#include "hamming/hamming.hh"

#include <chrono>
#include <iostream>
#include <string>

int main(int argc, char *argv[]) {
  std::string filename = std::string(argv[1]);
  std::size_t nsamples = std::stoi(std::string(argv[2]));

  auto start = std::chrono::steady_clock::now();
  auto data =
      hamming::from_fasta<hamming::DefaultDistIntType>(filename, nsamples);
  data.dump("distances.csv");
  auto stop = std::chrono::steady_clock::now();
  std::chrono::duration<double> elapsed_seconds = stop - start;
  std::cout << "Processing fasta data set took " << elapsed_seconds.count()
            << "s" << std::endl;
  return 0;
}
