printf("%d\t%d\t", rms_mapq, n);
printf("%s\t%s\t", r->s[0], r->s[1]);
//printf("%d\t%d\t", r->gl[0], r->gl[1]);
- printf("%d\t%d\t%d\n", r->cnt1, r->cnt2, r->cnt_anti);
+ printf("%d\t%d\t%d\t", r->cnt1, r->cnt2, r->cnt_anti);
+ printf("%d\t%d\n", r->cnt_ref, r->cnt_ambi);
bam_maqindel_ret_destroy(r);
}
return 0;
fprintf(stderr, " -i only show lines/consensus with indels\n");
fprintf(stderr, " -m INT filtering reads with bits in INT [%d]\n", d->mask);
fprintf(stderr, " -M INT cap mapping quality at INT [%d]\n", d->c->cap_mapQ);
- fprintf(stderr, " -t FILE list of reference sequences (assume the input is in SAM)\n");
+ fprintf(stderr, " -t FILE list of reference sequences (force -S)\n");
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");
}
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_fa && is_SAM && fn_list == 0) fn_list = samfaipath(fn_fa);
+
{
samfile_t *fp;
fp = is_SAM? samopen(argv[optind], "r", fn_list) : samopen(argv[optind], "rb", 0);