ifstream inName;
m->openInputFile(nameFile, inName);
- string first, second;
+ //string first, second;
int countName = 0;
set<string> thisnames1;
else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
if (pairDone) { //save one line
+ if (m->debug) { m->mothurOut("[DEBUG]: reading names: " + firstCol + '\t' + secondCol + ".\n"); }
vector<string> names;
- m->splitAtChar(second, names, ',');
+ m->splitAtChar(secondCol, names, ',');
//get aligned string for these seqs from the fasta file
string alignedString = "";