read->read(nameMap);
}else if (countfile != "") {
ct = new CountTable();
- ct->readTable(countfile);
+ ct->readTable(countfile, false);
read->read(ct);
}else { read->read(nameMap); }
map<string, string> variables;
variables["[filename]"] = fileroot;
- if (countfile != "") { variables["[tag2]"] = "unique_list"; }
variables["[clustertag]"] = tag;
string sabundFileName = getOutputFileName("sabund", variables);
string rabundFileName = getOutputFileName("rabund", variables);
+ if (countfile != "") { variables["[tag2]"] = "unique_list"; }
string listFileName = getOutputFileName("list", variables);
if (countfile == "") {