map<int, int> trimmedPos;
//check to make sure that is not whole seq
if ((rearPos - frontPos - 1) <= 0) {
- m->mothurOut("[ERROR]: when I trim " + query->getName() + ", the entire sequence is trimmed. Skipping."); m->mothurOutEndLine();
+ //m->mothurOut("[ERROR]: when I trim " + query->getName() + ", the entire sequence is trimmed. Skipping."); m->mothurOutEndLine();
query->setAligned("");
//trim topMatches
for (int i = 0; i < topMatches.size(); i++) {