void makeMatch(vector<string>& matches, int n) {
if (n == 1) return;
for (int i = 0; i < n / 2; ++i) {
matches[i] = "(" + matches[i] + "," + matches[n-1-i] + ")";
}
makeMatch(matches, n / 2);
}
Match* FusionMapper::mapRead(Read* r, bool& mapable, int distanceReq, int qualReq) {
vector<SeqMatch> mapping = mIndexer->mapRead(r);
//we only focus on the reads that can be mapped to two genome positions
if(mapping.size() < 2){
mapable = false;
return NULL;
}
mapable = true;
//if the left part of mapping result is reverse, use its reverse complement alternative and skip this one
if(!mIndexer->inRequiredDirection(mapping)) {
return NULL;
}
/*cout<<r->mName<<endl;
cout<<r->mSeq.mStr<<endl;
cout << mapping.size() << " mappings " << endl;
vector<SeqMatch>::iterator iter;
for(iter = mapping.begin(); iter!=mapping.end(); iter++){
iter->print();
cout << endl;
}
cout << endl;*/
// TODO: set int readBreak, int leftContig, int leftPos, int rightContig, int rightPos
Match* m = makeMatch(r, mapping);
return m;
}
string findContestMatch(int n) {
vector<string> matches;
for (int i = 0; i < n; ++i) {
matches.push_back(to_string(i+1));
}
makeMatch(matches, n);
return matches[0];
}