} ka_param_t;
typedef struct {
- float d, e;
- int bw;
-} ka_probpar_t;
+ int iio, iie, ido, ide;
+ int eio, eie, edo, ede;
+ int *matrix;
+ int row;
+ int band_width;
+} ka_param2_t;
#ifdef __cplusplus
extern "C" {
uint32_t *ka_global_core(uint8_t *seq1, int len1, uint8_t *seq2, int len2, const ka_param_t *ap,
int *_score, int *n_cigar);
- int ka_prob_glocal(const uint8_t *_ref, int l_ref, const uint8_t *_query, int l_query, const uint8_t *iqual,
- const ka_probpar_t *c, int *state, uint8_t *q);
-
+ int ka_global_score(const uint8_t *_seq1, int len1, const uint8_t *_seq2, int len2, const ka_param2_t *ap);
#ifdef __cplusplus
}
#endif
extern ka_param_t ka_param_blast; /* = { 5, 2, 5, 2, aln_sm_blast, 5, 50 }; */
-extern ka_probpar_t ka_probpar_def; /* { 0.0001, 0.1, 10 } */
+extern ka_param_t ka_param_qual; // only use this for global alignment!!!
+extern ka_param2_t ka_param2_qual; // only use this for global alignment!!!
#endif