}
bool isValid(int sid, int dir, int pos, const std::string& readseq, int LEN, int C) {
- if (sid <= 0 || sid > M || dir != 0 && dir != 1 || pos < 0 || pos + LEN > seqs[sid].getTotLen() || LEN > (int)readseq.length()) return false;
+ if (sid <= 0 || sid > M || (dir != 0 && dir != 1) || pos < 0 || pos + LEN > seqs[sid].getTotLen() || LEN > (int)readseq.length()) return false;
const std::string& seq = seqs[sid].getSeq(dir);
return countMismatch(seq, pos, readseq, LEN, C) <= C;
}
}
//inpF in fasta format, with sequence all in one line together
-//option 0 read all, 1 do not read sequences and names
+//option 0 read all, 1 do not read sequences
void Refs::loadRefs(char *inpF, int option) {
std::ifstream fin;
RefSeq seq;