* samtools-0.1.8-21 (r780)

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index f0e63ce62cd91cc6cada955eaa19c9b2493e1872..6d42471c007a6b34d5b7b1db3ee535c974564839 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -183,10 +183,15 @@ static inline void pileup_seq(const bam_pileup1_t *p, int pos, int ref_len, cons
                putchar(p->b->core.qual > 93? 126 : p->b->core.qual + 33);
        }
        if (!p->is_del) {
-               int rb, c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos)];
-               rb = (ref && pos < ref_len)? ref[pos] : 'N';
-               if (c == '=' || toupper(c) == toupper(rb)) c = bam1_strand(p->b)? ',' : '.';
-               else c = bam1_strand(p->b)? tolower(c) : toupper(c);
+               int c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos)];
+               if (ref) {
+                       int rb = pos < ref_len? ref[pos] : 'N';
+                       if (c == '=' || bam_nt16_table[c] == bam_nt16_table[rb]) c = bam1_strand(p->b)? ',' : '.';
+                       else c = bam1_strand(p->b)? tolower(c) : toupper(c);
+               } else {
+                       if (c == '=') c = bam1_strand(p->b)? ',' : '.';
+                       else c = bam1_strand(p->b)? tolower(c) : toupper(c);
+               }
                putchar(c);
        } else putchar(p->is_refskip? (bam1_strand(p->b)? '<' : '>') : '*');
        if (p->indel > 0) {
@@ -286,16 +291,18 @@ static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *p
        }
        // print pileup sequences
        printw(n, stdout); putchar('\t');
-       rms_aux = 0; // we need to recalculate rms_mapq when -c is not flagged on the command line
-       for (i = 0; i < n; ++i) {
-               const bam_pileup1_t *p = pu + i;
-               int tmp = p->b->core.qual < d->c->cap_mapQ? p->b->core.qual : d->c->cap_mapQ;
-               rms_aux += tmp * tmp;
-               pileup_seq(p, pos, d->len, d->ref);
-       }
+       for (i = 0; i < n; ++i)
+               pileup_seq(pu + i, pos, d->len, d->ref);
        // finalize rms_mapq
-       rms_aux = (uint64_t)(sqrt((double)rms_aux / n) + .499);
-       if (rms_mapq < 0) rms_mapq = rms_aux;
+       if (d->format & BAM_PLF_CNS) {
+               for (i = rms_aux = 0; i < n; ++i) {
+                       const bam_pileup1_t *p = pu + i;
+                       int tmp = p->b->core.qual < d->c->cap_mapQ? p->b->core.qual : d->c->cap_mapQ;
+                       rms_aux += tmp * tmp;
+               }
+               rms_aux = (uint64_t)(sqrt((double)rms_aux / n) + .499);
+               if (rms_mapq < 0) rms_mapq = rms_aux;
+       }
        putchar('\t');
        // print quality
        for (i = 0; i < n; ++i) {