phiX174_error_free_overlap.cpp

#include <iostream>
#include <cstring>
#include <vector>

int calculate_overlap(const std::string &a, const std::string &b, const int mer) noexcept
{
  for (int i = 0, n = 1 + a.size() - mer; i < n; ++i)
    if (strncmp(b.c_str(), a.c_str() + i, a.size() - i) == 0)
      return a.size() - i;
  return 0;
}

std::string assemble_genome(std::vector<std::string> reads, const int mer) noexcept
{
  std::string genome;
  genome.reserve(1000);
  genome += reads.front();

  std::string first_read = reads.front(), cur_read = "";
  int cur_index = 0;

  while (reads.size() > 1)
  {
    cur_read = std::move(reads[cur_index]);
    reads.erase(reads.begin() + cur_index);

    int max_overlap = -1;

    for (int j = 0; j < reads.size(); ++j)
    {
      int overlap = calculate_overlap(cur_read, reads[j], mer);
      if (overlap > max_overlap)
        max_overlap = overlap, cur_index = j;
    }

    genome += reads[cur_index].substr(max_overlap);
  }

  genome.erase(0, calculate_overlap(reads[0], first_read, mer));
  return genome;
}

int main()
{
  std::ios::sync_with_stdio(false);
  std::cin.tie(NULL);

  std::vector<std::string> reads;
  reads.reserve(1618);
  std::string s;

  while (std::cin >> s)
    if (reads.back() != s)
      reads.emplace_back(std::move(s));

  std::cout << assemble_genome(std::move(reads), 12) << std::endl;

  return 0;
}