phred_base.hpp

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// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: BSD-3-Clause

 
#pragma once
 
#include <algorithm>
 
#include <seqan3/alphabet/alphabet_base.hpp>
#include <seqan3/alphabet/detail/convert.hpp>
#include <seqan3/alphabet/quality/concept.hpp>
 
namespace seqan3
{

template <typename derived_type, size_t size>
class phred_base : public alphabet_base<derived_type, size, char>
{
public:
    using phred_type = int8_t;
 
private:
    using base_t = alphabet_base<derived_type, size, char>;

    friend base_t;

    constexpr phred_base() noexcept = default;                               
    constexpr phred_base(phred_base const &) noexcept = default;             
    constexpr phred_base(phred_base &&) noexcept = default;                  
    constexpr phred_base & operator=(phred_base const &) noexcept = default; 
    constexpr phred_base & operator=(phred_base &&) noexcept = default;      
    ~phred_base() noexcept = default;                                        

    friend derived_type;
 
public:
    // Import from base type:
    using base_t::alphabet_size;
    using base_t::assign_rank;
    using base_t::to_rank;
    using typename base_t::char_type;
    using typename base_t::rank_type;

    // This constructor needs to be public, because constructor templates are not inherited otherwise
    template <typename other_qual_type>
        requires (!std::same_as<phred_base, other_qual_type>) && (!std::same_as<derived_type, other_qual_type>)
              && quality_alphabet<other_qual_type>
    explicit constexpr phred_base(other_qual_type const & other) noexcept
    {
        assign_phred_to(seqan3::to_phred(other), static_cast<derived_type &>(*this));
    }


    constexpr phred_type to_phred() const noexcept
    {
        return rank_to_phred[to_rank()];
    }



    constexpr derived_type & assign_phred(phred_type const p) noexcept
    {
        return assign_rank(phred_to_rank[static_cast<rank_type>(p)]);
    }

 
private:
    static constexpr rank_type char_to_rank(char_type const chr)
    {
        int64_t difference = static_cast<int64_t>(chr) - static_cast<int64_t>(derived_type::offset_char);
        return std::clamp<int64_t>(difference, 0, alphabet_size - 1);
    }

    static constexpr char_type rank_to_char(rank_type const rank)
    {
        return rank + derived_type::offset_char;
    }

    static constexpr std::array<rank_type, 256> phred_to_rank{
        []() constexpr
        {
            std::array<rank_type, 256> ret{};
 
            for (int64_t i = std::numeric_limits<phred_type>::lowest(); i <= std::numeric_limits<phred_type>::max();
                 ++i)
            {
                if (i < derived_type::offset_phred) // map too-small to smallest possible
                    ret[static_cast<rank_type>(i)] = 0;
                else if (i >= derived_type::offset_phred + alphabet_size) // map too-large to highest possible
                    ret[static_cast<rank_type>(i)] = alphabet_size - 1;
                else // map valid range to identity
                    ret[static_cast<rank_type>(i)] = i - derived_type::offset_phred;
            }
 
            return ret;
        }()};

    static constexpr std::array<phred_type, alphabet_size> rank_to_phred{
        []() constexpr
        {
            std::array<phred_type, alphabet_size> ret{};
 
            for (size_t i = 0; i < alphabet_size; ++i)
                ret[i] = i + derived_type::offset_phred;
 
            return ret;
        }()};
};
 
} // namespace seqan3