From f717ea131837acd8cf85eaffb0e3584794f853a7 Mon Sep 17 00:00:00 2001
From: Nils Homer <nh13@users.noreply.github.com>
Date: Thu, 6 Aug 2020 10:10:58 -0700
Subject: [PATCH] Output mapping quality with XB

---
 bwamem_extra.c | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/bwamem_extra.c b/bwamem_extra.c
index 0d64e79..c47b93f 100644
--- 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);