48 lines
803 B
C
48 lines
803 B
C
#ifndef BWAMEM_H_
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#define BWAMEM_H_
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#include "bwt.h"
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struct __smem_i;
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typedef struct __smem_i smem_i;
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typedef struct {
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int64_t rbeg;
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int32_t qbeg, len;
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} memseed_t;
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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, max_chain_gap;
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} memopt_t;
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typedef struct {
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int n, m;
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int64_t pos;
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memseed_t *seeds;
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} memchain1_t;
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typedef struct {
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int n, m;
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memchain1_t *chains;
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} memchain_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 len, const uint8_t *query);
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const bwtintv_v *smem_next(smem_i *itr, int split_len);
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memopt_t *mem_opt_init(void);
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memchain_t mem_chain(const memopt_t *opt, const bwt_t *bwt, int len, const uint8_t *seq);
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#ifdef __cplusplus
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}
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#endif
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#endif
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