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

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author aaronquinlan
date Thu, 03 Nov 2011 10:25:04 -0400
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1 #ifndef BEDFILEPE_H
2 #define BEDFILEPE_H
3
4 #include <vector>
5 #include <map>
6 #include <string>
7 #include <iostream>
8 #include <fstream>
9 #include <sstream>
10 #include <cstring>
11 #include <algorithm>
12 #include "bedFile.h"
13 #include "lineFileUtilities.h"
14
15 using namespace std;
16
17
18 /*
19 Structure for paired-end records
20 */
21 struct BEDPE {
22
23 // UCSC BED fields
24 string chrom1;
25 CHRPOS start1;
26 CHRPOS end1;
27
28 string chrom2;
29 CHRPOS start2;
30 CHRPOS end2;
31
32 string name;
33 string score;
34
35 string strand1;
36 string strand2;
37
38 vector<string> otherFields;
39 };
40
41
42
43
44 //************************************************
45 // BedFile Class methods and elements
46 //************************************************
47 class BedFilePE {
48
49 public:
50
51 // Constructor
52 BedFilePE(string &);
53
54 // Destructor
55 ~BedFilePE(void);
56
57 // Open a BEDPE file for reading (creates an istream pointer)
58 void Open(void);
59
60 // Close an opened BEDPE file.
61 void Close(void);
62
63 // Get the next BED entry in an opened BED file.
64 BedLineStatus GetNextBedPE (BEDPE &bedpe, int &lineNum);
65
66
67 // Methods
68
69 void reportBedPETab(const BEDPE &a);
70 void reportBedPENewLine(const BEDPE &a);
71 void loadBedPEFileIntoMap();
72 void splitBedPEIntoBeds(const BEDPE &a, const int &lineNum, MATE *bedEntry1, MATE *bedEntry2);
73
74
75 void FindOverlapsPerBin(int bEnd, string chrom, CHRPOS start, CHRPOS end, string name, string strand,
76 vector<MATE> &hits, float overlapFraction, bool forceStrand, bool enforceDiffNames);
77
78
79 string bedFile;
80 unsigned int bedType;
81
82 masterMateMap bedMapEnd1;
83 masterMateMap bedMapEnd2;
84
85 private:
86 istream *_bedStream;
87
88 // methods
89 BedLineStatus parseLine (BEDPE &bedpe, const vector<string> &lineVector, int &lineNum);
90 bool parseBedPELine (BEDPE &bed, const vector<string> &lineVector, const int &lineNum);
91 };
92
93 #endif /* BEDFILEPE_H */