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comparison BEDTools-Version-2.14.3/src/fjoin/fjoin.h @ 1:bec36315bd12 default tip

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author aaronquinlan
date Sat, 19 Nov 2011 14:17:03 -0500
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0:dfcd8b6c1bda 1:bec36315bd12
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 "BamReader.h"
17 // #include "BamWriter.h"
18 // #include "BamAncillary.h"
19 // #include "BamAux.h"
20 // using namespace BamTools;
21
22
23 #include <vector>
24 #include <queue>
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 forceStrand,
40 bool reciprocal, bool obeySplits, bool bamInput, bool bamOutput);
41
42 // destructor
43 ~BedIntersect(void);
44
45 private:
46
47 //------------------------------------------------
48 // private attributes
49 //------------------------------------------------
50 string _bedAFile;
51 string _bedBFile;
52
53 bool _writeA; // should the original A feature be reported?
54 bool _writeB; // should the original B feature be reported?
55 bool _writeOverlap;
56 bool _writeAllOverlap;
57
58 bool _forceStrand;
59 bool _reciprocal;
60 float _overlapFraction;
61
62 bool _anyHit;
63 bool _noHit;
64 bool _writeCount; // do we want a count of the number of overlaps in B?
65 bool _obeySplits;
66 bool _bamInput;
67 bool _bamOutput;
68
69 bool _printable;
70
71 queue<BED*> _outputBuffer;
72 bool _lastPick;
73
74 map<string, vector<BED*> > _windowA;
75 map<string, vector<BED*> > _windowB;
76
77 // instance of a bed file class.
78 BedFile *_bedA, *_bedB;
79
80 //------------------------------------------------
81 // private methods
82 //------------------------------------------------
83 void IntersectBed(istream &bedInput);
84
85 void Scan(BED *x, vector<BED *> *windowX, BedLineStatus xStatus,
86 const BED &y, vector<BED *> *windowY, BedLineStatus yStatus);
87
88 void AddHits(BED *x, const BED &y);
89
90 void FlushOutputBuffer(bool final = false);
91
92 vector<BED*>* GetWindow(const string &chrom, bool isA);
93
94 void ChromSwitch(const string &chrom);
95
96 void IntersectBed();
97
98 void IntersectBam(string bamFile);
99
100 bool processHits(BED &a, vector<BED> &hits);
101
102 bool FindOverlaps(const BED &a, vector<BED> &hits);
103
104 bool FindOneOrMoreOverlap(const BED &a);
105
106 void ReportOverlapDetail(const int &overlapBases, const BED &a, const BED &b,
107 const CHRPOS &s, const CHRPOS &e);
108 void ReportOverlapSummary(const BED &a, const int &numOverlapsFound);
109
110 void ReportHits(set<BED> &A, set<BED> &B);
111
112 };
113
114 #endif /* INTERSECTBED_H */