Merge pull request lh3#293 from nh13/patch-2

Output mapping quality with XB
applib-sg-1009 · Mar 6, 2022 · 41e0078 · 41e0078
2 parents cb7e5df + e050ec9
commit 41e0078
Showing 1 changed file with 2 additions and 0 deletions.
diff --git a/bwamem_extra.c b/bwamem_extra.c
@@ -155,6 +155,8 @@ char **mem_gen_alt(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac
 		if (opt->flag & MEM_F_XB) {
 			kputc(',', &str);
 			kputw(t.score, &str);
+			kputc(',', &str);
+			kputw(t.mapq, &str);
 		}
 		kputc(';', &str);
 		free(t.cigar);