output_format_concept.hpp

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// -----------------------------------------------------------------------------------------------------
// Copyright (c) 2006-2019, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2019, 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/gap/gapped.hpp>
#include <seqan3/alphabet/nucleotide/dna5.hpp>
#include <seqan3/alphabet/quality/aliases.hpp>
#include <seqan3/alphabet/quality/phred42.hpp>
#include <seqan3/core/type_list.hpp>
#include <seqan3/io/alignment_file/header.hpp>
#include <seqan3/io/alignment_file/output_options.hpp>
#include <seqan3/io/alignment_file/sam_tag_dictionary.hpp>

namespace seqan3::detail
{

template <typename t>
class alignment_file_output_format
{};

} // namespace seqan3::detail

namespace seqan3
{

template <typename t>
SEQAN3_CONCEPT AlignmentFileOutputFormat =
    requires (detail::alignment_file_output_format<t>                              & v,
              std::ofstream                                                        & stream,
              alignment_file_output_options                                        & options,
              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,
              uint16_t                                                             & 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(stream,
              options,
              header,
              seq,
              qual,
              id,
              offset,
              ref_seq,
              ref_id,
              ref_offset,
              align,
              flag,
              mapq,
              mate,
              tag_dict,
              e_value,
              bit_score
              ) } -> void;
};


} // namespace seqan3

namespace seqan3::detail
{

template <typename t>
constexpr bool is_type_list_of_alignment_file_output_formats_v = false;

template <typename ... ts>
constexpr bool is_type_list_of_alignment_file_output_formats_v<type_list<ts...>>
                = (AlignmentFileOutputFormat<ts> && ...);

template <typename t>
SEQAN3_CONCEPT TypeListOfAlignmentFileOutputFormats = is_type_list_of_alignment_file_output_formats_v<t>;
} // namespace seqan3::detail