Biomodern-XbitVector

Biomodern.DibitVector and QuadVector is a space-efficient container for dibit and quadbit values, you can think of it as a specialization of std::vector for type uint2_t and uint4_t.

The implementation detail is refered to GCC and Clang's implementation of vector<bool> with adopting new C++20 features such as iterator concepts, operator<=> etc.

The synopsis of those two containers is:

template <
  std::unsigned_integral Block = std::uint8_t,
  std::copy_constructible Allocator = std::allocator<Block> 
>
class DibitVector;

which Block refers to the underlying storage type, the default type is uint8_t which can store 4 dibits or 2 quadbits in one block.

The member types and functions definition is just the same as vector<bool> with following additions:

block_type; // alias to Block.
size_type num_blocks(); // return the number of underlying blocks.
block_type* data();
block_type* data() const; // return the begin pointer to the underlying blocks.
void flip(); // flip all the dibits/quadbits of the vector.

Like vector<bool>, those two containers can work with all algorithms in <algorithm> even if ranges::sort which cannot sort vector<bool> currently. Note that the value_type of those two containers is uint8_t which is not a printable character, make sure to cast it to int before you print:

std::cout << static_cast<int>(v.front()) << "\n";
std::cout << +v.back() << "\n";

If you want to serialize those two containers, you can use my other project Biomodern.Serializer which proves a simple interface to serialize binary archive.

Compilers

• GCC 10.2

Usage

This project is header-only and has no dependency with other libraries, if you want use it, just copy and paste.

#include <algorithm>
#include <iostream>
#include <ranges>
#include "xbit_vector/xbit_vector.hpp"

int main() {
  biomodern::DibitVector<> v{3, 2, 1, 2, 3, 0, 0, 1, 2};
  assert(v.size() == 9);
  assert(v.num_blocks() == 3);

  auto base_view = std::views::transform([](auto c){ return "ACGT"[c]; });
  auto comp_view = std::views::transform([](auto c){ return 0b11u - c; });
  std::cout << "Reverse complement of ";
  std::ranges::copy(v | base_view, std::ostream_iterator<char>{std::cout, ""});
  std::cout << " is ";
  for (auto c : v | std::views::reverse | comp_view | base_view)
    std::cout << c;
}

Building and Testing

$ mkdir build && cd build
$ cmake ..
$ make
$ make test