+ vector<score_struct> path;
+
+ int rowIndex = highestStruct[i].row;
+ int pos = highestStruct[i].col;
+ int score = highestStruct[i].score;
+
+ while (pos >= 0 && score > 0) {
+ score_struct temp = ms[rowIndex][pos];
+ score = temp.score;
+
+ if (score > 0) { path.push_back(temp); }
+
+ rowIndex = temp.prev;
+ pos--;
+ }
+
+ reverse(path.begin(), path.end());
+
+ vector<trace_struct> trace = mapTraceRegionsToAlignment(path, refSeqs);
+
+ //cout << "traces\n";
+ //for(int j=0;j<trace.size();j++){
+ // cout << trace[j].col << '\t' << trace[j].oldCol << '\t' << refSeqs[trace[j].row]->getName() << endl;
+ //}
+
+ int traceStart = path[0].col;
+ int traceEnd = path[path.size()-1].col;
+// cout << "traceStart/End\t" << traceStart << '\t' << traceEnd << endl;