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

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author aaronquinlan
date Thu, 03 Nov 2011 10:25:04 -0400
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1 /*****************************************************************************
2 windowBed.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 WINDOWBED_H
13 #define WINDOWBED_H
14
15 #include "api/BamReader.h"
16 #include "api/BamWriter.h"
17 #include "api/BamAux.h"
18 using namespace BamTools;
19
20 #include "bedFile.h"
21 #include <vector>
22 #include <iostream>
23 #include <fstream>
24
25 using namespace std;
26
27 //************************************************
28 // Class methods and elements
29 //************************************************
30 class BedWindow {
31
32 public:
33
34 // constructor
35 BedWindow(string bedAFile, string bedBFile, int leftSlop, int rightSlop,
36 bool anyHit, bool noHit, bool writeCount, bool strandWindows,
37 bool matchOnSameStrand, bool matchOnDiffStrand, bool bamInput, bool bamOutput, bool isUncompressedBam);
38
39 // destructor
40 ~BedWindow(void);
41
42 private:
43
44 string _bedAFile;
45 string _bedBFile;
46 bool _anyHit;
47 bool _writeCount;
48 int _leftSlop;
49 int _rightSlop;
50 bool _noHit;
51 bool _strandWindows;
52 bool _matchOnSameStrand;
53 bool _matchOnDiffStrand;
54 bool _bamInput;
55 bool _bamOutput;
56 bool _isUncompressedBam;
57
58 // instance of a bed file class.
59 BedFile *_bedA, *_bedB;
60
61 // methods
62 void WindowIntersectBed();
63 void WindowIntersectBam(string bamFile);
64 void FindWindowOverlaps(const BED &a, vector<BED> &hits);
65 bool FindOneOrMoreWindowOverlaps(const BED &a);
66 void AddWindow(const BED &a, CHRPOS &fudgeStart, CHRPOS &fudgeEnd);
67
68 };
69 #endif /* WINDOWBED_H */