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 ;
phandle *ph ;
int t ;
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") ;
}
}
if (parname==NULL) {
fprintf(stderr, "no parameters\n") ;
return ;
}
pcheck(parname,'p') ;
printf("parameter file: %s\n", parname) ;
ph = openpars(parname) ;
dostrsub(ph) ;
getstring(ph, "genotypename:", &genotypename) ;
getstring(ph, "snpname:", &snpname) ;
getstring(ph, "indivname:", &indivname) ;
getstring(ph, "poplistname:", &poplistname) ;
getstring(ph, "snpeigname:", &snpeigname) ;
getstring(ph, "snpweightoutname:", &snpeigname) ; /* changed 09/18/07 */
getstring(ph, "output:", &outputname) ;
getstring(ph, "outputvecs:", &outputname) ;
getstring(ph, "evecoutname:", &outputname) ; /* changed 11/02/06 */
getstring(ph, "outputvals:", &outputvname) ;
getstring(ph, "evaloutname:", &outputvname) ; /* changed 11/02/06 */
getstring(ph, "badsnpname:", &badsnpname) ;
getstring(ph, "outliername:", &outliername) ;
getstring(ph, "outlieroutname:", &outliername) ; /* changed 11/02/06 */
getstring(ph, "phylipname:", &phylipname) ;
getstring(ph, "phylipoutname:", &phylipname) ; /* changed 11/02/06 */
getstring(ph, "weightname:", &weightname) ;
getstring(ph, "fstdetailsname:", &fstdetailsname) ;
getdbl(ph, "relthresh:", &relthresh) ;
getint(ph, "numeigs:", &numeigs) ;
getint(ph, "numoutevec:", &numeigs) ; /* changed 11/02/06 */
getint(ph, "markerscore:", &markerscore) ;
getint(ph, "chisqmode:", &chisqmode) ;
getint(ph, "missingmode:", &missingmode) ;
getint(ph, "fancynorm:", &fancynorm) ;
getint(ph, "usenorm:", &fancynorm) ; /* changed 11/02/06 */
getint(ph, "dotpopsmode:", &dotpopsmode) ;
getint(ph, "pcorrmode:", &pcorrmode) ; /* print correlations */
getint(ph, "pcpopsonly:", &pcpopsonly) ; /* but only within population */
getint(ph, "altnormstyle:", &altnormstyle) ;
getint(ph, "hashcheck:", &hashcheck) ;
getint(ph, "popgenmode:", &altnormstyle) ;
getint(ph, "noxdata:", &noxdata) ;
t = -1 ;
getint(ph, "xdata:", &t) ; if (t>=0) noxdata = 1-t ;
getint(ph, "nostatslim:", &nostatslim) ;
getint(ph, "popsizelimit:", &popsizelimit) ;
getint(ph, "minallelecnt:", &minallelecnt) ;
getint(ph, "chrom:", &xchrom) ;
getint(ph, "lopos:", &lopos) ;
getint(ph, "hipos:", &hipos) ;
getint(ph, "checksizemode:", &checksizemode) ;
getint(ph, "pubmean:", &pubmean) ;
getint(ph, "fstonly:", &fstonly) ;
getint(ph, "fsthiprecision:", &fsthiprec) ;
getint(ph, "ldregress:", &ldregress) ;
getint(ph, "nsnpldregress:", &ldregress) ; /* changed 11/02/06 */
getdbl(ph, "ldlimit:", &ldlimit) ; /* in morgans */
getdbl(ph, "maxdistldregress:", &ldlimit) ; /* in morgans */ /* changed 11/02/06 */
getint(ph, "minleneig:", &nostatslim) ;
getint(ph, "malexhet:", &malexhet) ;
getint(ph, "nomalexhet:", &malexhet) ; /* changed 11/02/06 */
getint(ph, "familynames:", &familynames) ;
getint(ph, "numoutliter:", &numoutliter) ;
getint(ph, "numoutlieriter:", &numoutliter) ; /* changed 11/02/06 */
getint(ph, "numoutleigs", &numoutleigs) ;
getint(ph, "numoutlierevec:", &numoutleigs) ; /* changed 11/02/06 */
getdbl(ph, "outlthresh:", &outlthresh) ;
getdbl(ph, "outliersigmathresh:", &outlthresh) ; /* changed 11/02/06 */
getdbl(ph, "blgsize:", &blgsize) ;
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) ;
getint(ph, "outputgroup:", &ogmode) ;
getint(ph, "packout:", &packout) ; /* now obsolete 11/02/06 */
getstring(ph, "twxtabname:", &twxtabname) ;
getdbl(ph, "r2thresh:", &r2thresh) ;
getdbl(ph, "r2genlim:", &r2genlim) ;
getdbl(ph, "r2physlim:", &r2physlim) ;
getint(ph, "killr2:", &killr2) ;
getint(ph, "numchrom:", &numchrom) ;
printf("### THE INPUT PARAMETERS\n");
printf("##PARAMETER NAME: VALUE\n");
writepars(ph);
}
void readcommands(int argc, char **argv)
{
int i,haploid=0;
phandle *ph ;
char str[5000] ;
char *tempname ;
int n, t ;
while ((i = getopt (argc, argv, "f:b:p:g:s:o:vVx")) != -1) {
switch (i)
{
case 'p':
parname = strdup(optarg) ;
break;
case 'f':
snpdetailsname = strdup(optarg) ;
break;
case 'g':
graphname = strdup(optarg) ;
break;
case 'o':
graphoutname = strdup(optarg) ;
break;
case 's':
seed = atoi(optarg) ;
break;
case 'b':
baseval = atof(optarg) ;
break;
case 'v':
printf("version: %s\n", WVERSION) ;
break;
case 'x':
doanalysis = NO ;
break;
case 'V':
verbose = YES ;
break;
case '?':
printf ("Usage: bad params.... \n") ;
fatalx("bad params\n") ;
}
}
if (parname==NULL) {
fprintf(stderr, "no parameters\n") ;
return ;
}
pcheck(parname,'p') ;
printf("parameter file: %s\n", parname) ;
ph = openpars(parname) ;
dostrsub(ph) ;
getstring(ph, "genotypename:", &genotypename) ;
getstring(ph, "snpname:", &snpname) ;
getstring(ph, "indivname:", &indivname) ;
getstring(ph, "graphname:", &graphname) ;
getstring(ph, "graphoutname:", &graphoutname) ;
int numeg = 4 ;
getstring(ph, "snpdetailsname:", &snpdetailsname) ;
getstring(ph, "outpop:", &outpop) ;
getstring(ph, "output:", &outputname) ;
getstring(ph, "badsnpname:", &badsnpname) ;
getstring(ph, "popfilename:", &popfilename) ;
getstring(ph, "f3log:", &f3name) ;
getstring(ph, "root:", &rootname) ;
getdbl(ph, "blgsize:", &blgsize) ;
getdbl(ph, "diag:", &diag) ;
getdbl(ph, "f2diag:", &f2diag) ;
getdbl(ph, "minvar:", &minvar) ;
getint(ph, "bigiter:", &bigiter) ;
getint(ph, "inbreed:", &inbreed) ;
getint(ph, "startiter:", &startiter) ;
getint(ph, "fancynorm:", &fancynorm) ;
getint(ph, "noxdata:", &noxdata) ;
t = -1 ;
getint(ph, "xdata:", &t) ; if (t>=0) noxdata = 1-t ;
getint(ph, "chrom:", &xchrom) ;
getint(ph, "nochrom:", &zchrom) ;
getint(ph, "doanalysis:", &doanalysis) ;
getint(ph, "quartet:", &quartet) ;
getint(ph, "nostatslim:", &nostatslim) ;
getint(ph, "popsizelimit:", &popsizelimit) ;
getint(ph, "gfromp:", &gfromp) ; // gen dis from phys
getint(ph, "seed:", &seed) ;
getint(ph, "details:", &details) ;
getint(ph, "forcezmode:", &forcezmode) ;
getint(ph, "dzeromode:", &dzeromode) ;
getdbl(ph, "baseval:", &baseval) ;
getdbl(ph, "jackquart:", &jackquart) ;
getint(ph, "jackweight:", &jackweight) ;
getint(ph, "pubjack:", &pubjack) ;
getstring(ph, "dumpname:", &dumpname) ;
getstring(ph, "loadname:", &loadname) ;
printf("### THE INPUT PARAMETERS\n");
printf("##PARAMETER NAME: VALUE\n");
writepars(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,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) ;
}
