d->max_depth = 0;
d->tid = -1; d->mask = BAM_DEF_MASK;
d->c = bam_maqcns_init();
+ d->c->is_soap = 1; // change the default model
d->ido = bam_maqindel_opt_init();
while ((c = getopt(argc, argv, "st:f:cT:N:r:l:d:im:gI:G:vM:S2aR:P")) >= 0) {
switch (c) {
- case 'a': d->c->is_soap = 1; break;
+ case 'a': d->c->is_soap = 0; break;
case 's': d->format |= BAM_PLF_SIMPLE; break;
case 't': fn_list = strdup(optarg); break;
case 'l': fn_pos = strdup(optarg); break;
fprintf(stderr, "Usage: samtools pileup [options] <in.bam>|<in.sam>\n\n");
fprintf(stderr, "Option: -s simple (yet incomplete) pileup format\n");
fprintf(stderr, " -S the input is in SAM\n");
- fprintf(stderr, " -a use the SOAPsnp model for SNP calling\n");
+ fprintf(stderr, " -a use the MAQ model for SNP calling\n");
fprintf(stderr, " -2 output the 2nd best call and quality\n");
fprintf(stderr, " -i only show lines/consensus with indels\n");
fprintf(stderr, " -m INT filtering reads with bits in INT [%d]\n", d->mask);
typedef struct {
bamFile fp;
- bam_iterf_t iter;
+ bam_iter_t iter;
} mplp_aux_t;
static int mplp_func(void *data, bam1_t *b)
{
mplp_aux_t *ma = (mplp_aux_t*)data;
- if (ma->iter) return bam_iterf_read(ma->fp, ma->iter, b);
+ if (ma->iter) return bam_iter_read(ma->fp, ma->iter, b);
return bam_read1(ma->fp, b);
}
exit(1);
}
if (i == 0) beg0 = beg, end0 = end;
- data[i]->iter = bam_iterf_query(idx, tid, beg, end);
+ data[i]->iter = bam_iter_query(idx, tid, beg, end);
bam_index_destroy(idx);
}
if (i == 0) h = h_tmp;
bam_header_destroy(h);
for (i = 0; i < n; ++i) {
bam_close(data[i]->fp);
- if (data[i]->iter) bam_iterf_destroy(data[i]->iter);
+ if (data[i]->iter) bam_iter_destroy(data[i]->iter);
free(data[i]);
}
free(data); free(plp); free(ref); free(n_plp);