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());
- //cout << "parents: (" << refSeqs[i]->getName() << ", " << refSeqs[j]->getName() << ")\n";
+
map<int, int> spots; //map from spot in original sequence to spot in filtered sequence for query and both parents
vector<data_struct> divs = runBellerophon(q, leftParent, rightParent, spots);
- //cout << divs.size() << endl;
- if (m->control_pressed) {
- delete q;
- delete leftParent;
- delete rightParent;
- return "no";
- }
+
+ if (m->control_pressed) { delete q; delete leftParent; delete rightParent; return "no"; }
-// cout << divs.size() << endl;
vector<data_struct> selectedDivs;
for (int k = 0; k < divs.size(); k++) {
vector<snps> snpsLeft = getSNPS(divs[k].parentA.getAligned(), divs[k].querySeq.getAligned(), divs[k].parentB.getAligned(), divs[k].winLStart, divs[k].winLEnd);
vector<snps> snpsRight = getSNPS(divs[k].parentA.getAligned(), divs[k].querySeq.getAligned(), divs[k].parentB.getAligned(), divs[k].winRStart, divs[k].winREnd);
- //cout << refSeqs[i]->getName() << '\t' << refSeqs[j]->getName() << '\t' << k << divs[k].parentA.getAligned() << endl << divs[k].parentB.getAligned() << endl;
+
if (m->control_pressed) { delete q; delete leftParent; delete rightParent; return "no"; }
int numSNPSLeft = snpsLeft.size();