Mercurial > repos > ashvark > qiime_1_8_0
comparison bwa-0.6.2/bwtgap.h @ 2:a294fbfcb1db draft default tip
Uploaded BWA
author | ashvark |
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date | Fri, 18 Jul 2014 07:55:59 -0400 |
parents | dd1186b11b3b |
children |
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1:a9636dc1e99a | 2:a294fbfcb1db |
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1 #ifndef BWTGAP_H_ | |
2 #define BWTGAP_H_ | |
3 | |
4 #include "bwt.h" | |
5 #include "bwtaln.h" | |
6 | |
7 typedef struct { // recursion stack | |
8 u_int32_t info; // score<<21 | i | |
9 u_int32_t n_mm:8, n_gapo:8, n_gape:8, state:2, n_seed_mm:6; | |
10 bwtint_t k, l; // (k,l) is the SA region of [i,n-1] | |
11 int last_diff_pos; | |
12 } gap_entry_t; | |
13 | |
14 typedef struct { | |
15 int n_entries, m_entries; | |
16 gap_entry_t *stack; | |
17 } gap_stack1_t; | |
18 | |
19 typedef struct { | |
20 int n_stacks, best, n_entries; | |
21 gap_stack1_t *stacks; | |
22 } gap_stack_t; | |
23 | |
24 #ifdef __cplusplus | |
25 extern "C" { | |
26 #endif | |
27 | |
28 gap_stack_t *gap_init_stack2(int max_score); | |
29 gap_stack_t *gap_init_stack(int max_mm, int max_gapo, int max_gape, const gap_opt_t *opt); | |
30 void gap_destroy_stack(gap_stack_t *stack); | |
31 bwt_aln1_t *bwt_match_gap(bwt_t *const bwt, int len, const ubyte_t *seq, bwt_width_t *w, | |
32 bwt_width_t *seed_w, const gap_opt_t *opt, int *_n_aln, gap_stack_t *stack); | |
33 void bwa_aln2seq(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s); | |
34 | |
35 #ifdef __cplusplus | |
36 } | |
37 #endif | |
38 | |
39 #endif |