Mercurial > repos > siyuan > prada
comparison pyPRADA_1.2/tools/bwa-0.5.7-mh/bwtsw2.h @ 0:acc2ca1a3ba4
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author | siyuan |
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date | Thu, 20 Feb 2014 00:44:58 -0500 |
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-1:000000000000 | 0:acc2ca1a3ba4 |
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1 #ifndef LH3_BWTSW2_H | |
2 #define LH3_BWTSW2_H | |
3 | |
4 #include <stdint.h> | |
5 #include "bntseq.h" | |
6 #include "bwt_lite.h" | |
7 #include "bwt.h" | |
8 | |
9 typedef struct { | |
10 int a, b, q, r, t, qr, bw; | |
11 int z, is, t_seeds, hard_clip; | |
12 float yita, mask_level, coef; | |
13 int n_threads, chunk_size; | |
14 } bsw2opt_t; | |
15 | |
16 typedef struct { | |
17 uint32_t k, l, flag:18, n_seeds:14; | |
18 int len, G, G2; | |
19 int beg, end; | |
20 } bsw2hit_t; | |
21 | |
22 typedef struct { | |
23 int n, max; | |
24 bsw2hit_t *hits; | |
25 int *n_cigar; | |
26 uint32_t **cigar; | |
27 } bwtsw2_t; | |
28 | |
29 typedef struct { | |
30 void *stack; | |
31 int max_l; | |
32 uint8_t *aln_mem; | |
33 } bsw2global_t; | |
34 | |
35 #ifdef __cplusplus | |
36 extern "C" { | |
37 #endif | |
38 | |
39 bsw2opt_t *bsw2_init_opt(); | |
40 bwtsw2_t **bsw2_core(const bsw2opt_t *opt, const bwtl_t *target, const bwt_t *query, bsw2global_t *pool); | |
41 void bsw2_aln(const bsw2opt_t *opt, const bntseq_t *bns, bwt_t * const target[2], const char *fn); | |
42 void bsw2_destroy(bwtsw2_t *b); | |
43 | |
44 bsw2global_t *bsw2_global_init(); | |
45 void bsw2_global_destroy(bsw2global_t *_pool); | |
46 | |
47 #ifdef __cplusplus | |
48 } | |
49 #endif | |
50 | |
51 #endif |