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