r112: bugfix: first mapq not counted

lh3 · Aug 14, 2016 · 2c964b0 · 2c964b0
1 parent c9b6d84
commit 2c964b0
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/group.c b/group.c
@@ -229,12 +229,13 @@ void lt_grp_push_read(const lt_opt_t *opt, lt_groups_t *g, const bam_hdr_t *h, c
 		}
 	}
 	if (i == kdq_size(g->q)) {
+		int q = c->qual < 60? c->qual : 60;
 		lt_group_t *p;
 		p = kdq_pushp(lt_group_t, g->q);
 		p->tid = c->tid, p->st = st, p->en = en, p->is_rev = is_rev, p->n_frag = 1;
 		p->l_open = is_rev? 1 : 0;
 		p->r_open = is_rev? 0 : 1;
-		p->sum_mq2 = 0;
+		p->sum_mq2 = q * q;
 		p->n = 0, p->m = 4;
 		p->a = (int*)malloc(p->m * sizeof(int));
 		p->a[p->n++] = en - st;

diff --git a/main.c b/main.c
@@ -3,7 +3,7 @@
 #include <sys/resource.h>
 #include <sys/time.h>
 
-#define LT_VERSION "r109"
+#define LT_VERSION "r112"
 
 int main_trim(int argc, char *argv[]);
 int main_ldup(int argc, char *argv[]);