- //Constructor , seq : the forward strand of the reference
- //tag does not contain ">"
- //polyALen : length of polyA tail we add
- RefSeq(const std::string& name, const std::string& seq, int polyALen) {
- fullLen = seq.length();
- totLen = fullLen + polyALen;
- this->name = name;
- this->seq = seq;
- this->seq.append(polyALen, 'A');
-
- assert(fullLen > 0 && totLen >= fullLen);
-
- int len = (fullLen - 1) / NBITS + 1;
- fmasks.clear(); fmasks.resize(len, 0);
- // ask read to be at least OLEN long!
- for (int i = std::max(fullLen - OLEN + 1, 0); i < fullLen; i++) setMask(i);
- }