//if user gave a namesfile then use it
if (namesfile != "") { readNamesFile(); }
- if (countfile != "") { ct.readTable(countfile); }
+ if (countfile != "") { ct.readTable(countfile, true, false); }
input = new InputData(listfile, "list");
list = input->getListVector();
m->mothurOut(list->getLabel()); m->mothurOutEndLine();
//for each bin in the list vector
+ vector<string> binLabels = list->getLabels();
for (int i = 0; i < list->size(); i++) {
if (m->control_pressed) { return 1; }
}
if (groups.size() != 0) { groupInfo += groups[groups.size()-1]; }
else { groupInfo = "not found"; }
- name = name + "\t" + groupInfo + "\t" + toString(i+1)+ "\tNumRep=" + toString(ct.getNumSeqs(name));
+ name = name + "\t" + groupInfo + "\t" + binLabels[i] + "\tNumRep=" + toString(ct.getNumSeqs(name));
out << ">" << name << endl;
out << sequence << endl;
}else {
- name = name + "\t" + toString(i+1) + "\tNumRep=" + toString(ct.getNumSeqs(name));
+ name = name + "\t" + binLabels[i] + "\tNumRep=" + toString(ct.getNumSeqs(name));
out << ">" << name << endl;
out << sequence << endl;
}
if (sequence != "not found") {
//if you don't have groups
if (groupfile == "") {
- name = name + "\t" + toString(i+1);
+ name = name + "\t" + binLabels[i];
out << ">" << name << endl;
out << sequence << endl;
}else {//if you do have groups
m->mothurOut(name + " is missing from your group file. Please correct. "); m->mothurOutEndLine();
return 1;
}else{
- name = name + "\t" + group + "\t" + toString(i+1);
+ name = name + "\t" + group + "\t" + binLabels[i];
out << ">" << name << endl;
out << sequence << endl;
}