|
0
|
1 /*****************************************************************************
|
|
|
2 pairToPair.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 PAIRTOPAIR_H
|
|
|
13 #define PAIRTOPAIR_H
|
|
|
14
|
|
|
15 #include "bedFile.h"
|
|
|
16 #include "bedFilePE.h"
|
|
|
17 #include <vector>
|
|
|
18 #include <iostream>
|
|
|
19 #include <fstream>
|
|
|
20
|
|
|
21 using namespace std;
|
|
|
22
|
|
|
23
|
|
|
24
|
|
|
25 //************************************************
|
|
|
26 // Class methods and elements
|
|
|
27 //************************************************
|
|
|
28 class PairToPair {
|
|
|
29
|
|
|
30 public:
|
|
|
31
|
|
|
32 // constructor
|
|
|
33 PairToPair(string &bedAFilePE, string &bedBFilePE, float &overlapFraction,
|
|
|
34 string searchType, bool ignoreStrand, bool reqDiffNames, int slop, bool strandedSlop);
|
|
|
35
|
|
|
36 // destructor
|
|
|
37 ~PairToPair(void);
|
|
|
38
|
|
|
39 void IntersectPairs();
|
|
|
40
|
|
|
41
|
|
|
42 private:
|
|
|
43
|
|
|
44 string _bedAFilePE;
|
|
|
45 string _bedBFilePE;
|
|
|
46
|
|
|
47 float _overlapFraction;
|
|
|
48 string _searchType;
|
|
|
49 bool _ignoreStrand;
|
|
|
50 bool _reqDiffNames;
|
|
|
51 int _slop;
|
|
|
52 bool _strandedSlop;
|
|
|
53
|
|
|
54 // instance of a paired-end bed file class.
|
|
|
55 BedFilePE *_bedA;
|
|
|
56
|
|
|
57 // instance of a bed file class.
|
|
|
58 BedFilePE *_bedB;
|
|
|
59
|
|
|
60 // methods
|
|
|
61 // void FindOverlaps(const BEDPE &a, vector<MATE> &hitsA1B1, vector<MATE> &hitsA1B2,
|
|
|
62 // vector<MATE> &hitsA2B1, vector<MATE> &hitsA2B2);
|
|
|
63 void FindOverlaps(const BEDPE &a);
|
|
|
64
|
|
|
65 void FindQualityHitsBetweenEnds(CHRPOS start, CHRPOS end,
|
|
|
66 const vector<MATE> &hits, vector<MATE> &qualityHits, int &numOverlaps);
|
|
|
67
|
|
|
68 bool FindHitsOnBothEnds(const BEDPE &a, const vector<MATE> &qualityHitsEnd1,
|
|
|
69 const vector<MATE> &qualityHitsEnd2);
|
|
|
70
|
|
|
71 void FindHitsOnEitherEnd(const BEDPE &a, const vector<MATE> &qualityHitsEnd1,
|
|
|
72 const vector<MATE> &qualityHitsEnd2);
|
|
|
73
|
|
|
74 };
|
|
|
75
|
|
|
76 #endif /* PAIRTOPAIR_H */
|
