typedef struct {
int gap_open;
int gap_ext;
- int gap_end;
+ int gap_end_open;
+ int gap_end_ext;
int *matrix;
int row;
int band_width;
} ka_param_t;
+typedef struct {
+ float d, e;
+ int bw;
+} ka_probpar_t;
+
#ifdef __cplusplus
extern "C" {
#endif
- 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);
+ 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);
#ifdef __cplusplus
}
#endif
-extern ka_param_t ka_param_blast; /* = { 5, 2, 2, aln_sm_blast, 5, 50 }; */
+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 } */
#endif