34 lines
555 B
C
34 lines
555 B
C
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#ifndef BWAMEM_H_
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#define BWAMEM_H_
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#include "bwt.h"
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typedef struct {
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const bwt_t *bwt;
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const uint8_t *query;
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int start, len, min_intv;
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bwtintv_v *tmpvec[2], *matches;
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} smem_i;
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typedef struct {
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int a, b, q, r, w;
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int min_seed_len, max_occ;
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} memopt_t;
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#ifdef __cplusplus
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extern "C" {
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#endif
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smem_i *smem_itr_init(const bwt_t *bwt);
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void smem_itr_destroy(smem_i *itr);
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void smem_set_query(smem_i *itr, int min_intv, int len, const uint8_t *query);
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int smem_next(smem_i *itr);
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memopt_t *mem_opt_init(void);
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#ifdef __cplusplus
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}
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#endif
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#endif
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