void Caller::compute_top_frequencies(const BasePileup& bp,
const vector<pair<int, int> >& base_offsets,
char& top_base, int& top_count,
char& second_base, int& second_count) {
const string& bases = bp.bases();
// frequency of each base (nidx / idxn converts to from / int)
int hist[5] = {0};
for (auto i : base_offsets) {
char base = Pileups::extract_match(bp, i.first);
++hist[nidx(base)];
}
int first = max_element(hist, hist + 4) - hist;
int second = first == 0 ? 1 : 0;
for (int i = 0; i < 4; ++i) {
if (i != first && hist[i] > hist[second]) {
second = i;
}
}
// break ties with reference
int refidx = nidx(bp.ref_base());
if (hist[first] == hist[refidx]) {
first = refidx;
} else if (hist[second] == hist[refidx]) {
second = refidx;
}
top_base = idxn(first);
top_count = hist[first];
second_base = idxn(second);
second_count = hist[second];
}
template<typename PointT> float
SmoothNormal<PointT>::calculateResidual(int idx){
std::vector<int> knbrs;
std::vector<float> kdist;
this->search_->nearestKSearch(idx, cluster_N_nbrs, knbrs, kdist);
Eigen::Map<Eigen::Vector3f> idxp((float*) this->input_->points[idx].data);
Eigen::Map<Eigen::Vector3f> idxn(this->normals_->points[idx].normal);
float res=0;
for(int i=0; i<knbrs.size(); i++){
Eigen::Map<Eigen::Vector3f> pt((float*) this->input_->points[knbrs[i]].data);
res = res + fabs(idxn.dot((pt-idxp)));
}
return res/(float) knbrs.size();
}
