-//ofstream out;
-//string name = toString(numi+1);
-//cout << name << endl;
-//name = name.substr(name.find_first_of("|")+1);
-//cout << name << endl;
-//name = name.substr(name.find_first_of("|")+1);
-//cout << name << endl;
-//name = name.substr(0, name.find_last_of("|"));
-//cout << name << endl;
-//string filename = name + ".seqsformaligner";
-//openOutputFile(filename, out);
-//for (int u = 0; u < refSeqs.size(); u++) { refSeqs[u]->printSequence(out); }
-//out.close();
-//filename = name + ".fasta";
-//openOutputFile(filename, out);
-//query->printSequence(out);
-//out.close();
-
-//for (int i = 0; i < refSeqs.size(); i++) { cout << refSeqs[i]->getName() << endl; }
-//cout << "before = " << refSeqs.size() << endl;