vector<results> Results = maligner->getOutput();
//realign query to parents to improve slayers detection rate
- //ChimeraReAligner realigner(templateSeqs, match, misMatch);
- //realigner.reAlign(query, Results);
-
+ ChimeraReAligner realigner(templateSeqs, match, misMatch);
+ realigner.reAlign(query, Results);
+cout << query->getName() << '\n' << query->getAligned() << endl;
//if (chimeraFlag == "yes") {
//get sequence that were given from maligner results