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#ifndef LH3_BWTSW2_H
#define LH3_BWTSW2_H
#include <stdint.h>
#include "bntseq.h"
#include "bwt_lite.h"
#include "bwt.h"
typedef struct {
int a, b, q, r, t, qr, bw;
int z, is, t_seeds, hard_clip;
float yita, mask_level, coef;
int n_threads, chunk_size;
} bsw2opt_t;
typedef struct {
uint32_t k, l, flag:18, n_seeds:14;
int len, G, G2;
int beg, end;
} bsw2hit_t;
typedef struct {
int n, max;
bsw2hit_t *hits;
int *n_cigar;
uint32_t **cigar;
} bwtsw2_t;
typedef struct {
void *stack;
int max_l;
uint8_t *aln_mem;
} bsw2global_t;
#ifdef __cplusplus
extern "C" {
bsw2opt_t *bsw2_init_opt();
bwtsw2_t **bsw2_core(const bsw2opt_t *opt, const bwtl_t *target, const bwt_t *query, bsw2global_t *pool);
void bsw2_aln(const bsw2opt_t *opt, const bntseq_t *bns, bwt_t * const target[2], const char *fn);
void bsw2_destroy(bwtsw2_t *b);
bsw2global_t *bsw2_global_init();
void bsw2_global_destroy(bsw2global_t *_pool);
#ifdef __cplusplus
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