for(int j=0;j<numBases;j++){
if(unaligned[j] != 'A' && unaligned[j] != 'T' && unaligned[j] != 'G' && unaligned[j] != 'C'){
ambigBases++;
for(int j=0;j<numBases;j++){
if(unaligned[j] != 'A' && unaligned[j] != 'T' && unaligned[j] != 'G' && unaligned[j] != 'C'){
ambigBases++;
//********************************************************************************************************************
int Sequence::getLongHomoPolymer(){
//********************************************************************************************************************
int Sequence::getLongHomoPolymer(){