r225: count N matches as mismatches

lh3 · Sep 17, 2024 · cea81a4 · cea81a4
1 parent 3bb365f
commit cea81a4
Show file tree

Hide file tree

Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/bwa-sw.c b/bwa-sw.c
@@ -402,7 +402,7 @@ static void sw_core(void *km, const rb3_swopt_t *opt, const rb3_fmi_t *f, const
 				sw_cell2sai(p, &ik);
 				rb3_fmd_extend_cached(f, rc, &ik, ok, 1);
 				for (c = 1; c < 6; ++c) {
-					int32_t sc = c == t->c? opt->match : -opt->mis;
+					int32_t sc = c == t->c && c != 5? opt->match : -opt->mis;
 					if (ok[c].size == 0) continue;
 					if (p->H + sc <= 0 || p->H + sc < max_min_sc) continue;
 					if (c != t->c && p->qlen < opt->end_len) continue;

diff --git a/main.c b/main.c
@@ -5,7 +5,7 @@
 #include "io.h"
 #include "ketopt.h"
 
-#define RB3_VERSION "3.6-r224-dirty"
+#define RB3_VERSION "3.6-r225-dirty"
 
 int main_build(int argc, char *argv[]);
 int main_merge(int argc, char *argv[]);