trim_quality.hpp

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// -----------------------------------------------------------------------------------------------------
// Copyright (c) 2006-2022, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2022, 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 <ranges>
 
#include <seqan3/alphabet/quality/qualified.hpp>
#include <seqan3/io/views/detail/take_until_view.hpp>
#include <seqan3/utility/views/deep.hpp>
 
namespace seqan3::detail
{
 
struct trim_fn
{
    template <typename threshold_t>
    constexpr auto operator()(threshold_t const threshold) const
    {
        static_assert(quality_alphabet<threshold_t> || std::integral<threshold_t>,
                      "The threshold must either be a quality alphabet or an integral type "
                      "in which case it is compared with the underlying Phred score type.");
 
        return adaptor_from_functor{*this, threshold};
    }
 
    template <std::ranges::input_range irng_t, typename threshold_t>
    constexpr auto operator()(irng_t && irange, threshold_t const threshold) const
    {
        static_assert(quality_alphabet<std::remove_reference_t<std::ranges::range_reference_t<irng_t>>>,
                      "views::trim_quality can only operate on ranges over seqan3::quality_alphabet.");
        static_assert(
            std::same_as<std::remove_cvref_t<threshold_t>, std::remove_cvref_t<std::ranges::range_reference_t<irng_t>>>
                || std::integral<std::remove_cvref_t<threshold_t>>,
            "The threshold must either be a letter of the underlying alphabet or an integral type "
            "in which case it is compared with the underlying Phred score type.");
 
        return detail::take_until(
            std::forward<irng_t>(irange),
            [threshold](auto const value)
            {
                if constexpr (std::same_as<std::remove_cvref_t<threshold_t>,
                                           std::remove_cvref_t<std::ranges::range_reference_t<irng_t>>>)
                {
                    return to_phred(value) < to_phred(threshold);
                }
                else
                {
                    using c_t = std::common_type_t<decltype(to_phred(value)), threshold_t>;
                    return static_cast<c_t>(to_phred(value)) < static_cast<c_t>(threshold);
                }
            });
    }
};
 
} // namespace seqan3::detail
 
namespace seqan3::views
{
inline constexpr auto trim_quality = deep{seqan3::detail::trim_fn{}};
 
} // namespace seqan3::views