while ((c = getopt(argc, argv, "FN1:l:cC:eHAGvbSuP:t:p:QgLi:IMs:D:U:X:d:T:Ywm:K:")) >= 0) {
switch (c) {
case '1': vc.n1 = atoi(optarg); break;
while ((c = getopt(argc, argv, "FN1:l:cC:eHAGvbSuP:t:p:QgLi:IMs:D:U:X:d:T:Ywm:K:")) >= 0) {
switch (c) {
case '1': vc.n1 = atoi(optarg); break;
case 'D': vc.fn_dict = strdup(optarg); break;
case 'F': vc.flag |= VC_FIX_PL; break;
case 'N': vc.flag |= VC_ACGT_ONLY; break;
case 'D': vc.fn_dict = strdup(optarg); break;
case 'F': vc.flag |= VC_FIX_PL; break;
case 'N': vc.flag |= VC_ACGT_ONLY; break;
vc.sublist = calloc(vc.n_sub, sizeof(int));
hout = bcf_hdr_subsam(hin, vc.n_sub, vc.subsam, vc.sublist);
}
vc.sublist = calloc(vc.n_sub, sizeof(int));
hout = bcf_hdr_subsam(hin, vc.n_sub, vc.subsam, vc.sublist);
}