try{
vector<string> reps;
string rep = "notFound";
+
+ if (m->debug) { m->mothurOut("[DEBUG]: group=" + group + " names.size() = " + toString(names.size()) + " " + names[0] + "\n"); }
if ((names.size() == 1)) {
return names[0];
if (countfile != "") { //if countfile is not blank then we can assume the list file contains only uniques, otherwise we assume list file contains everyone.
int numRep = 0;
if (group != "") { numRep = ct.getGroupCount(names[i], group); }
- else { numRep = ct.getGroupCount(names[i]); }
+ else { numRep = ct.getNumSeqs(names[i]); }
if (numRep > maxAbund) {
reps.clear();
reps.push_back(names[i]);
if (countfile != "") { //if countfile is not blank then we can assume the list file contains only uniques, otherwise we assume list file contains everyone.
int numRep = 0;
if (group != "") { numRep = ct.getGroupCount(names[i], group); }
- else { numRep = ct.getGroupCount(names[i]); }
+ else { numRep = ct.getNumSeqs(names[i]); }
for (int j = 1; j < numRep; j++) { //don't add yourself again
seqIndex.push_back(nameToIndex[names[i]]);
}