#ifndef KSW2_H_
#define KSW2_H_

#include <stdint.h>

#ifdef __cplusplus
extern "C" {
#endif

/**
 * Global alignment with moving a band
 *
 * @param km        memory pool, when used with kalloc
 * @param qlen      query length
 * @param query     query sequence with 0 <= query[i] < m
 * @param tlen      target length
 * @param target    target sequence with 0 <= target[i] < m
 * @param m         number of residue types
 * @param mat       m*m scoring mattrix in one-dimension array
 * @param gapo      gap open penalty; a gap of length l cost "-(gapo+l*gape)"
 * @param gape      gap extension penalty
 * @param w         band width
 * @param n_cigar   (out) number of CIGAR elements
 * @param cigar     (out) BAM-encoded CIGAR; caller need to deallocate with kfree(km, )
 *
 * @return          score of the alignment
 */
int ksw_global(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t gapo, int8_t gape, int w, int *n_cigar_, uint32_t **cigar_);
int ksw_global2(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t gapo, int8_t gape, int w, int *n_cigar_, uint32_t **cigar_);
int ksw_global2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t gapo, int8_t gape, int w, int *n_cigar_, uint32_t **cigar_);

void ksw_gen_simple_mat(int m, int8_t *mat, int8_t a, int8_t b);

#ifdef __cplusplus
}
#endif

#endif