quality_base.hpp

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// -----------------------------------------------------------------------------------------------------
// Copyright (c) 2022 deCODE Genetics
// Copyright (c) 2006-2020, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2020, Knut Reinert & MPI für molekulare Genetik
// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
// shipped with this file and also available at: https://github.com/biocpp/biocpp-core/blob/main/LICENSE.md
// -----------------------------------------------------------------------------------------------------
 
#pragma once
 
#include <bio/alphabet/base.hpp>
#include <bio/alphabet/detail/convert.hpp>
#include <bio/alphabet/quality/concept.hpp>
 
namespace bio::alphabet
{
 
template <typename derived_type, auto size>
class quality_base : public base<derived_type, size, char>
{
public:
    using phred_type = int8_t;
 
private:
    using base_t = base<derived_type, size, char>;
 
    constexpr quality_base() noexcept                                 = default; 
    constexpr quality_base(quality_base const &) noexcept             = default; 
    constexpr quality_base(quality_base &&) noexcept                  = default; 
    constexpr quality_base & operator=(quality_base const &) noexcept = default; 
    constexpr quality_base & operator=(quality_base &&) noexcept      = default; 
    ~quality_base() noexcept                                          = default; 
 
    constexpr quality_base(phred_type const p) noexcept { static_cast<derived_type *>(this)->assign_phred(p); }
 
    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 <meta::different_from<derived_type> other_qual_type>
        requires quality<other_qual_type>
    explicit constexpr quality_base(other_qual_type const & other) noexcept
    {
        assign_phred_to(bio::alphabet::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)]);
    }
 
protected:
    static constexpr std::array<rank_type, 256> phred_to_rank = []() constexpr
    {
        std::array<rank_type, 256> ret{};
 
        // NOLINTNEXTLINE(bugprone-signed-char-misuse)
        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 +
                            static_cast<int64_t>(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<rank_type, 256> char_to_rank = []() constexpr
    {
        std::array<rank_type, 256> ret{};
 
        // NOLINTNEXTLINE(bugprone-signed-char-misuse)
        for (int64_t i = std::numeric_limits<char_type>::lowest(); i <= std::numeric_limits<char_type>::max(); ++i)
        {
            if (i < derived_type::offset_char) // map too-small to smallest possible
                ret[static_cast<rank_type>(i)] = 0;
            else if (i >= derived_type::offset_char +
                            static_cast<int64_t>(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_char;
        }
 
        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;
    }();
 
    static constexpr std::array<char_type, alphabet_size> rank_to_char = []() constexpr
    {
        std::array<char_type, alphabet_size> ret{};
 
        for (size_t i = 0; i < alphabet_size; ++i)
            ret[i] = i + derived_type::offset_char;
 
        return ret;
    }();
 
    friend constexpr phred_type tag_invoke(custom::to_phred, derived_type const alph) noexcept
    {
        return alph.to_phred();
    }
 
    friend constexpr derived_type & tag_invoke(custom::assign_phred_to,
                                               phred_type const p,
                                               derived_type &   alph) noexcept
    {
        return alph.assign_phred(p);
    }
};
 
} // namespace bio::alphabet