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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"
#define BSW2_FLAG_MATESW 0x100
#define BSW2_FLAG_TANDEM 0x200
#define BSW2_FLAG_MOVED 0x400
#define BSW2_FLAG_RESCUED 0x800
typedef struct {
int skip_sw:8, cpy_cmt:8, hard_clip:16;
int a, b, q, r, t, qr, bw, max_ins, max_chain_gap;
int z, is, t_seeds, multi_2nd;
float mask_level, coef;
int n_threads, chunk_size;
} bsw2opt_t;
typedef struct {
bwtint_t k, l;
uint32_t flag:18, n_seeds:13, is_rev:1;
int len, G, G2;
int beg, end;
} bsw2hit_t;
typedef struct {
int flag, nn, n_cigar, chr, pos, qual, mchr, mpos, pqual, isize, nm;
uint32_t *cigar;
} bsw2aux_t;
typedef struct {
int n, max;
bsw2hit_t *hits;
bsw2aux_t *aux;
} bwtsw2_t;
typedef struct {
void *stack;
int max_l;
uint8_t *aln_mem;
} bsw2global_t;
typedef struct {
int l, tid;
char *name, *seq, *qual, *sam, *comment;
} bsw2seq1_t;
#ifdef __cplusplus
extern "C" {
#endif
bsw2opt_t *bsw2_init_opt();
bwtsw2_t **bsw2_core(const bntseq_t *bns, 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, const char *fn, const char *fn2);
void bsw2_destroy(bwtsw2_t *b);
bsw2global_t *bsw2_global_init();
void bsw2_global_destroy(bsw2global_t *_pool);
void bsw2_pair(const bsw2opt_t *opt, int64_t l_pac, const uint8_t *pac, int n, bsw2seq1_t *seq, bwtsw2_t **hit);
#ifdef __cplusplus
}
#endif
#endif
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