int has_error(const char* seq, const char *qual, int n) {
//std::cout << "seq::" << seq << "\n";
//std::cout << "qul::" << qual << "\n";
int k = qual_mer_dna::k();
int filled_ = 0;
int i=0;
while (seq[i]) {
int code = _mer.code(seq[i]);
if(code < 0) {
return 1;
}
char q = qual[i];
_mer.shift_left(code, q);
_rev_mer.shift_right(_rev_mer.complement(code), q);
//std::cout << "mer:" << _mer.to_str() << ", qual:" << _mer.qual_str() << "\n";
//std::cout << "rev:" << _rev_mer.to_str() << ", qual:" << _rev_mer.qual_str() << "\n";
i++; filled_++;
if (filled_>=k || seq[i] == 0) {
//std::cout << "using mer:" << _mer.to_str() << "\n";
qual_mer_dna &mer = (_mer < _rev_mer) ? _mer : _rev_mer;
if(!(*filter_)(mer)) {
return 1;
}
filled_-= k/2; //1; //k/8;
}
}
return 0;
}
mer_qual_iterator& operator++() {
while(true) {
while(cseq_ == eseq_) {
++index_;
while(index_ >= (*job_)->nb_filled) {
index_ = 0;
job_->next();
if(job_->is_empty()) {
delete job_;
job_ = 0;
return *this;
}
}
init_from_job();
filled_ = 0;
}
do {
const int code = m_.code(*cseq_++);
const char qual = cqual_ < equal_ ? *cqual_++ : std::numeric_limits<char>::max();
if(code >= 0 && qual >= min_qual_) {
m_.shift_left(code);
if(canonical_)
rcm_.shift_right(rcm_.complement(code));
filled_ = std::min(filled_ + 1, mer_dna::k());
} else
filled_ = 0;
} while(filled_ < m_.k() && cseq_ < eseq_);
if(filled_ >= m_.k())
break;
}
return *this;
}
