mothurOut("Done."); mothurOutEndLine();
}else { createProcessesPairs(); }
-string o = "closestmatch.eachgap.fasta";
-ofstream out7;
-openOutputFile(o, out7);
+//string o = "closestmatch.eachgap.fasta";
+//ofstream out7;
+//openOutputFile(o, out7);
-for (int i = 0; i < bestfit.size(); i++) {
- out7 << ">" << querySeqs[i]->getName() << "-"<< bestfit[i]->getName() << endl;
- out7 << bestfit[i]->getAligned() << endl;
-}
-out7.close();
+//for (int i = 0; i < bestfit.size(); i++) {
+ //out7 << ">" << querySeqs[i]->getName() << "-"<< bestfit[i]->getName() << endl;
+ //out7 << bestfit[i]->getAligned() << endl;
+//}
+//out7.close();
//find P
mothurOut("Getting conservation... "); cout.flush();
if (consfile == "") {