double accuracy(const dvec_t& dec_values, const ivec_t& ty){
int correct = 0;
int total = (int) ty.size();
size_t i;
for(i = 0; i < ty.size(); ++i)
if(ty[i] == (dec_values[i] >= 0? 1: -1)) ++correct;
printf("Accuracy = %g%% (%d/%d)\n",
(double)correct/total*100,correct,total);
return (double) correct / total;
}
/** Function debug_print_fragments ()
* Given fragment IDs then print concatenated fragments from input fastq files
*/
void debug_print_fragments (const ivec_t& fragIDs, const std::string& fq,
const std::string& fq2) {
std::cout << "\nnum fragments: " << fragIDs.size() << "\n";
iset_t ids (fragIDs.begin(), fragIDs.end());
std::ifstream ifhfq, ifhfq2;
xny::openfile<std::ifstream>(ifhfq, fq);
xny::openfile<std::ifstream>(ifhfq2, fq2);
bio::fastq_input_iterator<> iter_fq (ifhfq), end, iter_fq2(ifhfq2);
int fragID = 0;
for (; iter_fq != end, iter_fq2 != end; ++ iter_fq, ++ iter_fq2) {
if (ids.count(fragID)) {
std::string frag = std::get<1>(*iter_fq) + std::get<1> (*iter_fq2);
std::cout << frag << "\n";
}
++ fragID;
}
xny::closefile(ifhfq);
xny::closefile(ifhfq2);
} //debug_print_fragments
/** Function update_uf()
* Given fragment IDs of the same cluster, update the union find
* structure [uf_clust] to reflect this information
*/
void update_uf (ivec_t& uf_clst, const ivec_t& clusters) {
int sz = clusters.size ();
for (int i = 0; i < sz - 1; ++ i) {
for (int j = i + 1; j < sz; ++ j) {
int fragID_i = clusters[i],
fragID_j = clusters[j];
int root_i = uf_find (fragID_i, uf_clst),
root_j = uf_find (fragID_j, uf_clst);
uf_clst[root_j] = root_i;
}
}
} // update_uf
/** Function make_cluster()
*
* Given a list of fragments denoted by seeds, make pairwise comparison
* and clustering conforming max_mismatch criteria
*
* Output: clusters in 2d vector format, where each row of the vector
* stores the clustered fragment IDs.
*/
void make_cluster (iivec_t& clusters, const ii64vec_t& list_seeds,
const ivec_t& init_cluster, int max_mismatch, const ivec_t& uf_clst) {
if (list_seeds.size() == 0) {
abording ("DuplRm.cpp -- make_cluster(): SC failed");
}
//--------- union find: (1) initialize the cluster ---------
int sz = init_cluster.size();
bvec_t visited (sz, false);
ivec_t clst (sz);
for (int i = 0; i < sz; ++ i) clst[i] = i;
//--------- pairwise comparison ---------
for (int i = 0; i < sz - 1; ++ i) {
if (visited[i]) continue; // to speed up
int idx_i = init_cluster[i];
for (int j = i + 1; j < sz; ++ j) {
if (visited[j]) continue; // to speed up, avoid of comparison
// if this is already clustered
int idx_j = init_cluster[j];
// check global uf structure according to fragID
int root_uf_i = uf_clsfind ((int) list_seeds[idx_i].back(), uf_clst),
root_uf_j = uf_clsfind ((int) list_seeds[idx_j].back(), uf_clst);
if (root_uf_i != root_uf_j) {
int root_i = uf_find (i, clst),
root_j = uf_find (j, clst);
if (root_i != root_j) {
if (is_similar (list_seeds[idx_i], list_seeds[idx_j],
max_mismatch)) {
clst[root_j] = root_i;
visited[j] = true;
}
}
} // if
} // for (int j = i + 1
} // for (int i = 0
//----- generate final cluster { clusterID --> fragment IDs } ------
std::map<int, ivec_t> clstID_fragIDs;
std::map<int, ivec_t>::iterator it;
for (int i = 0; i < sz; ++ i) {
int idx_i = init_cluster[i];
int fragID = list_seeds[idx_i].back();
int root_i = uf_clsfind (i, clst);
it = clstID_fragIDs.find (root_i);
if (it != clstID_fragIDs.end()) it->second.push_back(fragID);
else clstID_fragIDs[root_i] = ivec_t (1, fragID);
} // for (int i = 0
// go through the map and produce clusters in sorted vector format
for (it = clstID_fragIDs.begin(); it != clstID_fragIDs.end(); ++ it) {
if (it->second.size() > 1) {
std::sort (it->second.begin(), it->second.end());
clusters.push_back(it->second);
}
} // for (it
} // make_cluster