* samtools-0.1.3-3 (r240)

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 5f20c1ead0f156ce85eb3d771e0b2a0106e6bb53..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) {
@@ -280,7 +280,7 @@ int bam_pileup(int argc, char *argv[])
                fprintf(stderr, "        -l FILE   list of sites at which pileup is output\n");
                fprintf(stderr, "        -f FILE   reference sequence in the FASTA format\n\n");
                fprintf(stderr, "        -c        output the maq consensus sequence\n");
-               fprintf(stderr, "        -g        output in the extended GLT format (suppressing -c/-i/-s)\n");
+               fprintf(stderr, "        -g        output in the GLFv3 format (suppressing -c/-i/-s)\n");
                fprintf(stderr, "        -T FLOAT  theta in maq consensus calling model (for -c/-g) [%f]\n", d->c->theta);
                fprintf(stderr, "        -N INT    number of haplotypes in the sample (for -c/-g) [%d]\n", d->c->n_hap);
                fprintf(stderr, "        -r FLOAT  prior of a difference between two haplotypes (for -c/-g) [%f]\n", d->c->het_rate);
@@ -292,7 +292,7 @@ int bam_pileup(int argc, char *argv[])
        }
        if (fn_fa) d->fai = fai_load(fn_fa);
        free(fn_fa);
-       bam_maqcns_prepare(d->c);
+       if (d->format & (BAM_PLF_CNS|BAM_PLF_GLF)) bam_maqcns_prepare(d->c);
        if (d->format & BAM_PLF_GLF) {
                glf3_header_t *h;
                h = glf3_header_init();
@@ -300,7 +300,7 @@ int bam_pileup(int argc, char *argv[])
                glf3_header_write(d->fp, h);
                glf3_header_destroy(h);
        }
-       if (d->fai == 0)
+       if (d->fai == 0 && (d->format & (BAM_PLF_CNS|BAM_PLF_INDEL_ONLY)))
                fprintf(stderr, "[bam_pileup] indels will not be called when -f is absent.\n");
        if (fn_list) { // the input is SAM
                tamFile fp;
@@ -322,6 +322,10 @@ int bam_pileup(int argc, char *argv[])
                bamFile fp;
                fp = (strcmp(argv[optind], "-") == 0)? bam_dopen(fileno(stdin), "r") : bam_open(argv[optind], "r");
                d->h = bam_header_read(fp);
+               if (d->h == 0) {
+                       fprintf(stderr, "[bam_pileup] fail to read the BAM header. Abort!\n");
+                       return 1;
+               }
                if (fn_pos) d->hash = load_pos(fn_pos, d->h);
                bam_pileup_file(fp, d->mask, pileup_func, d);
                bam_close(fp);