//lim : >=0 If mismatch > lim , return; -1 find all mismatches
int countMismatch(const std::string& seq, int pos, const std::string& readseq, int LEN, int lim = -1) {
int nMis = 0; // number of mismatches
//lim : >=0 If mismatch > lim , return; -1 find all mismatches
int countMismatch(const std::string& seq, int pos, const std::string& readseq, int LEN, int lim = -1) {
int nMis = 0; // number of mismatches