comparison pyPRADA_1.2/tools/bwa-0.5.7-mh/bwt_lite.h @ 0:acc2ca1a3ba4

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author siyuan
date Thu, 20 Feb 2014 00:44:58 -0500
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-1:000000000000 0:acc2ca1a3ba4
1 #ifndef BWT_LITE_H_
2 #define BWT_LITE_H_
3
4 #include <stdint.h>
5
6 typedef struct {
7 uint32_t seq_len, bwt_size, n_occ;
8 uint32_t primary;
9 uint32_t *bwt, *occ, *sa, L2[5];
10 uint32_t cnt_table[256];
11 } bwtl_t;
12
13 #define bwtl_B0(b, k) ((b)->bwt[(k)>>4]>>((~(k)&0xf)<<1)&3)
14
15 #ifdef __cplusplus
16 extern "C" {
17 #endif
18
19 bwtl_t *bwtl_seq2bwtl(int len, const uint8_t *seq);
20 inline uint32_t bwtl_occ(const bwtl_t *bwt, uint32_t k, uint8_t c);
21 inline void bwtl_occ4(const bwtl_t *bwt, uint32_t k, uint32_t cnt[4]);
22 inline void bwtl_2occ4(const bwtl_t *bwt, uint32_t k, uint32_t l, uint32_t cntk[4], uint32_t cntl[4]);
23 void bwtl_destroy(bwtl_t *bwt);
24
25 #ifdef __cplusplus
26 }
27 #endif
28
29 #endif