Uploaded samtools_0.1.16-1_amd64.changes.

[samtools.git] / kaln.h

diff --git a/kaln.h b/kaln.h
index b04d8cc0b001c17c20654fc125e392b08aefb343..1ece132755e51212ab1aee8e56b7b316484e6d37 100644 (file)
--- a/kaln.h
+++ b/kaln.h
@@ -33,23 +33,35 @@
 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 {
+       int iio, iie, ido, ide;
+       int eio, eie, edo, ede;
+       int *matrix;
+       int row;
+       int band_width;
+} ka_param2_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_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,  2, aln_sm_blast, 5, 50 }; */
+extern ka_param_t ka_param_blast; /* = { 5, 2, 5, 2, aln_sm_blast, 5, 50 }; */
+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