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rebuild_seqs.cpp
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rebuild_seqs.cpp
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#include <hash_cdbg/dna_alphabet.hpp>
#include <hash_cdbg/boss.hpp>
#include <fstream>
#include <thread>
#include <mutex>
#include <sdsl/csa_wt.hpp>
#include <sdsl/suffix_arrays.hpp>
std::mutex mtx_seqs;
inline uint64_t hash(uint64_t val1, uint64_t val2) {
uint64_t lhs = std::hash<uint64_t>()(val1), rhs = std::hash<uint64_t>()(val2);
uint64_t seed = lhs;
seed ^= lhs + 0x9e3779b97f4a7c15 + (seed << 12) + (seed >> 4);
seed ^= rhs + 0x9e3779b97f4a7c15 + (seed << 12) + (seed >> 4);
return seed;
}
void compute_starters(size_t start,
size_t end,
dbg_boss& my_dbg,
std::unordered_map<dbg_boss::size_type, bool>& starter_hash){
dbg_boss::size_type prev_node;
for(size_t i=start;i<=end;i++) {
prev_node = my_dbg.incomming(my_dbg.solid_nodes_ss(i), '$', true);
if(prev_node!=0){
try {
std::lock_guard<std::mutex> lck(mtx_seqs);
if (starter_hash.count(prev_node) == 0) {
starter_hash[prev_node] = true;
}
}catch (std::logic_error&){
std::cout<<"some error in the threads"<<std::endl;
}
}
}
}
void build_sequences(size_t start,
size_t end,
size_t& seqs_rebuilt,
size_t& amb_seqs,
size_t& fm_seqs,
size_t& nf_seqs,
std::vector<dbg_boss::size_type>& starter_nodes,
dbg_boss& my_dbg,
sdsl::csa_wt<wt_huff<rrr_vector<127> >, 512, 1024>& fm_index,
std::ofstream& output_file){
dbg_boss::size_type first_node, tmp_node, neighbor, cand_node;
size_t outd, n_colors, n_ambigous=0, n_fm=0, n_nf=0, seq_counter=0;
bool ambigous;
uint8_t symbol;
std::stringstream ss;
uint64_t seq_color;
for(size_t i=start;i<=end;i++){
first_node = starter_nodes[i];
if(first_node!=0) { // tmp_node is the start of one or more sequences
for (uint64_t node_color = 1; node_color <= my_dbg.get_color_num(first_node); ++node_color) {
tmp_node = first_node;
seq_color = node_color;
bool flag = true;
ambigous = false;
std::string tmp_string, tmp_rev_string;
tmp_string = my_dbg.node2string(tmp_node);
for(auto & sym : tmp_string) sym = dna_alphabet::char2comp[sym];
while (flag) {
if (my_dbg.is_colored(tmp_node)) {
seq_color = hash(tmp_node, seq_color);
}
outd = my_dbg.outdegree(tmp_node);
if (outd == 1) {
symbol = my_dbg.edge_bwt[my_dbg.get_edges(tmp_node).first] >> 1U;
tmp_string.push_back(symbol);
tmp_node = my_dbg.outgoing(tmp_node, 1);
} else {
n_colors = 0;
for (size_t j = 1; j <= outd; j++) {
neighbor = my_dbg.outgoing(tmp_node, j);
if (my_dbg.is_contained(neighbor, seq_color)) {
cand_node = neighbor;
symbol = my_dbg.edge_bwt[my_dbg.get_edges(tmp_node).first + j - 1] >> 1U;
n_colors++;
}
}
if (n_colors == 1) {
tmp_node = cand_node;
tmp_string.push_back(symbol);
} else if (n_colors == 0) {
ambigous = true;
flag = false;
n_nf++;
break;
} else {
ambigous = true;
flag = false;
n_ambigous++;
break;
}
}
if (!my_dbg.solid_nodes[tmp_node]) {
flag = false;
}
}
if (!ambigous) {
tmp_string = tmp_string.substr(1, tmp_string.size()-2);
seq_counter++;
size_t fm_count = sdsl::count(fm_index,tmp_string);
if(fm_count==0){
tmp_rev_string = tmp_string;
std::reverse(tmp_rev_string.begin(), tmp_rev_string.end());
for(auto& sym: tmp_rev_string){
sym = dna_alphabet::comp2rev[sym];
}
fm_count = sdsl::count(fm_index,tmp_rev_string);
}
if(fm_count==0){
for(auto&sym : tmp_string) sym = dna_alphabet::comp2char[sym];
std::cout<<tmp_string<<std::endl;
}
if (fm_count == 0) {
n_fm++;
seq_counter--;
std::cout << "fm_count 0!" << std::endl;
continue;
}
// my (output rebuild sequence)
for (auto& sym: tmp_string) sym = dna_alphabet::comp2char[sym];
ss << ">first_node_id:" << first_node << '\n';
ss << tmp_string << '\n';
}
}
}
}
size_t printed_syms = 1;
if (printed_syms != 0) {
try {
std::lock_guard<std::mutex> lck(mtx_seqs);
output_file << ss.str();
}catch (std::logic_error&){
std::cout<<"some error in the threads"<<std::endl;
}
ss.clear();
}
try {
std::lock_guard<std::mutex> lck(mtx_seqs);
seqs_rebuilt+=seq_counter;
amb_seqs += n_ambigous;
fm_seqs += n_fm;
nf_seqs += n_nf;
} catch (std::logic_error&) {
std::cout<<"some error in the threads"<<std::endl;
}
}
int main(int argc, char* argv[]) {
if (argc < 5) {
std::cerr << "Usage: " << argv[0] << " INPUT_BOSS_INDEX INPUT_FM_INDEX N_TREADS OUTPUT_FILE" << std::endl;
return 1;
}
dbg_boss dbg_index;
sdsl::load_from_file(dbg_index, argv[1]);
sdsl::csa_wt<wt_huff<rrr_vector<127> >, 512, 1024> fm_index;
sdsl::load_from_file(fm_index, argv[2]);
size_t n_threads = size_t(std::stoi(argv[3]));
std::ofstream output_file;
output_file.open(std::string(argv[4]) + ".fasta");
std::vector<dbg_boss::size_type> starter_nodes;
dbg_boss::size_type start, end;
size_t rem = dbg_index.n_solid_nodes % n_threads;
std::cout<<"computing the start of every sequence"<<std::endl;
{
dbg_boss::size_type nodes_per_thread = dbg_index.n_solid_nodes / n_threads;
std::vector<std::thread> threads;
std::unordered_map<dbg_boss::size_type, bool> starters_hash;
for (size_t i = 0; i < n_threads; i++) {
start = i * nodes_per_thread + 1;
end = ((i + 1) * nodes_per_thread);
if (i == n_threads - 1) end += rem;
threads.emplace_back(std::thread(compute_starters,
start,
end,
std::ref(dbg_index),
std::ref(starters_hash)));
}
for (auto &it : threads) it.join();
starter_nodes.reserve(starters_hash.size());
for (auto const &imap: starters_hash) starter_nodes.push_back(imap.first);
}
std::vector<std::thread> threads;
dbg_boss::size_type seqs_per_thread = starter_nodes.size() / n_threads;
rem = starter_nodes.size() % n_threads;
size_t amb_seqs=0, fm_seqs=0, nf_seqs=0, reb_seqs=0;
std::cout<<"inferring the original sequences"<<std::endl;
for (size_t i = 0; i < n_threads; i++) {
start = i * seqs_per_thread;
end = ((i + 1) * seqs_per_thread)-1;
if (i == n_threads - 1) end += rem;
threads.emplace_back(std::thread(build_sequences,
start,
end,
std::ref(reb_seqs),
std::ref(amb_seqs),
std::ref(fm_seqs),
std::ref(nf_seqs),
std::ref(starter_nodes),
std::ref(dbg_index),
std::ref(fm_index),
std::ref(output_file)));
}
for (auto &it : threads) it.join();
output_file.close();
std::cout<<reb_seqs<<" were rebuilt and "<<amb_seqs<<" were ambiguous, " << fm_seqs << " were fm_count 0, " << nf_seqs << " were not found"<<std::endl;
}