input_format_concept.hpp

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// -----------------------------------------------------------------------------------------------------
// 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/seqan/seqan3/blob/master/LICENSE.md
// -----------------------------------------------------------------------------------------------------
 
#pragma once
 
#include <fstream>
#include <string>
#include <vector>
 
#include <seqan3/alphabet/cigar/cigar.hpp>
#include <seqan3/alphabet/gap/gapped.hpp>
#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/alphabet/nucleotide/dna5.hpp>
#include <seqan3/alphabet/quality/aliases.hpp>
#include <seqan3/alphabet/quality/phred42.hpp>
#include <seqan3/core/type_list/type_list.hpp>
#include <seqan3/io/alignment_file/header.hpp>
#include <seqan3/io/alignment_file/input_options.hpp>
#include <seqan3/io/alignment_file/misc.hpp>
#include <seqan3/io/alignment_file/sam_tag_dictionary.hpp>
 
namespace seqan3::detail
{
 
template <typename format_type>
struct alignment_file_input_format_exposer : public format_type
{
public:
    // Can't use `using format_type::read_alignment_record` as it produces a hard failure in the format concept check
    // for types that do not model the format concept, i.e. don't offer the proper read_alignment_record interface.
    template <typename ...ts>
    void read_alignment_record(ts && ...args)
    {
        format_type::read_alignment_record(std::forward<ts>(args)...);
    }
};
 
} // namespace seqan3::detail
 
namespace seqan3
{
 
template <typename t>
SEQAN3_CONCEPT alignment_file_input_format =
    requires (detail::alignment_file_input_format_exposer<t>                      & v,
              std::ifstream                                                       & stream,
              alignment_file_input_options<dna5>                                  & options,
              std::vector<dna5_vector>                                            & ref_sequences,
              alignment_file_header<>                                             & header,
              dna5_vector                                                         & seq,
              std::vector<phred42>                                                & qual,
              std::string                                                         & id,
              int32_t                                                             & offset,
              dna5_vector                                                         & ref_seq,
              std::optional<int32_t>                                              & ref_id,
              std::optional<int32_t>                                              & ref_offset,
              std::pair<std::vector<gapped<dna4>>, std::vector<gapped<dna4>>>     & align,
              std::vector<cigar>                                                  & cigar,
              sam_flag                                                            & flag,
              uint8_t                                                             & mapq,
              std::tuple<std::optional<int32_t>, std::optional<int32_t>, int32_t> & mate,
              sam_tag_dictionary                                                  & tag_dict,
              double                                                              & e_value,
              double                                                              & bit_score)
{
    t::file_extensions;
    // std::same_as<decltype(t::file_extensions), std::vector<std::string>>;
 
    { v.read_alignment_record(stream,
                              options,
                              ref_sequences,
                              header,
                              seq,
                              qual,
                              id,
                              offset,
                              ref_seq,
                              ref_id,
                              ref_offset,
                              align,
                              cigar,
                              flag,
                              mapq,
                              mate,
                              tag_dict,
                              e_value,
                              bit_score)};
 
    { v.read_alignment_record(stream,
                              options,
                              std::ignore,
                              header,
                              std::ignore,
                              std::ignore,
                              std::ignore,
                              std::ignore,
                              std::ignore,
                              std::ignore,
                              std::ignore,
                              std::ignore,
                              std::ignore,
                              std::ignore,
                              std::ignore,
                              std::ignore,
                              std::ignore,
                              std::ignore,
                              std::ignore)};
};
 
 
} // namespace seqan3
 
namespace seqan3::detail
{
 
template <typename t>
constexpr bool is_type_list_of_alignment_file_input_formats_v = false;
 
template <typename ...ts>
constexpr bool is_type_list_of_alignment_file_input_formats_v<type_list<ts...>> =
    (alignment_file_input_format<ts> && ...);
 
template <typename t>
SEQAN3_CONCEPT type_list_of_alignment_file_input_formats = is_type_list_of_alignment_file_input_formats_v<t>;
 
} // namespace seqan3::detail