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) ; }