fixed a silly bug in pileup

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index f0e63ce62cd91cc6cada955eaa19c9b2493e1872..dca85181f99bf1c7343650846039153a019e7ea9 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) {
@@ -466,6 +473,7 @@ int bam_pileup(int argc, char *argv[])
                        bam_plp_set_mask(iter, d->mask);
                        while ((ret = samread(fp, b)) >= 0) {
                                int skip = 0;
+                               if ((int)b->core.tid < 0) break;
                                // update d->ref if necessary
                                if (d->fai && (int)b->core.tid != d->tid) {
                                        free(d->ref);
@@ -761,7 +769,8 @@ int bam_mpileup(int argc, char *argv[])
        mplp.max_mq = 60;
        mplp.min_baseQ = 13;
        mplp.capQ_thres = 0;
-       while ((c = getopt(argc, argv, "gf:r:l:M:q:Q:uaORC:")) >= 0) {
+       mplp.flag = MPLP_NO_ORPHAN | MPLP_REALN;
+       while ((c = getopt(argc, argv, "gf:r:l:M:q:Q:uaORC:B")) >= 0) {
                switch (c) {
                case 'f':
                        mplp.fai = fai_load(optarg);
@@ -772,6 +781,7 @@ int bam_mpileup(int argc, char *argv[])
                case 'g': mplp.flag |= MPLP_GLF; break;
                case 'u': mplp.flag |= MPLP_NO_COMP | MPLP_GLF; break;
                case 'a': mplp.flag |= MPLP_NO_ORPHAN | MPLP_REALN; break;
+               case 'B': mplp.flag &= ~MPLP_REALN & ~MPLP_NO_ORPHAN; break;
                case 'O': mplp.flag |= MPLP_NO_ORPHAN; break;
                case 'R': mplp.flag |= MPLP_REALN; break;
                case 'C': mplp.capQ_thres = atoi(optarg); break;
@@ -791,6 +801,7 @@ int bam_mpileup(int argc, char *argv[])
                fprintf(stderr, "         -q INT      filter out alignment with MQ smaller than INT [%d]\n", mplp.min_mq);
                fprintf(stderr, "         -g          generate BCF output\n");
                fprintf(stderr, "         -u          do not compress BCF output\n");
+               fprintf(stderr, "         -B          disable BAQ computation\n");
                fprintf(stderr, "\n");
                fprintf(stderr, "Notes: Assuming diploid individuals.\n\n");
                return 1;