void getChainingA(Chains &chains, vector<Match_t> &matches, const long querylength, const SpliceOptions_t & spliceOptions) {
int i = 0;
//TODO: make sure the seeds in one cluster are from one chromosome
int overlap; // length of the overlap between two consecutive seeds,
// will be negative when there is a gap between the two seeds
const int max_overlap = 17; // the maximum value two seeds can overlap and peeled back
while (i < matches.size()) {
Chain chain;
//build new cluster
chain.push_back(matches[i]);
long coverage = matches[i].len;
int j = i + 1;
while (j < matches.size() ) {
// Make sure the seeds are ordered on ref position as well
if (matches[j].ref - chain.back().ref <= spliceOptions.maxSpliceLength
&& chain.back().ref + chain.back().len - matches[j].ref < 0) {
// overlap in query:
overlap = chain.back().query + chain.back().len - matches[j].query;
// The seeds do not overlap, so they can be added without any adjustment
if (overlap <= 0) {
chain.push_back(matches[j]);
coverage += matches[j].len;
}
// Do not allow an overlap of greater then max_overlap
else if (overlap < max_overlap) {
// peel back the two seeds a bit, so the overlap disappears if possible
if(chain.back().len - overlap > 2 && matches[j].len - overlap > 2) {
chain.back().len -= overlap;
chain.push_back(matches[j]);
chain.back().len -= overlap;
chain.back().ref += overlap;
chain.back().query += overlap;
coverage += matches[j].len;
}
}
}
j++;
}
if ((coverage * 100) / querylength >= spliceOptions.minCoverage) {
chains.push_back(chain);
i = j + 1;
} else {
i++;
}
}
}
void read(Chain &chain) {
char c;
read(chain.name, chain.type, chain.model_name, chain.m_cg);
while (true) {
read(c);
if (c == 'c') {
return;
}
else if (c == 'R') {
chain.push_back(Residue{});
read(chain.back());
}
else {
throw "This is not a standard '.jn' file! Illegal " + c;
}
}
}