sam_file/output_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/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/output_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_output_format_exposer : public format_type
{
public:
    // Can't use `using format_type::write_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 write_alignment_record interface.
    template <typename... ts>
    void write_alignment_record(ts &&... args)
    {
        format_type::write_alignment_record(std::forward<ts>(args)...);
    }

    template <typename stream_t, typename header_type>
    void write_header(stream_t & stream, sam_file_output_options const & options, header_type & header)
    {
        format_type::write_header(stream, options, header);
    }
};
 
} // namespace seqan3::detail
 
namespace seqan3
{

template <typename t>
concept sam_file_output_format = requires (detail::sam_file_output_format_exposer<t> & v,
                                           std::ofstream & stream,
                                           sam_file_output_options & options,
                                           sam_file_header<> & header,
                                           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;
 
    {
        v.write_alignment_record(stream,
                                 options,
                                 header,
                                 seq,
                                 qual,
                                 id,
                                 ref_seq,
                                 ref_id,
                                 ref_offset,
                                 cigar,
                                 flag,
                                 mapq,
                                 mate,
                                 tag_dict,
                                 e_value,
                                 bit_score)
    } -> std::same_as<void>;
};
 
// Workaround for https://github.com/doxygen/doxygen/issues/9379
#if SEQAN3_DOXYGEN_ONLY(1) 0
template <typename t>
class sam_file_output_format
{};
#endif



 
} // namespace seqan3
 
namespace seqan3::detail
{

template <typename t>
constexpr bool is_type_list_of_sam_file_output_formats_v = false;

template <typename... ts>
constexpr bool is_type_list_of_sam_file_output_formats_v<type_list<ts...>> = (sam_file_output_format<ts> && ...);

template <typename t>
concept type_list_of_sam_file_output_formats = is_type_list_of_sam_file_output_formats_v<t>;
} // namespace seqan3::detail