+
+ int alnLength = oligo.length();
+
+ for(int i=oligo.length()-1;i>=0;i--){
+ if(oligo[i] != '-'){ alnLength = i+1; break; }
+ }
+ oligo = oligo.substr(0,alnLength);
+ temp = temp.substr(0,alnLength);
+// cout << "barcode = " << oligo << " raw = " << rawSequence.substr(0,alnLength) << " raw aligned = " << temp << endl;
+ cout << seq.getName() << endl;
+ cout << temp << endl;
+ cout << oligo << endl;
+ cout << alnLength << endl;
+ cout << endl;