trim_quality.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 <ranges>
 
#include <bio/alphabet/quality/qualified.hpp>
#include <bio/ranges/views/deep.hpp>
 
namespace bio::ranges::detail
{
 
struct trim_fn
{
    template <typename threshold_t>
    constexpr auto operator()(threshold_t const threshold) const
    {
        static_assert(alphabet::quality<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 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(alphabet::quality<std::ranges::range_reference_t<irng_t>>,
                      "views::trim_quality can only operate on ranges over bio::alphabet::quality.");
        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 type.");
 
        return std::views::take_while(
          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 alphabet::to_phred(value) >= alphabet::to_phred(threshold);
              }
              else
              {
                  using c_t = std::common_type_t<decltype(alphabet::to_phred(value)), threshold_t>;
                  return static_cast<c_t>(alphabet::to_phred(value)) >= static_cast<c_t>(threshold);
              }
          });
    }
};
 
} // namespace bio::ranges::detail
 
namespace bio::ranges::views
{
 
inline constexpr auto trim_quality = deep{detail::trim_fn{}};
 
 
} // namespace bio::ranges::views