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());
-
+
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);
delete rightParent;
return "no";
}
-
+
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);
}
}
-
// compute bootstrap support
if (all.size() > 0) {
//sort them
string parentA = pA->getAligned();
string parentB = pB->getAligned();
int length = query.length();
-//cout << q->getName() << endl << q->getAligned() << endl << endl;
-//cout << pA->getName() << endl << pA->getAligned() << endl << endl;
-//cout << pB->getName() << endl << pB->getAligned() << endl << endl;
-//cout << " length = " << length << endl;
-//cout << q->getName() << endl;
-//cout << pA->getName() << '\t';
-//cout << pB->getName() << endl;
+/*cout << q->getName() << endl << q->getAligned() << endl << endl;
+cout << pA->getName() << endl << pA->getAligned() << endl << endl;
+cout << pB->getName() << endl << pB->getAligned() << endl << endl;
+cout << " length = " << length << endl;
+cout << q->getName() << endl;
+cout << pA->getName() << '\t';
+cout << pB->getName() << endl;*/
//check window size
if (length < (2*windowSize+windowStep)) {