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paf_parser.cpp
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paf_parser.cpp
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#include <string>
#include <sstream>
#include <iostream>
#include <fstream>
#include <vector>
#include <unordered_map>
#include <algorithm>
#include <thread>
#include <future>
#include <chrono>
#include <iomanip>
#include <mutex>
#include <experimental/filesystem>
using namespace std;
mutex mtx;
void readfile(string filename, unordered_map<string, vector<pair<int,string> > >& target_map, int num_threads,unsigned long long int block_len, int index)
{
// cout<< "thread" << index << endl;
string target_seq_name, query_seq_name, temp,line;
ifstream infile;
infile.open(filename);
int query_start;
unsigned long long int read_len=0;
unsigned long long int start=block_len*index;
// cout <<"Start: " << start << endl;
infile.seekg(start, ios::beg);
char ch;
if(start!=0)
{
infile.seekg(-2, infile.cur);
infile >> noskipws >>ch;
if(ch !='\n')
{
while(infile.peek() != '\n')
{
infile >> noskipws >>ch;
// cout << ch;
read_len++;
}
infile >> noskipws >>ch;
read_len++; //for above \n
}
}
while ((read_len<=block_len) && getline(infile, line))
{
read_len+=line.length()+1; //+1 for \n
// cout << "Thread"<< index << " read length: " << read_len << endl;
istringstream record(line);
if (!(record >> query_seq_name >> temp >> query_start >> temp >> temp >> target_seq_name))
{
cout<< "Indexing issue for chunks while reading" << endl;
break;
}
mtx.lock();
// cout << "thread" << index << " adds " << query_seq_name << " at " << query_start << " to " << target_seq_name << endl;
// cout << "Read length: "<<read_len << endl;
target_map[target_seq_name].push_back({query_start,query_seq_name});
mtx.unlock();
}
infile.close();
}
void sort_query(unordered_map<string, vector<pair<int,string> > >& target_map, int index, unsigned int chunk_size, int num_threads)
{
unordered_map<string, vector<pair<int,string> > >::iterator ptr = target_map.begin();
advance(ptr,index*chunk_size);
unsigned int i=0;
while(i<chunk_size)
{
//cout << ptr->first << endl;
// cout<< "Sorted " << ptr->first << endl;
sort(ptr->second.begin(), ptr->second.end());
i++;
ptr++;
}
if(index==num_threads-1)
{
while(ptr!=target_map.end())
{
sort(ptr->second.begin(), ptr->second.end());
ptr++;
}
}
}
int main(int argc, const char * argv[])
{
string line;
if(argc<4)
{
cout<< "Input & output filenames and number of threads needed" << endl;
exit(1);
}
string filename=argv[1];
int num_threads=stoi(argv[3]);
size_t filesize = experimental::filesystem::file_size(filename);
cout<< "Filesize: " << filesize << " bytes" << endl;
int i;
unordered_map<string, vector<pair<int,string> > > target_map;
// future<unordered_map<string, vector<pair<int,string> > > > target_map_future = async(launch::async, readfile, filename);
vector<thread> read_threads;
unsigned long long int block_len=filesize/num_threads;
cout<< "Block length: " << block_len << endl;
auto start_read = chrono::high_resolution_clock::now();
for(i=0;i<num_threads;i++)
{
read_threads.push_back(thread(readfile,filename,ref(target_map),num_threads,block_len,i));
}
for (thread &t : read_threads)
{
if (t.joinable())
{
t.join();
}
}
auto end_read=chrono::high_resolution_clock::now();
double time_taken_read=chrono::duration_cast<chrono::nanoseconds>(end_read - start_read).count();
time_taken_read *= 1e-9;
unsigned int target_map_size=target_map.size();
unsigned int chunk_size=(target_map_size > num_threads) ? target_map_size/num_threads: 1;
int num_threads_sort=(target_map_size > num_threads) ? num_threads : target_map_size;
vector<thread> sort_threads;
auto start_sort = chrono::high_resolution_clock::now();
for(i=0;i<num_threads_sort;i++)
{
sort_threads.push_back(thread(sort_query,ref(target_map),i,chunk_size,num_threads_sort));
}
for (thread &t : sort_threads)
{
if (t.joinable())
{
t.join();
}
}
auto end_sort=chrono::high_resolution_clock::now();
double time_taken_sort=chrono::duration_cast<chrono::nanoseconds>(end_sort - start_sort).count();
time_taken_sort *= 1e-9;
ofstream outfile;
string outfilename=argv[2];
outfile.open(outfilename);
int num_records=0;
for (auto x : target_map)
{
outfile << x.first << ": "<<endl;
for ( auto y : x.second)
{
outfile << y.first << " ";
outfile << y.second << " ";
num_records++;
}
outfile << endl;
}
outfile.close();
cout << "Number of records: " << num_records << endl;
cout << "Number of target sequences: " << target_map.size() << endl;
cout << "Time taken by read is : " << fixed << time_taken_read << setprecision(9) << " sec" << endl;
cout << "Time taken by sort is : " << fixed << time_taken_sort << setprecision(9) << " sec" << endl;
return 0;
}