X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_plcmd.c;h=b1ffdf900cfa7212937b54ead357bbd3bb8579a0;hb=63e4e54189bc9e7f43852edf865f95e713b93dc4;hp=38680df3357a42b80cf251a3b8c796e057d17d32;hpb=7bd63d5c2677364126702d76c56e4d75981c62f4;p=samtools.git

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 38680df..b1ffdf9 100644
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -195,7 +195,7 @@ static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *p
 		if (p->is_head) printf("^%c", p->b->core.qual > 93? 126 : p->b->core.qual + 33);
 		if (!p->is_del) {
 			int c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos)];
-			if (toupper(c) == toupper(rb)) c = bam1_strand(p->b)? ',' : '.';
+			if (c == '=' || toupper(c) == toupper(rb)) c = bam1_strand(p->b)? ',' : '.';
 			else c = bam1_strand(p->b)? tolower(c) : toupper(c);
 			putchar(c);
 			if (p->indel > 0) {