void
loadannots()
{
ifstream annots;
annots.open(scangen_args.phenotype_arg);
if (annots.fail()){
cerr << "Cannot open phenotype file: " << strerror(errno) << endl;
exit(EXIT_FAILURE);
}
back_insert_iterator<vstring> dest(phenos);
copy(iisstring(annots),iisstring(),dest);
annots.close();
ifstream glist;
if (species=="droso"){
cout << "Reading droso genes list..." << endl;
glist.open( (scangen_datapath+"/droso/annot/genelist.dat").c_str() );
} else if (species=="eutherian"){
cout << "Reading eutherian genes list..." << endl;
glist.open( (scangen_datapath+"/eutherian/annot/genelist.dat").c_str() );
}
if (glist.fail()){
cerr << "Cannot open gene list file: " << strerror(errno) << endl;
exit(EXIT_FAILURE);
}
back_insert_iterator<vstring> destg(gbacks);
copy(iisstring(glist),iisstring(),destg);
glist.close();
for (ivstring ivs=phenos.begin();ivs!=phenos.end();ivs++){
for (ivstring ivs2=gbacks.begin();ivs2!=gbacks.end();ivs2++){
if (*ivs2==*ivs){
gbacks.erase(ivs2);
break;
}
}
}
// for (ivstring ivs=phenos.begin();ivs!=phenos.end();ivs++){
// cout << *ivs << endl;
// }
}
void
comppheno()
{
// attribute phenotype to CRMs
for (unsigned int i=0;i<nbchrom;i++){
for (ivginst ivg=groupedinst[i].begin();ivg!=groupedinst[i].end();ivg++){
(*ivg).isdiscarded();
if (!(*ivg).discarded){
for (ivstring ivs=phenos.begin();ivs!=phenos.end();ivs++){
if ((*ivg).besttss.gene==*ivs){
(*ivg).goodpheno=1;
break;
} else {
(*ivg).goodpheno=0;
}
}
} else {
(*ivg).goodpheno=0;
}
}
}
return;
}
/*!
* @if jp
* @brief 与えられた文字列リストから重複を削除
* @else
* @brief Eliminate duplication from the given string list
* @endif
*/
vstring unique_sv(vstring sv)
{
return std::for_each(sv.begin(), sv.end(), unique_strvec()).str;
}
