X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=kaln.h;h=1ece132755e51212ab1aee8e56b7b316484e6d37;hp=b04d8cc0b001c17c20654fc125e392b08aefb343;hb=9f4bebab2e0917c676ae739b2d05cb22ad6c4ed5;hpb=317f5e8dd22cc9e1e5e05fbcaeb3b9aca7447351

diff --git a/kaln.h b/kaln.h
index b04d8cc..1ece132 100644
--- 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