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, " -l FILE list of sites at which pileup is output\n");
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, " -l FILE list of sites at which pileup is output\n");