Mercurial > repos > ashvark > qiime_1_8_0
comparison bwa-0.6.2/bwtsw2.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 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 #define BSW2_FLAG_MATESW 0x100 | |
10 #define BSW2_FLAG_TANDEM 0x200 | |
11 #define BSW2_FLAG_MOVED 0x400 | |
12 #define BSW2_FLAG_RESCUED 0x800 | |
13 | |
14 typedef struct { | |
15 int skip_sw:16, hard_clip:16; | |
16 int a, b, q, r, t, qr, bw, max_ins; | |
17 int z, is, t_seeds, multi_2nd; | |
18 float mask_level, coef; | |
19 int n_threads, chunk_size; | |
20 } bsw2opt_t; | |
21 | |
22 typedef struct { | |
23 bwtint_t k, l; | |
24 uint32_t flag:18, n_seeds:13, is_rev:1; | |
25 int len, G, G2; | |
26 int beg, end; | |
27 } bsw2hit_t; | |
28 | |
29 typedef struct { | |
30 int flag, nn, n_cigar, chr, pos, qual, mchr, mpos, pqual, isize, nm; | |
31 uint32_t *cigar; | |
32 } bsw2aux_t; | |
33 | |
34 typedef struct { | |
35 int n, max; | |
36 bsw2hit_t *hits; | |
37 bsw2aux_t *aux; | |
38 } bwtsw2_t; | |
39 | |
40 typedef struct { | |
41 void *stack; | |
42 int max_l; | |
43 uint8_t *aln_mem; | |
44 } bsw2global_t; | |
45 | |
46 typedef struct { | |
47 int l, tid; | |
48 char *name, *seq, *qual, *sam; | |
49 } bsw2seq1_t; | |
50 | |
51 #ifdef __cplusplus | |
52 extern "C" { | |
53 #endif | |
54 | |
55 bsw2opt_t *bsw2_init_opt(); | |
56 bwtsw2_t **bsw2_core(const bntseq_t *bns, const bsw2opt_t *opt, const bwtl_t *target, const bwt_t *query, bsw2global_t *pool); | |
57 void bsw2_aln(const bsw2opt_t *opt, const bntseq_t *bns, bwt_t * const target, const char *fn, const char *fn2); | |
58 void bsw2_destroy(bwtsw2_t *b); | |
59 | |
60 bsw2global_t *bsw2_global_init(); | |
61 void bsw2_global_destroy(bsw2global_t *_pool); | |
62 | |
63 void bsw2_pair(const bsw2opt_t *opt, int64_t l_pac, const uint8_t *pac, int n, bsw2seq1_t *seq, bwtsw2_t **hit); | |
64 | |
65 #ifdef __cplusplus | |
66 } | |
67 #endif | |
68 | |
69 #endif |