void CompTool::search_forward_matches(const string seq1_name, const string seq2_name, int* SA, BWT& bwt,
const int kmer_size, const int slide_letters, const int max_num_matches){
stringstream out_file;
out_file << seq1_name << "__" << seq2_name << ".match." << kmer_size << ".forward";
ofstream ofs(out_file.str().c_str());
ofs << "#" << seq2_name << "\t" << seq1_name << endl; // header
for(int i = 0; i < seq2_size_ - kmer_size; i += slide_letters){
int8_t* query = &seq2_[i];
int lb, ub; // lower- and upper-bound of matches in suffix array
bwt.search(query, kmer_size, lb, ub);
if(lb <= ub){
for(int j = lb; j <= ub; j++){
if(j == lb + max_num_matches) break;
ofs << i << "\t" << SA[j] << endl;
}
}
}
}
void CompTool::search_reverse_matches(const string seq1_name, const string seq2_name, int* SA, BWT& bwt,
const int kmer_size, const int slide_letters, const int max_num_matches){
stringstream out_file;
out_file << seq1_name << "__" << seq2_name << ".match." << kmer_size << ".reverse";
ofstream ofs(out_file.str().c_str());
ofs << "#" << seq2_name << "\t" << seq1_name << endl; // header
int8_t* query = new int8_t[kmer_size];
for(int i = kmer_size-1; i < seq2_size_ - 1; i += slide_letters){
// convert k-mers to reverse complements
for(int j = 0; j < kmer_size; j++)
query[j] = num_char_ - seq2_[i-j];
int lb, ub; // lower- and upper-bound of matches in suffix array
bwt.search(query, kmer_size, lb, ub);
if(lb <= ub){
for(int j = lb; j <= ub; j++){
if(j == lb + max_num_matches) break;
ofs << i << "\t" << SA[j] << endl;
}
}
}
delete[] query;
}