temp = validParameter.validFile(parameters, "trim", false); if (temp == "not found") { temp = "f"; }
trim = m->isTrue(temp);
- temp = validParameter.validFile(parameters, "split", false); if (temp == "not found") { temp = "f"; }
+ temp = validParameter.validFile(parameters, "split", false); if (temp == "not found") { temp = "f"; }
trimera = m->isTrue(temp);
search = validParameter.validFile(parameters, "search", false); if (search == "not found") { search = "distance"; }
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();
query->setAligned("");
//trim topMatches
for (int i = 0; i < topMatches.size(); i++) {