullB();
58 void FindWindowOverlaps(BED &, vector<BED> &);
59
60 };
61 #endif /* CLOSEST_H */