void readcommands(int argc, char **argv)
{
int i;
char *parname = NULL ;
phandle *ph ;
char str[5000] ;
char *tempname ;
int n ;
while ((i = getopt (argc, argv, "p:vV")) != -1) {
switch (i)
{
case 'p':
parname = strdup(optarg) ;
break;
case 'v':
printf("version: %s\n", WVERSION) ;
break;
case 'V':
verbose = YES ;
break;
case '?':
printf ("Usage: bad params.... \n") ;
fatalx("bad params\n") ;
}
}
pcheck(parname,'p') ;
printf("parameter file: %s\n", parname) ;
ph = openpars(parname) ;
dostrsub(ph) ;
getint(ph, "packmode:", &packmode) ; // controls internals
getstring(ph, "genotypename:", &genotypename) ;
getstring(ph, "snpname:", &snpname) ;
getstring(ph, "indivname:", &indivname) ;
getstring(ph, "pcaname:", &pcaname) ;
getint(ph, "numpc:", &numpc) ;
getint(ph, "qtmode:", &qtmode) ;
getint(ph, "hashcheck:", &hashcheck) ;
getstring(ph, "outputname:", &outputname);
writepars(ph) ;
closepars(ph) ;
}
int
main (int argc , char **argv)
{
phandle *ph ;
char *parname ;
parname = strdup("actpar") ;
ph = openpars(parname) ;
writepars(ph) ;
printf("\n\n") ;
dostrsub(ph) ;
writepars(ph) ;
closepars(ph) ;
}
void readcommands(int argc, char **argv)
{
int i,haploid=0;
char *parname = NULL ;
phandle *ph ;
char str[5000] ;
char *tempname ;
int n ;
while ((i = getopt (argc, argv, "p:vVf")) != -1) {
switch (i)
{
case 'p':
parname = strdup(optarg) ;
break;
case 'v':
printf("version: %s\n", WVERSION) ;
break;
case 'V':
verbose = YES ;
break;
case 'f':
phasedmode = YES ;
break;
case '?':
printf ("Usage: bad params.... \n") ;
fatalx("bad params\n") ;
}
}
pcheck(parname,'p') ;
printf("parameter file: %s\n", parname) ;
ph = openpars(parname) ;
dostrsub(ph) ;
getstring(ph, "geno1:", &geno1) ;
getstring(ph, "snp1:", &snp1) ;
getstring(ph, "ind1:", &ind1) ;
getstring(ph, "geno2:", &geno2) ;
getstring(ph, "snp2:", &snp2) ;
getstring(ph, "ind2:", &ind2) ;
getstring(ph, "indoutfilename:", &indoutfilename) ;
getstring(ph, "indivoutname:", &indoutfilename) ;
getstring(ph, "snpoutfilename:", &snpoutfilename) ;
getstring(ph, "snpoutname:", &snpoutfilename) ;
getstring(ph, "genooutfilename:", &genooutfilename) ;
getstring(ph, "genotypeoutname:", &genooutfilename) ;
getstring(ph, "outputformat:", &omode) ;
getint(ph, "docheck:", &docheck) ;
getint(ph, "hashcheck:", &hashcheck) ;
getint(ph, "strandcheck:", &strandcheck) ;
getint(ph, "phasedmode:", &phasedmode) ;
writepars(ph) ;
closepars(ph) ;
}
void
readcommands (int argc, char **argv)
{
int i;
char *parname = NULL;
phandle *ph;
while ((i = getopt (argc, argv, "i:o:p:n:m:t:V")) != -1)
{
switch (i)
{
case 'i':
iname = strdup (optarg);
break;
case 'o':
oname = strdup (optarg);
break;
case 't':
twxtab = strdup (optarg);
break;
case 'n':
nval = atof (optarg);
break;
case 'm':
minleneig = atoi (optarg);
break;
case 'p':
parname = strdup (optarg);
break;
case 'V':
verbose = YES;
break;
case '?':
printf ("Usage: bad params.... \n");
fatalx ("bad params\n");
}
}
if (parname == NULL)
return;
printf ("parameter file: %s\n", parname);
ph = openpars (parname);
getstring (ph, "input:", &iname);
getstring (ph, "output:", &oname);
getdbl (ph, "nval:", &nval);
getint (ph, "minleneig:", &minleneig);
writepars (ph);
closepars (ph);
}
void readcommands(int argc, char **argv)
{
int i,haploid=0;
char *parname = NULL ;
phandle *ph ;
char str[5000] ;
char *tempname ;
int n ;
while ((i = getopt (argc, argv, "p:vV")) != -1) {
switch (i)
{
case 'p':
parname = strdup(optarg) ;
break;
case 'v':
printf("version: %s\n", WVERSION) ;
break;
case 'V':
verbose = YES ;
break;
case '?':
printf ("Usage: bad params.... \n") ;
fatalx("bad params\n") ;
}
}
pcheck(parname,'p') ;
printf("parameter file: %s\n", parname) ;
ph = openpars(parname) ;
dostrsub(ph) ;
/**
DIR2: /fg/nfiles/admixdata/ms2
SSSS: DIR2/outfiles
genotypename: DIR2/autos_ccshad_fakes
eglistname: DIR2/eurlist
output: eurout
*/
getstring(ph, "genotypename:", &genotypename) ;
getstring(ph, "genotypelist:", &genotypelist) ;
getstring(ph, "snpname:", &snpname) ;
getstring(ph, "indivname:", &indivname) ;
getstring(ph, "badsnpname:", &badsnpname) ;
getstring(ph, "flipsnpname:", &flipsnpname) ;
getstring(ph, "flipstrandname:", &flipstrandname) ;
getstring(ph, "indoutfilename:", &indoutfilename) ;
getstring(ph, "indivoutname:", &indoutfilename) ; /* changed 11/02/06 */
getstring(ph, "snpoutfilename:", &snpoutfilename) ;
getstring(ph, "snpoutname:", &snpoutfilename) ; /* changed 11/02/06 */
getstring(ph, "genooutfilename:", &genooutfilename) ;
getstring(ph, "genotypeoutname:", &genooutfilename) ; /* changed 11/02/06 */
getstring(ph, "outputformat:", &omode) ;
getstring(ph, "outputmode:", &omode) ;
getstring(ph, "polarize:", &polarid) ;
getint(ph, "zerodistance:", &zerodistance) ;
getint(ph, "checksizemode:", &checksizemode) ;
getint(ph, "badpedignore:", &badpedignore) ;
getint(ph, "numchrom:", &numchrom) ;
getstring(ph, "xregionname:", &xregionname) ;
getdbl(ph, "hwfilter:", &nhwfilter) ;
getstring(ph, "deletesnpoutname:", &deletesnpoutname);
getint(ph, "outputgroup:", &ogmode) ;
getint(ph, "malexhet:", &malexhet) ;
getint(ph, "nomalexhet:", &malexhet) ; /* changed 11/02/06 */
getint(ph, "tersemode:", &tersem) ;
getint(ph, "familynames:", &familynames) ;
getint(ph, "packout:", &packout) ; /* now obsolete 11/02/06 */
getint(ph, "decimate:", &decim) ;
getint(ph, "dmindis:", &dmindis) ;
getint(ph, "dmaxdis:", &dmaxdis) ;
getint(ph, "fastdup:", &fastdup) ;
getint(ph, "flipreference:", &flipreference) ;
getint(ph, "fastdupnum:", &fastdupnum) ;
getdbl(ph, "fastdupthresh:", &fastdupthresh) ;
getdbl(ph, "fastdupkill:", &fastdupkill) ;
getint(ph, "killr2:", &killr2) ;
getint(ph, "hashcheck:", &hashcheck) ;
getint(ph, "outputall:", &outputall) ;
getint(ph, "sevencolumnped:", &sevencolumnped) ;
getint(ph, "phasedmode:", &phasedmode) ;
getdbl(ph, "r2thresh:", &r2thresh) ;
getdbl(ph, "r2genlim:", &r2genlim) ;
getdbl(ph, "r2physlim:", &r2physlim) ;
getint(ph, "chrom:", &xchrom) ;
getint(ph, "lopos:", &lopos) ;
getint(ph, "hipos:", &hipos) ;
getint(ph, "minchrom:", &minchrom) ;
getint(ph, "maxchrom:", &maxchrom) ;
getdbl(ph, "maxmissfrac:", &maxmissfrac) ;
getint(ph, "maxmissing:", &maxmiss) ;
getstring(ph, "poplistname:", &poplistname) ;
getstring(ph, "newsnpname:", &newsnpname) ;
getstring(ph, "newindivname:", &newindivname) ;
getint(ph, "deletedup:", &deletedup) ;
getint(ph, "mkdiploid:", &mkdiploid) ;
writepars(ph) ;
closepars(ph) ;
}
