+ int traceStart = path[0].col;
+ int traceEnd = path[path.size()-1].col;
+// cout << "traceStart/End\t" << traceStart << '\t' << traceEnd << endl;
+
+ string queryInRange = query->getAligned();
+ queryInRange = queryInRange.substr(traceStart, (traceEnd-traceStart+1));
+// cout << "here" << endl;
+ string chimeraSeq = constructChimericSeq(trace, refSeqs);
+ string antiChimeraSeq = constructAntiChimericSeq(trace, refSeqs);
+
+ percentIdenticalQueryChimera = computePercentID(queryInRange, chimeraSeq);
+ double percentIdenticalQueryAntiChimera = computePercentID(queryInRange, antiChimeraSeq);
+// cout << i << '\t' << percentIdenticalQueryChimera << '\t' << percentIdenticalQueryAntiChimera << endl;
+
+ if(percentIdenticalQueryAntiChimera > maxPercentIdenticalQueryAntiChimera){
+ maxPercentIdenticalQueryAntiChimera = percentIdenticalQueryAntiChimera;
+ maxTrace = trace;
+ maxIndex = i;
+ }