- for(int i=0; i<A.getLength(); i++){
- if(A.getUnaligned()[i] != '.' || B.getUnaligned()[i] != '.'){
+ string seqA = A.getAligned();
+ string seqB = B.getAligned();
+
+ int alignLength = seqA.length();
+
+ for(int i=0; i<alignLength; i++){
+ if(seqA[i] != '.' || seqB[i] != '.'){