Implement the glocal HMM; discard the extention HMM

[samtools.git] / kaln.h

diff --git a/kaln.h b/kaln.h
index 74da142e5f7fa2b005b1b6c3318c923f92531c0c..3bcaac150c7e08c7869099c28158cffc130c40c1 100644 (file)
--- a/kaln.h
+++ b/kaln.h
@@ -50,12 +50,16 @@ typedef struct {
 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 float *_qual,
+                                          const ka_probpar_t *c, int *state, uint8_t *q);
 
 #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 } */
 
 #endif