sam_file/input_format_concept.hpp

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// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: BSD-3-Clause

 
#pragma once
 
#include <fstream>
#include <optional>
#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/io/sam_file/header.hpp>
#include <seqan3/io/sam_file/input_options.hpp>
#include <seqan3/io/sam_file/sam_flag.hpp>
#include <seqan3/io/sam_file/sam_tag_dictionary.hpp>
#include <seqan3/utility/type_list/type_list.hpp>
 
namespace seqan3::detail
{

template <typename format_type>
struct sam_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>
concept sam_file_input_format = requires (detail::sam_file_input_format_exposer<t> & v,
                                          std::ifstream & stream,
                                          sam_file_input_options<dna5> & options,
                                          std::vector<dna5_vector> & ref_sequences,
                                          sam_file_header<> & header,
                                          std::streampos & position_buffer,
                                          dna5_vector & seq,
                                          std::vector<phred42> & qual,
                                          std::string & id,
                                          dna5_vector & ref_seq,
                                          std::optional<int32_t> & ref_id,
                                          std::optional<int32_t> & ref_offset,
                                          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,
                                position_buffer,
                                seq,
                                qual,
                                id,
                                ref_seq,
                                ref_id,
                                ref_offset,
                                cigar,
                                flag,
                                mapq,
                                mate,
                                tag_dict,
                                e_value,
                                bit_score)
    };
 
    {
        v.read_alignment_record(stream,
                                options,
                                std::ignore,
                                header,
                                position_buffer,
                                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)
    };
};
 
// Workaround for https://github.com/doxygen/doxygen/issues/9379
#if SEQAN3_DOXYGEN_ONLY(1) 0
template <typename t>
class sam_file_input_format
{};
#endif


 
} // namespace seqan3
 
namespace seqan3::detail
{

template <typename t>
constexpr bool is_type_list_of_sam_file_input_formats_v = false;

template <typename... ts>
constexpr bool is_type_list_of_sam_file_input_formats_v<type_list<ts...>> = (sam_file_input_format<ts> && ...);

template <typename t>
concept type_list_of_sam_file_input_formats = is_type_list_of_sam_file_input_formats_v<t>;
 
} // namespace seqan3::detail