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

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author aaronquinlan
date Thu, 03 Nov 2011 10:25:04 -0400
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1 /*****************************************************************************
2 intersectBed.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 INTERSECTBED_H
13 #define INTERSECTBED_H
14
15 #include "bedFile.h"
16 #include "chromsweep.h"
17 #include "api/BamReader.h"
18 #include "api/BamWriter.h"
19 #include "api/BamAux.h"
20 #include "BamAncillary.h"
21 using namespace BamTools;
22
23
24 #include <vector>
25 #include <iostream>
26 #include <fstream>
27 #include <stdlib.h>
28 using namespace std;
29
30
31
32 class BedIntersect {
33
34 public:
35
36 // constructor
37 BedIntersect(string bedAFile, string bedBFile, bool anyHit,
38 bool writeA, bool writeB, bool writeOverlap, bool writeAllOverlap,
39 float overlapFraction, bool noHit, bool writeCount, bool sameStrand, bool diffStrand,
40 bool reciprocal, bool obeySplits, bool bamInput, bool bamOutput, bool isUncompressedBam,
41 bool sortedInput);
42
43 // destructor
44 ~BedIntersect(void);
45
46 private:
47
48 //------------------------------------------------
49 // private attributes
50 //------------------------------------------------
51 string _bedAFile;
52 string _bedBFile;
53
54 bool _writeA; // should the original A feature be reported?
55 bool _writeB; // should the original B feature be reported?
56 bool _writeOverlap;
57 bool _writeAllOverlap;
58
59 bool _sameStrand;
60 bool _diffStrand;
61 bool _reciprocal;
62 float _overlapFraction;
63
64 bool _anyHit;
65 bool _noHit;
66 bool _writeCount; // do we want a count of the number of overlaps in B?
67 bool _obeySplits;
68 bool _bamInput;
69 bool _bamOutput;
70 bool _isUncompressedBam;
71 bool _sortedInput;
72 bool _printable;
73
74 // instance of a bed file class.
75 BedFile *_bedA, *_bedB;
76
77 //------------------------------------------------
78 // private methods
79 //------------------------------------------------
80 void IntersectBed(istream &bedInput);
81
82 void IntersectBed();
83
84 void IntersectBam(string bamFile);
85
86 bool processHits(const BED &a, const vector<BED> &hits);
87
88 bool FindOverlaps(const BED &a, vector<BED> &hits);
89
90 bool FindOneOrMoreOverlap(const BED &a);
91
92 void ReportOverlapDetail(int overlapBases, const BED &a, const BED &b, CHRPOS s, CHRPOS e);
93
94 void ReportOverlapSummary(const BED &a, const int &numOverlapsFound);
95
96 };
97
98 #endif /* INTERSECTBED_H */