nameMap->readMap();
}else if (countfile != "") {
ct = new CountTable();
- ct->readTable(countfile, false);
+ ct->readTable(countfile, false, false);
nameMap= new NameAssignment();
vector<string> tempNames = ct->getNamesOfSeqs();
for (int i = 0; i < tempNames.size(); i++) { nameMap->push_back(tempNames[i]); }