void extern readPhenoFile(vector<Individual*>& sample, vector<Locus*>& locus, vector<CSNP*>& snp)
{
par.qt = false;
par.bt = true;
checkFileExists(par.phenofile);
ifstream PHE(par.phenofile.c_str(), ios::in);
map<string, Individual*> uid;
map<string, Individual*>::iterator ii;
for(int i=0; i<sample.size(); i++)
{
uid.insert(make_pair(sample[i]->fid+"_"+sample[i]->iid, sample[i]));
sample[i]->phenotype = -9;
sample[i]->phenotypes.resize(0);
sample[i]->missing = true;
}
vector<int> pheno_idx;
pheno_idx.resize(0);
if(par.pheno_names.size()>0)
{
string pfid, piid, ph;
char cline[par.MAX_LINE_LENGTH];
PHE.getline(cline, par.MAX_LINE_LENGTH, '\n');
string sline = cline;
if(sline!="")
{
string buf;
stringstream ss(sline);
vector<string> tokens;
while(ss>>buf)
tokens.push_back(buf);
if(tokens[0] != "FID")
error("First header field must be FID");
if(tokens[1] != "IID")
error("Second header field must be IID");
for(int j=0; j<par.pheno_names.size(); j++)
for(int i=2; i<tokens.size(); i++)
if(tokens[i] == par.pheno_names[j])
{
pheno_idx.push_back(i-1);
}
if(pheno_idx.size()<par.pheno_names.size())
error("Did not find phenotypes");
} // end of if sline != ""
int
_ecore_thread_win32_join(win32_thread *x,
void **res)
{
if (!PHE(x, PHS()))
{
WaitForSingleObject(x->thread, INFINITE);
CloseHandle(x->thread);
}
if (res) *res = x->val;
free(x);
return 0;
}
