phred_base.hpp

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// -----------------------------------------------------------------------------------------------------
// Copyright (c) 2006-2021, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2021, 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/seqan/seqan3/blob/master/LICENSE.md
// -----------------------------------------------------------------------------------------------------
 
#pragma once
 
#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; 
 
#ifdef SEQAN3_DEPRECATED_310
    SEQAN3_DEPRECATED_310 constexpr phred_base(phred_type const p) noexcept
    {
        static_cast<derived_type *>(this)->assign_phred(p);
    }
#endif // SEQAN3_DEPRECATED_310
 
    friend derived_type;
 
public:
    // Import from base type:
    using base_t::alphabet_size;
    using base_t::to_rank;
    using base_t::assign_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 std::array<rank_type, 256> constexpr 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 std::array<phred_type, alphabet_size> constexpr 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 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;
    }
};
 
} // namespace seqan3