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;
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);
}
gaint gaexpr (char *expr, struct gastat *pst) {
struct gagrid *pgr;
struct gastn *stn;
struct smem *stack;
char *ptr, *pos;
gadouble val;
gaint cmdlen,i,j,rc,curr;
gaint state,cont,err;
gaint size;
if (gaqsig()) return(1);
pass++;
cmdlen = strlen(expr);
/* size = cmdlen * ( 7 + sizeof(struct smem) ); */
size = sizeof(struct smem[cmdlen+10]);
stack = (struct smem *)malloc(size);
if (stack==NULL) {
gaprnt (0,"Memory Allocation Error: parser stack\n");
return (1);
}
state=1;
curr = -1;
pos = expr;
cont=1; err=0;
while (cont) { /* Loop while parsing exprssn */
if (state) { /* Expect operand or '(' */
if (*pos=='(') { /* Handle left paren */
curr++;
stack[curr].type = 2;
pos++;
}
else if (*pos=='-') { /* Handle unary '-' operator */
curr++;
stack[curr].type = -1;
stack[curr].obj.pgr = gagrvl(-1.0);
curr++;
stack[curr].type=1; stack[curr].obj.op = 0;
pos++;
}
else if (*pos>='0' && *pos<='9') { /* Handle numeric value */
if ((ptr=getdbl(pos,&val))==NULL) {
cont=0; err=1;
i = 1 + pos - expr;
gaprnt (0,"Syntax Error: Invalid numeric value\n");
} else {
curr++;
stack[curr].type = -1;
stack[curr].obj.pgr = gagrvl(val);
/* stkdmp(stack,curr); */
rc = eval(0, stack, &curr);
if (rc) {
err=1; cont=0;
}
state = 0;
pos=ptr;
}
}
else if (*pos>='a' && *pos<='z') { /* Handle variable */
if ((ptr=varprs(pos, pst))==NULL) {
cont=0; err=1;
} else {
curr++;
if (pst->type) {
stack[curr].type = -1;
stack[curr].obj.pgr = pst->result.pgr;
} else {
stack[curr].type = -2;
stack[curr].obj.stn = pst->result.stn;
}
/* stkdmp(stack,curr); */
rc = eval(0, stack, &curr);
if (rc) {
err=1; cont=0;
}
state = 0;
pos=ptr;
}
}
else {
cont=0; err=1;
gaprnt (0,"Syntax Error: Expected operand or '('\n");
}
} else { /* Expect operator or ')' */
if (*pos==')') { /* Handle right paren */
curr++;
stack[curr].type = 3;
pos++;
rc = eval(0, stack, &curr); /* Process stack */
if (rc) {
err=1; cont=0;
pos--;
}
}
/* Handle operator */
else if ( (*pos=='*')||(*pos=='/')||(*pos=='+')||(*pos=='-') ) {
curr++;
stack[curr].type=1;
if (*pos=='*') stack[curr].obj.op=0;
if (*pos=='/') stack[curr].obj.op=1;
if (*pos=='+') stack[curr].obj.op=2;
if (*pos=='-') {
stack[curr].obj.op=2;
curr++;
stack[curr].type = -1;
stack[curr].obj.pgr = gagrvl(-1.0);
curr++;
stack[curr].type=1; stack[curr].obj.op = 0;
}
/* stkdmp(stack,curr); */
pos++;
state=1;
}
else {
gaprnt (0,"Syntax Error: Expected operator or ')'\n");
cont=0; err=1;
}
}
if (*pos=='\0'||*pos=='\n') cont=0;
}
if (!err) {
rc = eval(1, stack, &curr);
/* stkdmp(stack,curr); */
if (rc) {
err=1;
} else {
if (curr==0) {
if (stack[0].type == -1) {
pst->type = 1;
pst->result.pgr = stack[0].obj.pgr;
} else if (stack[0].type == -2) {
pst->type = 0;
pst->result.stn = stack[0].obj.stn;
} else {
gaprnt (0,"GAEXPR Logic Error Number 29\n");
err=1;
}
}
else {
gaprnt (0,"Syntax Error: Unmatched Parens\n");
err=1;
}
}
}
if (err) {
if (pass==1) {
i = 1 + pos - expr;
sprintf (pout," Error ocurred at column %i\n",i);
gaprnt (0,pout);
}
/* release any memory still hung off the stack */
for (i=0; i<curr; i++) {
if (stack[i].type==-1) {
pgr = stack[i].obj.pgr;
gagfre(pgr);
} else if (stack[i].type==-2) {
stn = stack[i].obj.stn;
for (j=0; j<BLKNUM; j++) {
if (stn->blks[j] != NULL) free(stn->blks[j]);
}
free(stn);
}
}
}
free(stack);
pass--;
return (err);
}
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) ;
}