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comparison gene_fraction/src/Alignments.h @ 0:f95150c37d38 draft default tip

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planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
author chrisd
date Sun, 21 Feb 2016 23:31:55 -0500
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-1:000000000000 0:f95150c37d38
1 #ifndef ALIGNMENTS_H
2 #define ALIGNMENTS_H
3
4 #include <string>
5 #include <vector>
6
7 /**
8 * Stores information about an alignment
9 */
10 struct alignment_fields {
11 std::string QNAME;
12 int FLAG;
13 std::string RNAME;
14 int POS;
15 int MAPQ;
16 std::string CIGAR;
17 std::string RNEXT;
18 int PNEXT;
19 int TLEN;
20 std::string SEQ;
21 std::string QUAL;
22 };
23
24 /**
25 * Class for dealing with alignments
26 */
27 class Alignments {
28 public:
29 /**
30 * Ctor that initializes alignment
31 */
32 Alignments(std::string alignment);
33
34 /**
35 * Stores information about each of the eleven
36 * required alignment fields
37 */
38 void fill_alignment_fields(const std::string &alignment);
39
40 std::vector<std::pair<int,char>> cigar();
41
42 inline std::string alignment() const { return _alignment; };
43
44 inline std::string qname() const { return field.QNAME; };
45 inline std::string rname() const { return field.RNAME; };
46 inline std::string cigar() const { return field.CIGAR; };
47 inline std::string rnext() const { return field.RNEXT; };
48 inline std::string seq() const { return field.SEQ; };
49 inline std::string qual() const { return field.QUAL; };
50
51 inline int flag() const { return field.FLAG; };
52 inline int pos() const { return field.POS; };
53 inline int mapq() const { return field.MAPQ; };
54 inline int pnext() const { return field.PNEXT; };
55 inline int tlen() const { return field.TLEN; };
56
57 private:
58 /**
59 * Returns a pair of cigar operations as (occurrence, operation)
60 * Ex: 10M5I -> (10, M), (5, I)
61 */
62 std::vector<std::pair<int,char>> get_cigar_operations(const std::string &cigar);
63
64 std::string _alignment;
65 alignment_fields field;
66 };
67
68 #endif /* ALIGNMENTS_H */