m->mothurOut("\n[NOTE]: The count file should contain only unique names, so mothur assumes your fasta, list and taxonomy files also contain only uniques.\n\n");
}
CountTable ct;
- ct.readTable(countfile, true);
+ ct.readTable(countfile, true, false);
if (!ct.hasGroupInfo()) { m->mothurOut("[ERROR]: your count file does not contain group info, aborting.\n"); return 0; }
vector<string> gNamesOfGroups = ct.getNamesOfGroups();
m->setGroups(groupsToKeep);
m->clearAllGroups();
m->saveNextLabel = "";
- m->printedHeaders = false;
- m->currentBinLabels.clear();
- m->binLabelsInFile.clear();
+ m->printedSharedHeaders = false;
+ m->currentSharedBinLabels.clear();
+ m->sharedBinLabelsInFile.clear();
InputData input(sharedfile, "sharedfile");
lookup = input.getSharedRAbundVectors();