X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=blobdiff_plain;f=kaln.h;h=1ece132755e51212ab1aee8e56b7b316484e6d37;hp=74da142e5f7fa2b005b1b6c3318c923f92531c0c;hb=307c147168f7154e3755712797078c513e0b242a;hpb=9e59c3bca7bf72427f3d5934ba56c3fe1cbd8285

diff --git a/kaln.h b/kaln.h
index 74da142..1ece132 100644
--- a/kaln.h
+++ b/kaln.h
@@ -42,20 +42,26 @@ typedef struct {
 } 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" {
 #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, 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