comparison bwa-0.6.2/bwa.h @ 2:a294fbfcb1db draft default tip

Uploaded BWA
author ashvark
date Fri, 18 Jul 2014 07:55:59 -0400
parents dd1186b11b3b
children
comparison
equal deleted inserted replaced
1:a9636dc1e99a 2:a294fbfcb1db
1 #ifndef BWA_H_
2 #define BWA_H_
3
4 #include <stdint.h>
5
6 #define BWA_DEF_MAX_SCORE 2048
7 #define BWA_MAX_QUERY_LEN 1024
8
9 // BWA index
10 struct bwa_idx_t;
11 typedef struct bwa_idx_t bwa_idx_t;
12
13 // Buffer for BWA alignment
14 struct bwa_buf_t;
15 typedef struct bwa_buf_t bwa_buf_t;
16
17 // BWA alignment options
18 typedef struct {
19 int s_gapo, s_gape; // gap open and extension penalties; the mismatch penalty is fixed at 3
20 int max_diff, max_gapo, max_gape; // max differences (-1 to use fnr for length-adjusted max diff), gap opens and gap extensions
21 int seed_len, max_seed_diff; // seed length and max differences allowed in the seed
22 float fnr; // parameter for automatic length-adjusted max differences
23 } bwa_opt_t;
24
25 // default BWA alignment options
26 extern bwa_opt_t bwa_def_opt; // = { 11, 4, -1, 1, 6, 32, 2, 0.04 }
27
28 // an interval hit in the SA coordinate; basic unit in .sai files
29 typedef struct {
30 uint32_t n_mm:16, n_gapo:8, n_gape:8;
31 int score;
32 uint64_t k, l; // [k,l] is the SA interval; each interval has l-k+1 hits
33 } bwa_sai1_t;
34
35 // all interval hits in the SA coordinate
36 typedef struct {
37 int n; // number of interval hits
38 bwa_sai1_t *sai;
39 } bwa_sai_t;
40
41 // an alignment
42 typedef struct {
43 uint32_t n_n:8, n_gap:12, n_mm:12; // number of ambiguous bases, gaps and mismatches in the alignment
44 int32_t ref_id; // referece sequence index (the first seq is indexed by 0)
45 uint32_t offset; // coordinate on the reference; zero-based
46 uint32_t n_cigar:16, flag:16; // number of CIGAR operations; SAM flag
47 uint32_t *cigar; // CIGAR in the BAM 28+4 encoding; having n_cigar operations
48 } bwa_aln_t;
49
50 typedef struct {
51 int mapQs, mapQ, c1, c2;
52 uint64_t sa;
53 bwa_sai1_t *which;
54 bwa_sai_t sai;
55 bwa_aln_t one;
56 } bwa_one_t;
57
58 typedef struct {
59 double avg, std, ap_prior;
60 uint64_t low, high, high_bayesian;
61 } bwa_pestat_t;
62
63 #ifdef __cplusplus
64 extern "C" {
65 #endif
66
67 // load a BWA index
68 bwa_idx_t *bwa_idx_load(const char *prefix);
69 void bwa_idx_destroy(bwa_idx_t *p);
70
71 // allocate a BWA alignment buffer; if unsure, set opt to &bwa_def_opt and max_score to BWA_DEF_MAX_SCORE
72 bwa_buf_t *bwa_buf_init(const bwa_opt_t *opt, int max_score);
73 void bwa_buf_destroy(bwa_buf_t *p);
74
75 /**
76 * Find all the SA intervals
77 *
78 * @param idx BWA index; multiple threads can share the same index
79 * @param buf BWA alignment buffer; each thread should have its own buffer
80 * @param seq NULL terminated C string, consisting of A/C/G/T/N only
81 *
82 * @return SA intervals seq is matched to
83 */
84 bwa_sai_t bwa_sai(const bwa_idx_t *idx, bwa_buf_t *buf, const char *seq);
85
86 /**
87 * Construct an alignment in the base-pair coordinate
88 *
89 * @param idx BWA index
90 * @param buf BWA alignment buffer
91 * @param seq NULL terinated C string
92 * @param sa Suffix array value
93 * @param n_gaps Number of gaps (typically equal to bwa_sai1_t::n_gapo + bwa_sai1_t::n_gape
94 *
95 * @return An alignment
96 */
97 void bwa_sa2aln(const bwa_idx_t *idx, bwa_buf_t *buf, const char *seq, uint64_t sa, int n_gaps, bwa_aln_t *aln);
98
99 bwa_one_t *bwa_se(const bwa_idx_t *idx, bwa_buf_t *buf, const char *seq, int gen_cigar);
100
101 void bwa_one_destroy(bwa_one_t *one);
102
103 #ifdef __cplusplus
104 }
105 #endif
106
107 #endif