doinit.c
  case 'a': m_msg->aln.showall = 1;
  case 'B': m_msg->z_bits = 0;
  case 'b': m_msg->mshow
  case 'C': m_msg->nmlen
  case 'd': m_msg->ashow);
  case 'D': ppst->debug_lib = 1;
  case 'E': m_msg->e_cut
  case 'F': m_msg->e_low
  case 'f': ppst->gdelval
  case 'g': ppst->ggapval
  case 'H':  m_msg->nohist = 1; break;
  case 'i':  m_msg->revcomp = 1; break;
  case 'I':  m_msg->self = 1; break;
  case 'J':  m_msg->ql_start, ql_stop
  case 'K':  max_buf_cnt (PCOMPLIB)
  case 'l':  m_msg->flstr
  case 'L':  m_msg->long_info = 1
  case 'M':  m_msg->n1_low,&m_msg->n1_high
  case 'm':  m_msg->markx
  case 'n':  m_msg->qdnaseq = 1
  case 'N':  m_msg->maxn
  case 'p':  m_msg->qdnaseq = 0;
  case 'O':  m_msg->outfile
  case 'q':
  case 'Q':  m_msg->quiet = 1;
  case 'r':  ppst->p_d_mat,&ppst->p_d_mis
  case 'R':  m_msg->dfile
  case 's':  standard_pam(smstr); ppst->pamoff=atoi(bp+1);
  case 'S':  ppst->ext_sq_set = 1;
  case 't':  ppst->tr_type
  case 'T':  PCOMPLIB: worker_1,worker_n
      	     _t: max_workers
  case 'v':  ppst->zs_win
  case 'w':  m_msg->aln.llen
  case 'W':  m_msg->aln.llcntx);
  case 'X':  m_msg->sq0off,&m_msg->sq1off
  case 'x':  ppst->pam_x
  case 'z':  ppst->zsflag
  case 'Z':  ppst->zdb_size

initfa.c
  case '1': ppst->param_u.fa.iniflag=1;
  case '3': m_msg->nframe = 3; /* TFASTA */
	    m_msg->nframe = 1;	/* for TFASTXY */
	    m_msg->qframe = 1;  /* for FASTA, FASTX */
  case 'A': ppst->sw_flag= 1;
  case 'c': ppst->param_u.fa.optcut
  case 'h': ppst->gshift
  case 'j': ppst->gsubs
  case 'o': ppst->param_u.fa.optflag = 0;
  case 'y': ppst->param_u.fa.optwid

initsw.c
  case '3': m_msg->qframe = m_msg->nframe = 1;