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#ifndef BWTGAP_H_
#define BWTGAP_H_
#include "bwt.h"
#include "bwtaln.h"
typedef struct { // recursion stack
u_int32_t info; // score<<21 | i
u_int32_t n_mm:8, n_gapo:8, n_gape:8, state:2, n_seed_mm:6;
u_int32_t n_ins:16, n_del:16;
int last_diff_pos;
bwtint_t k, l; // (k,l) is the SA region of [i,n-1]
} gap_entry_t;
typedef struct {
int n_entries, m_entries;
gap_entry_t *stack;
} gap_stack1_t;
typedef struct {
int n_stacks, best, n_entries;
gap_stack1_t *stacks;
} gap_stack_t;
#ifdef __cplusplus
extern "C" {
#endif
gap_stack_t *gap_init_stack2(int max_score);
gap_stack_t *gap_init_stack(int max_mm, int max_gapo, int max_gape, const gap_opt_t *opt);
void gap_destroy_stack(gap_stack_t *stack);
bwt_aln1_t *bwt_match_gap(bwt_t *const bwt, int len, const ubyte_t *seq, bwt_width_t *w,
bwt_width_t *seed_w, const gap_opt_t *opt, int *_n_aln, gap_stack_t *stack);
void bwa_aln2seq(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s);
#ifdef __cplusplus
}
#endif
#endif
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