* samtools-0.1.3-3 (r240)

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 38680df3357a42b80cf251a3b8c796e057d17d32..b1ffdf900cfa7212937b54ead357bbd3bb8579a0 100644 (file)
--- 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) {