bwtgap.h

#ifndef BWTGAP_H_
#define BWTGAP_H_

#include "bwt.h"
//#include "bwtaln.h"
#include "jigsawaln.h"

typedef struct { // recursion stack
	u_int32_t info; // score<<21 | a<<20 | i
	u_int32_t n_mm:8, n_gapo_t:8, n_gape_t:8, n_gapo_q:8, n_gape_q:8;
	//mismatch, gap opening and extension in target and query sequences respectively
	u_int32_t state:2, n_seed_mm:6;
	bwtint_t k, l; // (k,l) is the SA region of [i,n-1]
	int last_diff_pos;
} 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_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(const bwt_t *bwt, uint32_t len, const ubyte_t *seq[2], bwt_width_t *w[2],
							  /*bwt_width_t *seed_w[2],*/ 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