* aggressive gapped aligner is implemented in calmd.

[samtools.git] / kaln.h

diff --git a/kaln.h b/kaln.h
index b04d8cc0b001c17c20654fc125e392b08aefb343..4b6869c7f71ab67b3257a86c4bcd5dc7bbf2e826 100644 (file)
--- a/kaln.h
+++ b/kaln.h
@@ -33,7 +33,8 @@
 typedef struct {
        int gap_open;
        int gap_ext;
-       int gap_end;
+       int gap_end_open;
+       int gap_end_ext;
 
        int *matrix;
        int row;
@@ -50,6 +51,6 @@ extern "C" {
 }
 #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 }; */
 
 #endif