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Biomodern.Istring

Biomodern.Istring is just type alias to the basic_string<int8_t>, which can be using for representing the encoded string of nucleotide sequence which 0-3 indicate ACGT, and 4 indicates the unknown base N. The head only istring.hpp contains several utility functions for the nucleotide sequence such as:

istring operator ""_s(const char*); // user-defined literals for the istring
size_t Codec::hash(istring); // integer encoding for istring
istring Codec::rhash(size_t, size_t); // map integer back to the istring
string Codec::rev_comp(string_view);
istring Codec::rev_comp(istring_view); // get reverse complement for the std::string/istring

Compilers

  • GCC 10.2

Usage

#include <cassert>
#include <iostream>
#include "istring.hpp"

int main() {
  using namespace std::string_literals;
  using namespace biomodern::utility;
  
  const auto s = 12031_s;
  assert(Codec::hash(s) == 0b01'10'00'11'01);
  assert(Codec::rhash(0b01'10'00'11'01, 5) == s);
  assert(Codec::to_istring("ACNGGTT") == 0142233_s);
  assert(Codec::rev_comp("ACNGGTT") == "AACCNGT"s);
  assert(Codec::rev_comp(s) == 20312_s);
  std::cout << s << "\n";
}