nucleotide.hpp

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#pragma once
 
#include <array>
#include <cstdint> // for uint8_t
#include <stdexcept> // for std::invalid_argument
#include <fstream>
 
enum class Nucleotide : uint8_t
{
    A = 0, 
    C = 1, 
    G = 2, 
    T = 3,  
    INVALID 
};
 
static constexpr std::array<Nucleotide, 256> char_to_nucleotide = []() {
    std::array<Nucleotide, 256> result;
    result.fill(Nucleotide::INVALID);
 
    // Initialize valid nucleotide mappings
    result['A'] = Nucleotide::A;
    result['a'] = Nucleotide::A;
    result['C'] = Nucleotide::C;
    result['c'] = Nucleotide::C;
    result['G'] = Nucleotide::G;
    result['g'] = Nucleotide::G;
    result['T'] = Nucleotide::T;
    result['t'] = Nucleotide::T;
 
    return result;
}();
 
static constexpr std::array<char, 4> nucleotide_to_char = {
    'A', 'C', 'G', 'T'
};
 
bool is_valid_nucleotide(char nucleotide);
 
std::ostream& operator<<(std::ostream& os, const Nucleotide& nucleotide);