std::vector<iArray*> getTestIndividuals(const char *pName){
iArray *testList = typecast_stringarray_to_iArray(readarray(std::string(pName)));
int numTrues=0;
for(int i=0;i<testList->x;i++)
if(testList->array[i])
numTrues++;
//printf("numTrues:%d\n",numTrues);
//testList->print("testlist",NULL);
std::vector<iArray*> returnVal;
int pos1 = getNext(testList,0);
while(pos1!=-1){
int pos2 = getNext(testList,pos1+1);
while(pos2!=-1){
if(pos2!=-1){
//printf("p1:%d\tp2:%d\n",pos1,pos2);
iArray *pr = allocIntArray(2);
pr->array[0]=pos1;pr->array[1]=pos2;
returnVal.push_back(pr);
}
pos2 = getNext(testList,pos2+1);
}
pos1 = getNext(testList,pos1+1);
}
killArray(testList);
return returnVal;
}
int main(int argc, char *argv[]){
toCargs *pars;
if(argc<12){
std::cout << "\t-> Please input -g GENOTYPEFILE -LD {0,1} -back BACK -threshold prune_val -filename OUTPUTDATA -snps KEEPLIST\n";
return 0;
}
//get commandline args
pars = readArgs(argc,argv);
pars->doPrune = 1;
//check if fileexists
if(fexists(pars->data_filename)){
printf("\t-> outputfile:%s exists, will exit\n",pars->data_filename.c_str());
return 0;
}
if(fexists(pars->usedSnps_filename)){
printf("\t-> outputfile:%s exists will exit\n",pars->usedSnps_filename.c_str());
return 0;
}
//run prune
prune object;
print_functionPars(pars);
fromCres *fromObject = object.main_run(pars);
//write results
write_iMatrix_to_file(pars->data_filename,fromObject->data);
write_iArray_to_file(pars->usedSnps_filename,fromObject->usedSnps);
killArray(fromObject->usedSnps);
killMatrix(fromObject->data);
killMatrix(pars->data);
return 0;
}
