- Sequence* q = new Sequence(query->getName(), query->getAligned());
- Sequence* leftParent = new Sequence(refSeqs[i]->getName(), refSeqs[i]->getAligned());
- Sequence* rightParent = new Sequence(refSeqs[j]->getName(), refSeqs[j]->getAligned());
+ Sequence q(query.getName(), query.getAligned());
+ Sequence leftParent(refSeqs[i].getName(), refSeqs[i].getAligned());
+ Sequence rightParent(refSeqs[j].getName(), refSeqs[j].getAligned());
+
+ //cout << q->getName() << endl << q->getAligned() << endl << endl;
+ //cout << leftParent.getName() << '\t' << leftParent.getAligned().length() << endl << endl;
+ //cout << rightParent.getName() << '\t' << rightParent.getAligned().length() << endl << endl;
+ //cout << q.getName() << '\t' << q.getAligned().length() << endl << endl;
+ //cout << rightParent->getName() << endl << rightParent->getAligned() << endl << endl;
+ //cout << " length = " << rightParent->getAligned().length() << endl;