sam_file/record.hpp

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// -----------------------------------------------------------------------------------------------------
// Copyright (c) 2006-2022, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2022, 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 <seqan3/io/record.hpp>
 
namespace seqan3
{
template <typename field_types, typename field_ids>
class sam_record : public record<field_types, field_ids>
{
    using base_t = record<field_types, field_ids>;
 
    using tuple_base_t = typename base_t::base_type;
 
    template <field f>
    using field_constant = typename base_t::template field_constant<f>;
 
    using base_t::get_impl;
 
public:
    sam_record() = default;                               
    sam_record(sam_record const &) = default;             
    sam_record & operator=(sam_record const &) = default; 
    sam_record(sam_record &&) = default;                  
    sam_record & operator=(sam_record &&) = default;      
    ~sam_record() = default;                              
 
    using base_t::base_t;
 
    decltype(auto) id() &&
    {
        return get_impl(field_constant<seqan3::field::id>{}, static_cast<tuple_base_t &&>(*this));
    }
    decltype(auto) id() const &&
    {
        return get_impl(field_constant<seqan3::field::id>{}, static_cast<tuple_base_t const &&>(*this));
    }
    decltype(auto) id() &
    {
        return get_impl(field_constant<seqan3::field::id>{}, static_cast<tuple_base_t &>(*this));
    }
    decltype(auto) id() const &
    {
        return get_impl(field_constant<seqan3::field::id>{}, static_cast<tuple_base_t const &>(*this));
    }
 
    decltype(auto) sequence() &&
    {
        return get_impl(field_constant<seqan3::field::seq>{}, static_cast<tuple_base_t &&>(*this));
    }
    decltype(auto) sequence() const &&
    {
        return get_impl(field_constant<seqan3::field::seq>{}, static_cast<tuple_base_t const &&>(*this));
    }
    decltype(auto) sequence() &
    {
        return get_impl(field_constant<seqan3::field::seq>{}, static_cast<tuple_base_t &>(*this));
    }
    decltype(auto) sequence() const &
    {
        return get_impl(field_constant<seqan3::field::seq>{}, static_cast<tuple_base_t const &>(*this));
    }
 
    decltype(auto) base_qualities() &&
    {
        return get_impl(field_constant<seqan3::field::qual>{}, static_cast<tuple_base_t &&>(*this));
    }
    decltype(auto) base_qualities() const &&
    {
        return get_impl(field_constant<seqan3::field::qual>{}, static_cast<tuple_base_t const &&>(*this));
    }
    decltype(auto) base_qualities() &
    {
        return get_impl(field_constant<seqan3::field::qual>{}, static_cast<tuple_base_t &>(*this));
    }
    decltype(auto) base_qualities() const &
    {
        return get_impl(field_constant<seqan3::field::qual>{}, static_cast<tuple_base_t const &>(*this));
    }
 
    SEQAN3_DEPRECATED_340 decltype(auto) sequence_position() &&
    {
        return static_cast<int32_t>(0);
    }
    SEQAN3_DEPRECATED_340 decltype(auto) sequence_position() const &&
    {
        return static_cast<int32_t>(0);
    }
    SEQAN3_DEPRECATED_340 decltype(auto) sequence_position() &
    {
        return static_cast<int32_t>(0);
    }
    SEQAN3_DEPRECATED_340 decltype(auto) sequence_position() const &
    {
        return static_cast<int32_t>(0);
    }
 
    SEQAN3_DEPRECATED_340 decltype(auto) alignment() &&
    {}
    SEQAN3_DEPRECATED_340 decltype(auto) alignment() const &&
    {}
    SEQAN3_DEPRECATED_340 decltype(auto) alignment() &
    {}
    SEQAN3_DEPRECATED_340 decltype(auto) alignment() const &
    {}
 
    decltype(auto) reference_id() &&
    {
        return get_impl(field_constant<seqan3::field::ref_id>{}, static_cast<tuple_base_t &&>(*this));
    }
    decltype(auto) reference_id() const &&
    {
        return get_impl(field_constant<seqan3::field::ref_id>{}, static_cast<tuple_base_t const &&>(*this));
    }
    decltype(auto) reference_id() &
    {
        return get_impl(field_constant<seqan3::field::ref_id>{}, static_cast<tuple_base_t &>(*this));
    }
    decltype(auto) reference_id() const &
    {
        return get_impl(field_constant<seqan3::field::ref_id>{}, static_cast<tuple_base_t const &>(*this));
    }
 
    decltype(auto) reference_sequence() = delete;
 
    decltype(auto) reference_position() &&
    {
        return get_impl(field_constant<seqan3::field::ref_offset>{}, static_cast<tuple_base_t &&>(*this));
    }
    decltype(auto) reference_position() const &&
    {
        return get_impl(field_constant<seqan3::field::ref_offset>{}, static_cast<tuple_base_t const &&>(*this));
    }
    decltype(auto) reference_position() &
    {
        return get_impl(field_constant<seqan3::field::ref_offset>{}, static_cast<tuple_base_t &>(*this));
    }
    decltype(auto) reference_position() const &
    {
        return get_impl(field_constant<seqan3::field::ref_offset>{}, static_cast<tuple_base_t const &>(*this));
    }
 
    decltype(auto) header_ptr() &&
    {
        return get_impl(field_constant<seqan3::field::header_ptr>{}, static_cast<tuple_base_t &&>(*this));
    }
    decltype(auto) header_ptr() const &&
    {
        return get_impl(field_constant<seqan3::field::header_ptr>{}, static_cast<tuple_base_t const &&>(*this));
    }
    decltype(auto) header_ptr() &
    {
        return get_impl(field_constant<seqan3::field::header_ptr>{}, static_cast<tuple_base_t &>(*this));
    }
    decltype(auto) header_ptr() const &
    {
        return get_impl(field_constant<seqan3::field::header_ptr>{}, static_cast<tuple_base_t const &>(*this));
    }
 
    decltype(auto) flag() &&
    {
        return get_impl(field_constant<seqan3::field::flag>{}, static_cast<tuple_base_t &&>(*this));
    }
    decltype(auto) flag() const &&
    {
        return get_impl(field_constant<seqan3::field::flag>{}, static_cast<tuple_base_t const &&>(*this));
    }
    decltype(auto) flag() &
    {
        return get_impl(field_constant<seqan3::field::flag>{}, static_cast<tuple_base_t &>(*this));
    }
    decltype(auto) flag() const &
    {
        return get_impl(field_constant<seqan3::field::flag>{}, static_cast<tuple_base_t const &>(*this));
    }
 
    decltype(auto) mate_reference_id() &&
    {
        return std::get<0>(get_impl(field_constant<seqan3::field::mate>{}, static_cast<tuple_base_t &&>(*this)));
    }
    decltype(auto) mate_reference_id() const &&
    {
        return std::get<0>(get_impl(field_constant<seqan3::field::mate>{}, static_cast<tuple_base_t const &&>(*this)));
    }
    decltype(auto) mate_reference_id() &
    {
        return std::get<0>(get_impl(field_constant<seqan3::field::mate>{}, static_cast<tuple_base_t &>(*this)));
    }
    decltype(auto) mate_reference_id() const &
    {
        return std::get<0>(get_impl(field_constant<seqan3::field::mate>{}, static_cast<tuple_base_t const &>(*this)));
    }
 
    decltype(auto) mate_position() &&
    {
        return std::get<1>(get_impl(field_constant<seqan3::field::mate>{}, static_cast<tuple_base_t &&>(*this)));
    }
    decltype(auto) mate_position() const &&
    {
        return std::get<1>(get_impl(field_constant<seqan3::field::mate>{}, static_cast<tuple_base_t const &&>(*this)));
    }
    decltype(auto) mate_position() &
    {
        return std::get<1>(get_impl(field_constant<seqan3::field::mate>{}, static_cast<tuple_base_t &>(*this)));
    }
    decltype(auto) mate_position() const &
    {
        return std::get<1>(get_impl(field_constant<seqan3::field::mate>{}, static_cast<tuple_base_t const &>(*this)));
    }
 
    decltype(auto) template_length() &&
    {
        return std::get<2>(get_impl(field_constant<seqan3::field::mate>{}, static_cast<tuple_base_t &&>(*this)));
    }
    decltype(auto) template_length() const &&
    {
        return std::get<2>(get_impl(field_constant<seqan3::field::mate>{}, static_cast<tuple_base_t const &&>(*this)));
    }
    decltype(auto) template_length() &
    {
        return std::get<2>(get_impl(field_constant<seqan3::field::mate>{}, static_cast<tuple_base_t &>(*this)));
    }
    decltype(auto) template_length() const &
    {
        return std::get<2>(get_impl(field_constant<seqan3::field::mate>{}, static_cast<tuple_base_t const &>(*this)));
    }
 
    decltype(auto) mapping_quality() &&
    {
        return get_impl(field_constant<seqan3::field::mapq>{}, static_cast<tuple_base_t &&>(*this));
    }
    decltype(auto) mapping_quality() const &&
    {
        return get_impl(field_constant<seqan3::field::mapq>{}, static_cast<tuple_base_t const &&>(*this));
    }
    decltype(auto) mapping_quality() &
    {
        return get_impl(field_constant<seqan3::field::mapq>{}, static_cast<tuple_base_t &>(*this));
    }
    decltype(auto) mapping_quality() const &
    {
        return get_impl(field_constant<seqan3::field::mapq>{}, static_cast<tuple_base_t const &>(*this));
    }
 
    decltype(auto) cigar_sequence() &&
    {
        return get_impl(field_constant<seqan3::field::cigar>{}, static_cast<tuple_base_t &&>(*this));
    }
    decltype(auto) cigar_sequence() const &&
    {
        return get_impl(field_constant<seqan3::field::cigar>{}, static_cast<tuple_base_t const &&>(*this));
    }
    decltype(auto) cigar_sequence() &
    {
        return get_impl(field_constant<seqan3::field::cigar>{}, static_cast<tuple_base_t &>(*this));
    }
    decltype(auto) cigar_sequence() const &
    {
        return get_impl(field_constant<seqan3::field::cigar>{}, static_cast<tuple_base_t const &>(*this));
    }
 
    decltype(auto) tags() &&
    {
        return get_impl(field_constant<seqan3::field::tags>{}, static_cast<tuple_base_t &&>(*this));
    }
    decltype(auto) tags() const &&
    {
        return get_impl(field_constant<seqan3::field::tags>{}, static_cast<tuple_base_t const &&>(*this));
    }
    decltype(auto) tags() &
    {
        return get_impl(field_constant<seqan3::field::tags>{}, static_cast<tuple_base_t &>(*this));
    }
    decltype(auto) tags() const &
    {
        return get_impl(field_constant<seqan3::field::tags>{}, static_cast<tuple_base_t const &>(*this));
    }
};
} // namespace seqan3
 
namespace std
{
 
template <typename field_types, typename field_ids>
struct tuple_size<seqan3::sam_record<field_types, field_ids>> :
    tuple_size<typename seqan3::sam_record<field_types, field_ids>::base_type>
{};
 
template <size_t elem_no, typename field_types, typename field_ids>
struct tuple_element<elem_no, seqan3::sam_record<field_types, field_ids>> :
    tuple_element<elem_no, typename seqan3::sam_record<field_types, field_ids>::base_type>
{};
 
} // namespace std