output_format_concept.hpp

Go to the documentation of this file.

// -----------------------------------------------------------------------------------------------------
// Copyright (c) 2006-2021, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2021, 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/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)...);
    }
};
 
} // namespace seqan3::detail
 
namespace seqan3
{
 
template <typename t>
SEQAN3_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,
              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;
 
    SEQAN3_RETURN_TYPE_CONSTRAINT(v.write_alignment_record(stream,
                                                           options,
                                                           header,
                                                           seq,
                                                           qual,
                                                           id,
                                                           offset,
                                                           ref_seq,
                                                           ref_id,
                                                           ref_offset,
                                                           align,
                                                           cigar,
                                                           flag,
                                                           mapq,
                                                           mate,
                                                           tag_dict,
                                                           e_value,
                                                           bit_score),
                                  std::same_as, void);
};
 
 
} // 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>
SEQAN3_CONCEPT type_list_of_sam_file_output_formats = is_type_list_of_sam_file_output_formats_v<t>;
} // namespace seqan3::detail