X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=kaln.h;h=1ece132755e51212ab1aee8e56b7b316484e6d37;hp=b24597cfc2ee159529c5746916597591ecababe2;hb=b990d9d3dd518a9cf7b7f4a165c584d8d8d1cfb0;hpb=62781a2daa24d74a3c590e2669fad1fa7cabf933

diff --git a/kaln.h b/kaln.h
index b24597c..1ece132 100644
--- a/kaln.h
+++ b/kaln.h
@@ -42,9 +42,12 @@ 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" {
@@ -52,14 +55,13 @@ extern "C" {
 
 	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);
-
+	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_probpar_t ka_probpar_def; /* { 0.0001, 0.1, 10 } */
+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