i64 totient_with_factor(const IntPairVec& vfac)
{
i64 prod = 1;
for(unsigned int i = 0; i < vfac.size(); ++i){
i64 px = vfac[i].first;
i64 npow = vfac[i].second;
prod *= (px-1);
prod *= power(px, npow-1);
}
return prod;
}
void generate_all_numbers(int num, IntPairVec& pairs, vector<int>& vn, int cpos)
{
if(cpos == pairs.size()){
vn.push_back(num);
return;
}
for( int i = 0; true ; ++i ){
int n1 = num * power(pairs[cpos].first, i);
if(n1 > 100000) break;
generate_all_numbers(n1, pairs, vn, cpos+1);
}
}
int main(int argc, char* argv[]) {
using namespace kmer_match;
using maligner_dp::AlignmentHeader;
opt::program_name = argv[0];
parse_args(argc, argv);
cerr << "................................................\n"
<< "MALIGNER settings:\n"
<< "\tquery_maps_file: " << opt::query_maps_file << "\n"
<< "\tref_maps_file: " << opt::ref_maps_file << "\n"
<< "\tmax. consecutive unmatched sites: " << opt::max_unmatched_sites << "\n"
<< "\tmax. unmatched rate: " << opt::max_unmatched_rate << "\n"
<< "\trelative_error: " << opt::rel_error << "\n"
<< "\tabsolute_error: " << opt::min_abs_error << "\n"
<< "\tminimum query frags: " << opt::min_frag << "\n"
<< "\tmax matches per query: " << opt::max_match << "\n"
<< "................................................\n\n";
ErrorModel error_model(opt::rel_error, opt::min_abs_error);
auto start_time = chrono::steady_clock::now();
/////////////////////////////////////////////////////////////
// Read Reference Maps
MapWrapperVec ref_maps = read_ref_maps(opt::ref_maps_file, opt::ref_is_circular, opt::ref_is_bounded);
// Store a vector of pointers to the underlying Maps.
MapWrapperPVec p_ref_maps(ref_maps.size());
for(size_t i = 0; i < ref_maps.size(); i++) {
p_ref_maps[i] = &ref_maps[i];
}
// Store reference maps in an unordered map.
MapDB ref_map_db;
for(auto i = ref_maps.begin(); i != ref_maps.end(); i++) {
ref_map_db.insert( MapDB::value_type(i->map_.name_, *i) );
}
cerr << "Read " << ref_maps.size() << " reference maps.\n";
////////////////////////////////////////////////////////////////
// Build Chunk Database
MapChunkDB chunkDB(p_ref_maps, opt::max_unmatched_sites);
cerr << "Made MapChunkDB with " << chunkDB.map_chunks_.size() << " chunks.\n";
// Write alignment header
std::cout << AlignmentHeader();
size_t aln_count = 0;
size_t map_with_aln = 0;
size_t counter = 0;
size_t interval_report = 100;
Scorer scorer(opt::query_miss_penalty, opt::ref_miss_penalty, opt::min_sd, opt::sd_rate);
// Iterate through query maps file.
Map query_map;
MapReader query_map_reader(opt::query_maps_file);
for(; query_map_reader.next(query_map); counter++) {
if(counter == interval_report) {
std::cerr << ".";
counter = 0;
}
MapWrapper query = MapWrapper(std::move(query_map), false, false);
if(int(query.num_frags()) < opt::min_frag) {
continue;
}
std::cerr << "Aligning " << query.get_name() << "\n";
const FragVec& frags = query.get_frags();
// Note: We ignore boundary fragments
IntPairVec bounds = error_model.compute_bounds(frags.begin() + 1, frags.end() - 1);
// Determine the maximum number of unmatched sites allowed
const double mur = opt::max_unmatched_rate;
size_t max_unmatched = mur > 0.0 ?
size_t((mur/(1-mur)) * bounds.size()) : std::numeric_limits<size_t>::max();
RefAlignmentVec ref_alns = chunkDB.get_compatible_alignments_best(bounds, max_unmatched);
// std::cerr << qi->name_ << "\n";
// std::cerr << frags << "\n";
// std::cerr << "max_unmatched: " << max_unmatched << "\n";
// std::cerr << "num_frags: " << bounds.size() << "\n";
// std::cerr << "num aln: " << " " << ref_alns.size() << std::endl;
// Sort the alignments in ascending order of miss_rate
std::sort(ref_alns.begin(), ref_alns.end(), ReferenceAlignmentMissRateSort());
AlignmentVec alns = convert_alignments(ref_alns, query, ref_map_db, scorer);
cerr << "Converted " << alns.size() << " alignments.\n";
int query_aln_count = 0;
bool map_has_alignment = false;
for(auto a = alns.begin(); a != alns.end(); a++) {
if(query_aln_count == opt::max_match) break;
const maligner_dp::Alignment& aln = *a;
bool have_aln = false;
if(aln.score_per_inner_chunk <= opt::max_score_per_inner_chunk) {
maligner_dp::print_alignment(std::cout, aln);
++aln_count;
++query_aln_count;
have_aln = true;
map_has_alignment = true;
}
}
if(map_has_alignment) {
++map_with_aln;
}
}
cerr << "\ntotal alignments: " << aln_count << "\n";
cerr << map_with_aln << " maps with alignments.\n";
auto end_time = chrono::steady_clock::now();
cerr << chrono::duration <double, milli> (end_time - start_time).count() << " ms" << endl;
std::cerr << "maligner done.\n";
return EXIT_SUCCESS;
}
