dev/html/sam__file_2input_8hpp_source.html

// -----------------------------------------------------------------------------------------------------

// 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 <cassert>

#include <seqan3/std/concepts>

#include <seqan3/std/filesystem>

#include <fstream>

#include <seqan3/std/ranges>

#include <string>

#include <variant>

#include <vector>


#include <seqan3/alignment/decorator/gap_decorator.hpp>

#include <seqan3/alphabet/adaptation/char.hpp>

#include <seqan3/alphabet/aminoacid/aa27.hpp>

#include <seqan3/alphabet/cigar/cigar.hpp>

#include <seqan3/alphabet/nucleotide/dna15.hpp>

#include <seqan3/alphabet/nucleotide/dna5.hpp>

#include <seqan3/alphabet/quality/phred42.hpp>

#include <seqan3/alphabet/quality/qualified.hpp>

#include <seqan3/io/detail/in_file_iterator.hpp>

#include <seqan3/io/detail/misc_input.hpp>

#include <seqan3/io/detail/record.hpp>

#include <seqan3/io/exception.hpp>

#include <seqan3/io/sam_file/format_bam.hpp>

#include <seqan3/io/sam_file/format_sam.hpp>

#include <seqan3/io/sam_file/input_format_concept.hpp>

#include <seqan3/io/sam_file/record.hpp>

#include <seqan3/io/sam_file/sam_flag.hpp>

#include <seqan3/io/stream/concept.hpp>

#include <seqan3/utility/tuple/concept.hpp>

#include <seqan3/utility/type_list/traits.hpp>

#include <seqan3/utility/type_traits/detail/transformation_trait_or.hpp>

#include <seqan3/utility/views/repeat_n.hpp>

#include <seqan3/utility/views/slice.hpp>


namespace seqan3

{


// ---------------------------------------------------------------------------------------------------------------------

// sam_file_input_traits

// ---------------------------------------------------------------------------------------------------------------------


template <typename t>

SEQAN3_CONCEPT sam_file_input_traits = requires (t v)

{

    // field::seq

    requires writable_alphabet<typename t::sequence_alphabet>;

    requires writable_alphabet<typename t::sequence_legal_alphabet>;

    requires explicitly_convertible_to<typename t::sequence_legal_alphabet, typename t::sequence_alphabet>;

    requires sequence_container<typename t::template sequence_container<typename t::sequence_alphabet>>;


    // field::id

    requires sequence_container<typename t::template id_container<char>>;


    // field::qual

    requires writable_quality_alphabet<typename t::quality_alphabet>;

    requires sequence_container<typename t::template quality_container<typename t::quality_alphabet>>;


    // field::ref_seq

    // either ref_info_not_given or a range over ranges over alphabet (e.g. std::vector<dna4_vector>)

    requires std::same_as<typename t::ref_sequences, ref_info_not_given> || requires ()

    {

        requires alphabet<std::ranges::range_reference_t<std::ranges::range_reference_t<typename t::ref_sequences>>>;

    };


    // field::ref_id

    requires alphabet<std::ranges::range_reference_t<std::ranges::range_reference_t<typename t::ref_ids>>> &&

             (!std::same_as<typename t::ref_sequences, ref_info_not_given> ||

              writable_alphabet<std::ranges::range_reference_t<std::ranges::range_reference_t<typename t::ref_ids>>>);

    requires std::ranges::forward_range<std::ranges::range_reference_t<typename t::ref_ids>>;

    requires std::ranges::forward_range<typename t::ref_ids>;


    // field::offset is fixed to int32_t

    // field::ref_offset is fixed to std::optional<int32_t>

    // field::flag is fixed to seqan3::sam_flag

    // field::mapq is fixed to uint8_t

    // field::evalue is fixed to double

    // field::bitscore is fixed to double

    // field::mate is fixed to std::tuple<ref_id_container<ref_id_alphabet>, ref_offset_type, int32_t>


    // field::alignment

    // the alignment type cannot be configured.

    // Type of tuple entry 1 (reference) is set to

    // 1) a std::ranges::subrange over std::ranges::range_value_t<typename t::ref_sequences> if reference information was given

    // or 2) a "dummy" sequence type:

    // views::repeat_n(sequence_alphabet{}, size_t{}) | std::views::transform(detail::access_restrictor_fn{})

    // Type of tuple entry 2 (query) is set to

    // 1) a std::ranges::subrange over std::ranges::range_value_t<typename t::ref_sequences> if reference information was given

    // or 2) a "dummy" sequence type:

};


// ---------------------------------------------------------------------------------------------------------------------

// sam_file_input_default_traits

// ---------------------------------------------------------------------------------------------------------------------


template <typename ref_sequences_t = ref_info_not_given, typename ref_ids_t = std::deque<std::string>>

struct sam_file_input_default_traits

{

    using sequence_alphabet                     = dna5;


    using sequence_legal_alphabet               = dna15;


    template <typename _sequence_alphabet>

    using sequence_container                    = std::vector<_sequence_alphabet>;


    template <typename _id_alphabet>

    using id_container                          = std::basic_string<_id_alphabet>;


    using quality_alphabet                      = phred42;


    template <typename _quality_alphabet>

    using quality_container                     = std::vector<_quality_alphabet>;


    using ref_sequences                         = ref_sequences_t;


    using ref_ids                               = ref_ids_t;

};


// ---------------------------------------------------------------------------------------------------------------------

// sam_file_input

// ---------------------------------------------------------------------------------------------------------------------


template <

    sam_file_input_traits traits_type_ = sam_file_input_default_traits<>,

    detail::fields_specialisation selected_field_ids_ = fields<field::seq,

                                                               field::id,

                                                               field::offset,

                                                               field::ref_id,

                                                               field::ref_offset,

                                                               field::alignment,

                                                               field::cigar,

                                                               field::mapq,

                                                               field::qual,

                                                               field::flag,

                                                               field::mate,

                                                               field::tags,

                                                               field::header_ptr>,

    detail::type_list_of_sam_file_input_formats valid_formats_ = type_list<format_sam, format_bam>>

class sam_file_input

{

public:

    using traits_type           = traits_type_;

    using selected_field_ids    = selected_field_ids_;

    using valid_formats         = valid_formats_;

    using stream_char_type      = char;


private:

    using dummy_ref_type = decltype(views::repeat_n(typename traits_type::sequence_alphabet{}, size_t{}) |

                                    std::views::transform(detail::access_restrictor_fn{}));


    using ref_sequence_unsliced_type =

        detail::lazy_conditional_t<std::ranges::range<typename traits_type::ref_sequences const>,

                                  detail::lazy<std::ranges::range_reference_t,

                                               typename traits_type::ref_sequences const>,

                                  dummy_ref_type>;


    using ref_sequence_sliced_type = decltype(std::declval<ref_sequence_unsliced_type>() | views::slice(0, 0));

public:

    using sequence_type            = typename traits_type::template sequence_container<

                                         typename traits_type::sequence_alphabet>;

    using id_type                  = typename traits_type::template id_container<char>;

    using offset_type              = int32_t;

    using ref_sequence_type = std::conditional_t<std::same_as<typename traits_type::ref_sequences, ref_info_not_given>,

                                                 dummy_ref_type,

                                                 ref_sequence_sliced_type>;

    using ref_id_type              = std::optional<int32_t>;

    using ref_offset_type          = std::optional<int32_t>;

    using mapq_type                = uint8_t;

    using quality_type             = typename traits_type::template quality_container<

                                         typename traits_type::quality_alphabet>;

    using flag_type                = sam_flag;

    using cigar_type               = std::vector<cigar>;

    using mate_type                = std::tuple<ref_id_type, ref_offset_type, int32_t>;

    using header_type              = sam_file_header<typename traits_type::ref_ids>;


private:

    using alignment_query_type = std::conditional_t<

                                     selected_field_ids::contains(field::seq),

                                     gap_decorator<

                                         decltype(std::declval<sequence_type &>() | views::slice(0, 0))>,

                                     typename traits_type::template sequence_container<

                                         gapped<typename traits_type::sequence_alphabet>>>;


public:

    using alignment_type = std::tuple<gap_decorator<ref_sequence_type>, alignment_query_type>;


    using field_types = type_list<sequence_type,

                                  id_type,

                                  offset_type,

                                  ref_id_type,

                                  ref_offset_type,

                                  alignment_type,

                                  std::vector<cigar>,

                                  mapq_type,

                                  quality_type,

                                  flag_type,

                                  mate_type,

                                  sam_tag_dictionary,

                                  header_type *>;


    using field_ids = fields<field::seq,

                             field::id,

                             field::offset,

                             field::ref_id,

                             field::ref_offset,

                             field::alignment,

                             field::cigar,

                             field::mapq,

                             field::qual,

                             field::flag,

                             field::mate,

                             field::tags,

                             field::header_ptr>;


    static_assert([] () constexpr

                  {

                      for (field f : selected_field_ids::as_array)

                          if (!field_ids::contains(f))

                              return false;

                      return true;

                  }(),

                  "You selected a field that is not valid for alignment files, please refer to the documentation "

                  "of sam_file_input::field_ids for the accepted values.");


    using record_type = sam_record<detail::select_types_with_ids_t<field_types, field_ids, selected_field_ids>,

                                   selected_field_ids>;


    using value_type        = record_type;

    using reference         = record_type &;

    using const_reference   = void;

    using size_type         = size_t;

    using difference_type   = std::make_signed_t<size_t>;

    using iterator          = detail::in_file_iterator<sam_file_input>;

    using const_iterator    = void;

    using sentinel          = std::default_sentinel_t;


    sam_file_input() = delete;

    sam_file_input(sam_file_input const &) = delete;

    sam_file_input & operator=(sam_file_input const &) = delete;

    sam_file_input(sam_file_input &&) = default;

    sam_file_input & operator=(sam_file_input &&) = default;

    ~sam_file_input() = default;


    sam_file_input(std::filesystem::path filename,

                   selected_field_ids const & SEQAN3_DOXYGEN_ONLY(fields_tag) = selected_field_ids{}) :

        primary_stream{new std::ifstream{}, stream_deleter_default}

    {

        init_by_filename(std::move(filename));

    }


    template <input_stream stream_t, sam_file_input_format file_format>

        requires std::same_as<typename std::remove_reference_t<stream_t>::char_type, stream_char_type>

    sam_file_input(stream_t & stream,

                   file_format const & SEQAN3_DOXYGEN_ONLY(format_tag),

                   selected_field_ids const & SEQAN3_DOXYGEN_ONLY(fields_tag) = selected_field_ids{}) :

        primary_stream{&stream, stream_deleter_noop}

    {

        init_by_format<file_format>();

    }


    template <input_stream stream_t, sam_file_input_format file_format>

        requires std::same_as<typename std::remove_reference_t<stream_t>::char_type, stream_char_type>

    sam_file_input(stream_t && stream,

                   file_format const & SEQAN3_DOXYGEN_ONLY(format_tag),

                   selected_field_ids const & SEQAN3_DOXYGEN_ONLY(fields_tag) = selected_field_ids{}) :

        primary_stream{new stream_t{std::move(stream)}, stream_deleter_default}

    {

        init_by_format<file_format>();

    }


    sam_file_input(std::filesystem::path filename,

                   typename traits_type::ref_ids & ref_ids,

                   typename traits_type::ref_sequences & ref_sequences,

                   selected_field_ids const & SEQAN3_DOXYGEN_ONLY(fields_tag) = selected_field_ids{}) :

        primary_stream{new std::ifstream{}, stream_deleter_default}

    {

        // initialize reference information

        set_references(ref_ids, ref_sequences);


        init_by_filename(std::move(filename));

    }


    template <input_stream stream_t, sam_file_input_format file_format>

    sam_file_input(stream_t & stream,

                   typename traits_type::ref_ids & ref_ids,

                   typename traits_type::ref_sequences & ref_sequences,

                   file_format const & SEQAN3_DOXYGEN_ONLY(format_tag),

                   selected_field_ids const & SEQAN3_DOXYGEN_ONLY(fields_tag) = selected_field_ids{}) :

        primary_stream{&stream, stream_deleter_noop}

    {

        // initialize reference information

        set_references(ref_ids, ref_sequences);


        init_by_format<file_format>();

    }


    template <input_stream stream_t, sam_file_input_format file_format>

    sam_file_input(stream_t && stream,

                   typename traits_type::ref_ids & ref_ids,

                   typename traits_type::ref_sequences & ref_sequences,

                   file_format const & SEQAN3_DOXYGEN_ONLY(format_tag),

                   selected_field_ids const & SEQAN3_DOXYGEN_ONLY(fields_tag) = selected_field_ids{}) :

        primary_stream{new stream_t{std::move(stream)}, stream_deleter_default}

    {

        // initialize reference information

        set_references(ref_ids, ref_sequences);


        init_by_format<file_format>();

    }


    // explicitly delete rvalues for reference information

    sam_file_input(std::filesystem::path,

                   typename traits_type::ref_ids &&,

                   typename traits_type::ref_sequences &&,

                   selected_field_ids const &) = delete;


    template <input_stream stream_t, sam_file_input_format file_format>

    sam_file_input(stream_t &&,

                   typename traits_type::ref_ids &&,

                   typename traits_type::ref_sequences &&,

                   file_format const &,

                   selected_field_ids const &) = delete;


    iterator begin()

    {

        // buffer first record

        if (!first_record_was_read)

        {

            read_next_record();

            first_record_was_read = true;

        }


        return {*this};

    }


    sentinel end() noexcept

    {

        return {};

    }


    reference front() noexcept

    {

        return *begin();

    }


    sam_file_input_options<typename traits_type::sequence_legal_alphabet> options;


    header_type & header()

    {

        // make sure header is read

        if (!first_record_was_read)

        {

            read_next_record();

            first_record_was_read = true;

        }


        return *header_ptr;

    }


protected:


    void init_by_filename(std::filesystem::path filename)

    {

        primary_stream->rdbuf()->pubsetbuf(stream_buffer.data(), stream_buffer.size());

        static_cast<std::basic_ifstream<char> *>(primary_stream.get())->open(filename,

                                                                             std::ios_base::in | std::ios::binary);

        // open stream

        if (!primary_stream->good())

            throw file_open_error{"Could not open file " + filename.string() + " for reading."};


        secondary_stream = detail::make_secondary_istream(*primary_stream, filename);

        detail::set_format(format, filename);

    }


    template <typename format_type>

    void init_by_format()

    {

        static_assert(list_traits::contains<format_type, valid_formats>,

                      "You selected a format that is not in the valid_formats of this file.");


        format = detail::sam_file_input_format_exposer<format_type>{};

        secondary_stream = detail::make_secondary_istream(*primary_stream);

    }


    std::unique_ptr<header_type> header_ptr{new header_type{}};


    record_type record_buffer;

    std::vector<char> stream_buffer{std::vector<char>(1'000'000)};


    using stream_ptr_t = std::unique_ptr<std::basic_istream<stream_char_type>,

                                         std::function<void(std::basic_istream<stream_char_type>*)>>;

    static void stream_deleter_noop(std::basic_istream<stream_char_type> *) {}

    static void stream_deleter_default(std::basic_istream<stream_char_type> * ptr) { delete ptr; }


    stream_ptr_t primary_stream{nullptr, stream_deleter_noop};

    stream_ptr_t secondary_stream{nullptr, stream_deleter_noop};


    bool first_record_was_read{false};

    bool at_end{false};


    using format_type = typename detail::variant_from_tags<valid_formats,

                                                           detail::sam_file_input_format_exposer>::type;


    format_type format;


    typename traits_type::ref_sequences const * reference_sequences_ptr{nullptr};


    template <std::ranges::forward_range ref_sequences_t>

    void set_references(typename traits_type::ref_ids & ref_ids, ref_sequences_t && ref_sequences)

    {

        assert(std::ranges::distance(ref_ids) == std::ranges::distance(ref_sequences));


        header_ptr = std::unique_ptr<header_type>{std::make_unique<header_type>(ref_ids)};

        reference_sequences_ptr = &ref_sequences;


        // initialise reference map and ref_dict if ref_ids are non-empty

        for (int32_t idx = 0; idx < std::ranges::distance(ref_ids); ++idx)

        {

            header_ptr->ref_id_info.emplace_back(std::ranges::distance(ref_sequences[idx]), "");


            if constexpr (std::ranges::contiguous_range<std::ranges::range_reference_t<

                                                            typename traits_type::ref_ids>> &&

                          std::ranges::sized_range<std::ranges::range_reference_t<typename traits_type::ref_ids>> &&

                          std::ranges::borrowed_range<std::ranges::range_reference_t<typename traits_type::ref_ids>>)

            {

                auto && id = header_ptr->ref_ids()[idx];

                header_ptr->ref_dict[std::span{std::ranges::data(id), std::ranges::size(id)}] = idx;

            }

            else

            {

                header_ptr->ref_dict[header_ptr->ref_ids()[idx]] = idx;

            }

        }

    }


    void read_next_record()

    {

        // clear the record

        record_buffer.clear();

        detail::get_or_ignore<field::header_ptr>(record_buffer) = header_ptr.get();


        // at end if we could not read further

        if (std::istreambuf_iterator<stream_char_type>{*secondary_stream} ==

            std::istreambuf_iterator<stream_char_type>{})

        {

            at_end = true;

            return;

        }


        auto call_read_func = [this] (auto & ref_seq_info)

        {

            std::visit([&] (auto & f)

            {

                f.read_alignment_record(*secondary_stream,

                                        options,

                                        ref_seq_info,

                                        *header_ptr,

                                        detail::get_or_ignore<field::seq>(record_buffer),

                                        detail::get_or_ignore<field::qual>(record_buffer),

                                        detail::get_or_ignore<field::id>(record_buffer),

                                        detail::get_or_ignore<field::offset>(record_buffer),

                                        detail::get_or_ignore<field::ref_seq>(record_buffer),

                                        detail::get_or_ignore<field::ref_id>(record_buffer),

                                        detail::get_or_ignore<field::ref_offset>(record_buffer),

                                        detail::get_or_ignore<field::alignment>(record_buffer),

                                        detail::get_or_ignore<field::cigar>(record_buffer),

                                        detail::get_or_ignore<field::flag>(record_buffer),

                                        detail::get_or_ignore<field::mapq>(record_buffer),

                                        detail::get_or_ignore<field::mate>(record_buffer),

                                        detail::get_or_ignore<field::tags>(record_buffer),

                                        detail::get_or_ignore<field::evalue>(record_buffer),

                                        detail::get_or_ignore<field::bit_score>(record_buffer));

            }, format);

        };


        assert(!format.valueless_by_exception());


        if constexpr (!std::same_as<typename traits_type::ref_sequences, ref_info_not_given>)

            call_read_func(*reference_sequences_ptr);

        else

            call_read_func(std::ignore);

    }


    friend iterator;

};


template <input_stream stream_type, sam_file_input_format file_format, detail::fields_specialisation selected_field_ids>

sam_file_input(stream_type && stream, file_format const &, selected_field_ids const &)

    -> sam_file_input<typename sam_file_input<>::traits_type, // actually use the default

                      selected_field_ids,

                      type_list<file_format>>;


template <input_stream stream_type, sam_file_input_format file_format, detail::fields_specialisation selected_field_ids>

sam_file_input(stream_type & stream, file_format const &, selected_field_ids const &)

    -> sam_file_input<typename sam_file_input<>::traits_type, // actually use the default

                      selected_field_ids,

                      type_list<file_format>>;


template <input_stream stream_type, sam_file_input_format file_format>

sam_file_input(stream_type && stream, file_format const &)

    -> sam_file_input<typename sam_file_input<>::traits_type, // actually use the default

                      typename sam_file_input<>::selected_field_ids, // actually use the default

                      type_list<file_format>>;


template <input_stream stream_type, sam_file_input_format file_format>

sam_file_input(stream_type & stream, file_format const &)

    -> sam_file_input<typename sam_file_input<>::traits_type, // actually use the default

                      typename sam_file_input<>::selected_field_ids, // actually use the default

                      type_list<file_format>>;


template <std::ranges::forward_range ref_ids_t,

          std::ranges::forward_range ref_sequences_t,

          detail::fields_specialisation selected_field_ids>

sam_file_input(std::filesystem::path path, ref_ids_t &, ref_sequences_t &, selected_field_ids const &)

    -> sam_file_input<sam_file_input_default_traits<std::remove_reference_t<ref_sequences_t>,

                                                    std::remove_reference_t<ref_ids_t>>,

                      selected_field_ids,

                      typename sam_file_input<>::valid_formats>;  // actually use the default


template <std::ranges::forward_range ref_ids_t,

          std::ranges::forward_range ref_sequences_t>

sam_file_input(std::filesystem::path path, ref_ids_t &, ref_sequences_t &)

    -> sam_file_input<sam_file_input_default_traits<std::remove_reference_t<ref_sequences_t>,

                                                    std::remove_reference_t<ref_ids_t>>,

                      typename sam_file_input<>::selected_field_ids, // actually use the default

                      typename sam_file_input<>::valid_formats>;     // actually use the default


template <input_stream stream_type,

          std::ranges::forward_range ref_ids_t,

          std::ranges::forward_range ref_sequences_t,

          sam_file_input_format file_format,

          detail::fields_specialisation selected_field_ids>

sam_file_input(stream_type && stream, ref_ids_t &, ref_sequences_t &, file_format const &, selected_field_ids const &)

    -> sam_file_input<sam_file_input_default_traits<std::remove_reference_t<ref_sequences_t>,

                                                    std::remove_reference_t<ref_ids_t>>,

                      selected_field_ids,

                      type_list<file_format>>;


template <input_stream stream_type,

          std::ranges::forward_range ref_ids_t,

          std::ranges::forward_range ref_sequences_t,

          sam_file_input_format file_format,

          detail::fields_specialisation selected_field_ids>

sam_file_input(stream_type & stream, ref_ids_t &, ref_sequences_t &, file_format const &, selected_field_ids const &)

    -> sam_file_input<sam_file_input_default_traits<std::remove_reference_t<ref_sequences_t>,

                                                    std::remove_reference_t<ref_ids_t>>,

                      selected_field_ids,

                      type_list<file_format>>;


template <input_stream stream_type,

          std::ranges::forward_range ref_ids_t,

          std::ranges::forward_range ref_sequences_t,

          sam_file_input_format file_format>

sam_file_input(stream_type && stream, ref_ids_t &, ref_sequences_t &, file_format const &)

    -> sam_file_input<sam_file_input_default_traits<std::remove_reference_t<ref_sequences_t>,

                                                    std::remove_reference_t<ref_ids_t>>,

                      typename sam_file_input<>::selected_field_ids, // actually use the default

                      type_list<file_format>>;


template <input_stream stream_type,

          std::ranges::forward_range ref_ids_t,

          std::ranges::forward_range ref_sequences_t,

          sam_file_input_format file_format>

sam_file_input(stream_type & stream, ref_ids_t &, ref_sequences_t &, file_format const &)

    -> sam_file_input<sam_file_input_default_traits<std::remove_reference_t<ref_sequences_t>,

                                                    std::remove_reference_t<ref_ids_t>>,

                      typename sam_file_input<>::selected_field_ids, // actually use the default

                      type_list<file_format>>;


} // namespace seqan3

aa27.hpp
Provides seqan3::aa27, container aliases and string literals.

cigar.hpp
Provides the seqan3::cigar alphabet.

std::ifstream

std::basic_istream

std::basic_string

cassert

char.hpp
Provides alphabet adaptations for standard char types.

seqan3::alphabet_variant
A combined alphabet that can hold values of either of its alternatives..
Definition: alphabet_variant.hpp:131

seqan3::detail::in_file_iterator
Input iterator necessary for providing a range-like interface in input file.
Definition: in_file_iterator.hpp:41

seqan3::dna15
The 15 letter DNA alphabet, containing all IUPAC smybols minus the gap..
Definition: dna15.hpp:51

seqan3::dna5
The five letter DNA alphabet of A,C,G,T and the unknown character N..
Definition: dna5.hpp:51

seqan3::gap_decorator
A gap decorator allows the annotation of sequences with gap symbols while leaving the underlying sequ...
Definition: gap_decorator.hpp:83

seqan3::phred42
Quality type for traditional Sanger and modern Illumina Phred scores..
Definition: phred42.hpp:47

seqan3::sam_file_header
Stores the header information of alignment files.
Definition: header.hpp:32

seqan3::sam_file_input
A class for reading alignment files, e.g. SAM, BAM, BLAST ...
Definition: input.hpp:350

seqan3::sam_file_input::sam_file_input
sam_file_input(std::filesystem::path path, ref_ids_t &, ref_sequences_t &) -> sam_file_input< sam_file_input_default_traits< std::remove_reference_t< ref_sequences_t >, std::remove_reference_t< ref_ids_t > >, typename sam_file_input<>::selected_field_ids, typename sam_file_input<>::valid_formats >
Deduce ref_sequences_t and ref_ids_t, default the rest.

seqan3::sam_file_input::end
sentinel end() noexcept
Returns a sentinel for comparison with iterator.
Definition: input.hpp:765

seqan3::sam_file_input::size_type
size_t size_type
An unsigned integer type, usually std::size_t.
Definition: input.hpp:520

seqan3::sam_file_input::ref_id_type
std::optional< int32_t > ref_id_type
The type of field::ref_id is fixed to std::optional<int32_t>.
Definition: input.hpp:409

seqan3::sam_file_input::set_references
void set_references(typename traits_type::ref_ids &ref_ids, ref_sequences_t &&ref_sequences)
Updates the reference information members and the header.
Definition: input.hpp:912

seqan3::sam_file_input::const_reference
void const_reference
The const_reference type is void because files are not const-iterable.
Definition: input.hpp:518

seqan3::sam_file_input::sam_file_input
sam_file_input(std::filesystem::path path, ref_ids_t &, ref_sequences_t &, selected_field_ids const &) -> sam_file_input< sam_file_input_default_traits< std::remove_reference_t< ref_sequences_t >, std::remove_reference_t< ref_ids_t > >, selected_field_ids, typename sam_file_input<>::valid_formats >
Deduce selected fields, ref_sequences_t and ref_ids_t, default the rest.

seqan3::sam_file_input::sam_file_input
sam_file_input(stream_t &stream, file_format const &format_tag, selected_field_ids const &fields_tag=selected_field_ids{})
Construct from an existing stream and with specified format.
Definition: input.hpp:594

seqan3::sam_file_input::valid_formats
valid_formats_ valid_formats
A seqan3::type_list with the possible formats.
Definition: input.hpp:361

seqan3::sam_file_input::dummy_ref_type
decltype(views::repeat_n(typename traits_type::sequence_alphabet{}, size_t{})|std::views::transform(detail::access_restrictor_fn{})) dummy_ref_type
The dummy ref sequence type if no reference information were given.
Definition: input.hpp:369

seqan3::sam_file_input::stream_char_type
char stream_char_type
Character type of the stream(s).
Definition: input.hpp:363

seqan3::sam_file_input::sam_file_input
sam_file_input(stream_type &&stream, ref_ids_t &, ref_sequences_t &, file_format const &) -> sam_file_input< sam_file_input_default_traits< std::remove_reference_t< ref_sequences_t >, std::remove_reference_t< ref_ids_t > >, typename sam_file_input<>::selected_field_ids, type_list< file_format > >
Deduce ref_sequences_t and ref_ids_t, and file format.

seqan3::sam_file_input::sequence_type
typename traits_type::template sequence_container< typename traits_type::sequence_alphabet > sequence_type
The type of field::seq (default std::vector<seqan3::dna5>).
Definition: input.hpp:388

seqan3::sam_file_input::sam_file_input
sam_file_input(std::filesystem::path filename, selected_field_ids const &fields_tag=selected_field_ids{})
Construct from filename.
Definition: input.hpp:564

seqan3::sam_file_input::at_end
bool at_end
File is one position behind the last record.
Definition: input.hpp:885

seqan3::sam_file_input::sam_file_input
sam_file_input(stream_type &stream, file_format const &) -> sam_file_input< typename sam_file_input<>::traits_type, typename sam_file_input<>::selected_field_ids, type_list< file_format > >
Deduce file_format, and default the rest.

seqan3::sam_file_input::sentinel
std::default_sentinel_t sentinel
The type returned by end().
Definition: input.hpp:528

seqan3::sam_file_input::read_next_record
void read_next_record()
Tell the format to move to the next record and update the buffer.
Definition: input.hpp:941

seqan3::sam_file_input::sam_file_input
sam_file_input(stream_t &stream, typename traits_type::ref_ids &ref_ids, typename traits_type::ref_sequences &ref_sequences, file_format const &format_tag, selected_field_ids const &fields_tag=selected_field_ids{})
Construct from an existing stream and with specified format.
Definition: input.hpp:676

seqan3::sam_file_input::stream_buffer
std::vector< char > stream_buffer
A larger (compared to stl default) stream buffer to use when reading from a file.
Definition: input.hpp:863

seqan3::sam_file_input::primary_stream
stream_ptr_t primary_stream
The primary stream is the user provided stream or the file stream if constructed from filename.
Definition: input.hpp:878

seqan3::sam_file_input::format
format_type format
The actual std::variant holding a pointer to the detected/selected format.
Definition: input.hpp:892

seqan3::sam_file_input::ref_offset_type
std::optional< int32_t > ref_offset_type
The type of field::ref_offset is fixed to an std::optional<int32_t>.
Definition: input.hpp:416

seqan3::sam_file_input::traits_type
traits_type_ traits_type
A traits type that defines aliases and template for storage of the fields.
Definition: input.hpp:357

seqan3::sam_file_input::offset_type
int32_t offset_type
The type of field::offset is fixed to int32_t.
Definition: input.hpp:392

seqan3::sam_file_input::sam_file_input
sam_file_input(stream_type &stream, ref_ids_t &, ref_sequences_t &, file_format const &) -> sam_file_input< sam_file_input_default_traits< std::remove_reference_t< ref_sequences_t >, std::remove_reference_t< ref_ids_t > >, typename sam_file_input<>::selected_field_ids, type_list< file_format > >
Deduce selected fields, ref_sequences_t and ref_ids_t, and file format.

seqan3::sam_file_input::options
sam_file_input_options< typename traits_type::sequence_legal_alphabet > options
The options are public and its members can be set directly.
Definition: input.hpp:800

seqan3::sam_file_input::sam_file_input
sam_file_input(stream_type &&stream, file_format const &) -> sam_file_input< typename sam_file_input<>::traits_type, typename sam_file_input<>::selected_field_ids, type_list< file_format > >
Deduce file_format, and default the rest.

seqan3::sam_file_input::stream_deleter_noop
static void stream_deleter_noop(std::basic_istream< stream_char_type > *)
Stream deleter that does nothing (no ownership assumed).
Definition: input.hpp:873

seqan3::sam_file_input::ref_sequence_unsliced_type
detail::lazy_conditional_t< std::ranges::range< typename traits_type::ref_sequences const  >, detail::lazy< std::ranges::range_reference_t, typename traits_type::ref_sequences const  >, dummy_ref_type > ref_sequence_unsliced_type
The unsliced ref sequence type if reference information were given.
Definition: input.hpp:376

seqan3::sam_file_input::id_type
typename traits_type::template id_container< char > id_type
The type of field::id (default std::string by default).
Definition: input.hpp:390

seqan3::sam_file_input::operator=
sam_file_input & operator=(sam_file_input &&)=default
Move assignment is defaulted.

seqan3::sam_file_input::iterator
friend iterator
Befriend iterator so it can access the buffers.
Definition: input.hpp:990

seqan3::sam_file_input::secondary_stream
stream_ptr_t secondary_stream
The secondary stream is a compression layer on the primary or just points to the primary (no compress...
Definition: input.hpp:880

seqan3::sam_file_input::quality_type
typename traits_type::template quality_container< typename traits_type::quality_alphabet > quality_type
The type of field::qual (default std::vector<seqan3::phred42>).
Definition: input.hpp:421

seqan3::sam_file_input::sam_file_input
sam_file_input(stream_t &&stream, typename traits_type::ref_ids &ref_ids, typename traits_type::ref_sequences &ref_sequences, file_format const &format_tag, selected_field_ids const &fields_tag=selected_field_ids{})
This is an overloaded member function, provided for convenience. It differs from the above function o...
Definition: input.hpp:691

seqan3::sam_file_input::alignment_type
std::tuple< gap_decorator< ref_sequence_type >, alignment_query_type > alignment_type
The type of field::alignment (default: std::pair<std::vector<gapped<dna5>>, std::vector<gapped<dna5>>...
Definition: input.hpp:442

seqan3::sam_file_input::record_type
sam_record< detail::select_types_with_ids_t< field_types, field_ids, selected_field_ids >, selected_field_ids > record_type
The type of the record, a specialisation of seqan3::record; acts as a tuple of the selected field typ...
Definition: input.hpp:506

seqan3::sam_file_input::format_type
typename detail::variant_from_tags< valid_formats, detail::sam_file_input_format_exposer >::type format_type
Type of the format, an std::variant over the valid_formats.
Definition: input.hpp:889

seqan3::sam_file_input::sam_file_input
sam_file_input()=delete
Default constructor is explicitly deleted, you need to give a stream or file name.

seqan3::sam_file_input::begin
iterator begin()
Returns an iterator to current position in the file.
Definition: input.hpp:740

seqan3::sam_file_input::selected_field_ids
selected_field_ids_ selected_field_ids
A seqan3::fields list with the fields selected for the record.
Definition: input.hpp:359

seqan3::sam_file_input::sam_file_input
sam_file_input(stream_type &stream, ref_ids_t &, ref_sequences_t &, file_format const &, selected_field_ids const &) -> sam_file_input< sam_file_input_default_traits< std::remove_reference_t< ref_sequences_t >, std::remove_reference_t< ref_ids_t > >, selected_field_ids, type_list< file_format > >
Deduce selected fields, ref_sequences_t and ref_ids_t, and file format.

seqan3::sam_file_input::first_record_was_read
bool first_record_was_read
Tracks whether the very first record is buffered when calling begin().
Definition: input.hpp:883

seqan3::sam_file_input::sam_file_input
sam_file_input(std::filesystem::path filename, typename traits_type::ref_ids &ref_ids, typename traits_type::ref_sequences &ref_sequences, selected_field_ids const &fields_tag=selected_field_ids{})
Construct from filename and given additional reference information.
Definition: input.hpp:638

seqan3::sam_file_input::operator=
sam_file_input & operator=(sam_file_input const &)=delete
Copy assignment is explicitly deleted because you cannot have multiple access to the same file.

seqan3::sam_file_input::record_buffer
record_type record_buffer
Buffer for a single record.
Definition: input.hpp:861

seqan3::sam_file_input::sam_file_input
sam_file_input(sam_file_input &&)=default
Move construction is defaulted.

seqan3::sam_file_input::init_by_format
void init_by_format()
/brief Initialisation based on a format (construction via stream).
Definition: input.hpp:845

seqan3::sam_file_input::const_iterator
void const_iterator
The const iterator type is void because files are not const-iterable.
Definition: input.hpp:526

seqan3::sam_file_input::header_ptr
std::unique_ptr< header_type > header_ptr
The file header object.
Definition: input.hpp:855

seqan3::sam_file_input::header
header_type & header()
Access the file's header.
Definition: input.hpp:814

seqan3::sam_file_input::sam_file_input
sam_file_input(sam_file_input const &)=delete
Copy construction is explicitly deleted because you cannot have multiple access to the same file.

seqan3::sam_file_input::mapq_type
uint8_t mapq_type
The type of field::mapq is fixed to uint8_t.
Definition: input.hpp:418

seqan3::sam_file_input::flag_type
sam_flag flag_type
The type of field::flag is fixed to seqan3::sam_flag.
Definition: input.hpp:423

seqan3::sam_file_input::sam_file_input
sam_file_input(stream_t &&stream, file_format const &format_tag, selected_field_ids const &fields_tag=selected_field_ids{})
This is an overloaded member function, provided for convenience. It differs from the above function o...
Definition: input.hpp:607

seqan3::sam_file_input::ref_sequence_sliced_type
decltype(std::declval< ref_sequence_unsliced_type >()|views::slice(0, 0)) ref_sequence_sliced_type
The ref sequence type if reference information were given.
Definition: input.hpp:379

seqan3::sam_file_input::sam_file_input
sam_file_input(stream_type &&stream, file_format const &, selected_field_ids const &) -> sam_file_input< typename sam_file_input<>::traits_type, selected_field_ids, type_list< file_format > >
Deduce selected fields, file_format, and default the rest.

seqan3::sam_file_input::sam_file_input
sam_file_input(stream_type &&stream, ref_ids_t &, ref_sequences_t &, file_format const &, selected_field_ids const &) -> sam_file_input< sam_file_input_default_traits< std::remove_reference_t< ref_sequences_t >, std::remove_reference_t< ref_ids_t > >, selected_field_ids, type_list< file_format > >
Deduce selected fields, ref_sequences_t and ref_ids_t, and file format.

seqan3::sam_file_input::stream_deleter_default
static void stream_deleter_default(std::basic_istream< stream_char_type > *ptr)
Stream deleter with default behaviour (ownership assumed).
Definition: input.hpp:875

seqan3::sam_file_input::~sam_file_input
~sam_file_input()=default
Destructor is defaulted.

seqan3::sam_file_input::mate_type
std::tuple< ref_id_type, ref_offset_type, int32_t > mate_type
The type of field::mate is fixed to std::tuple<ref_id_type, ref_offset_type, int32_t>).
Definition: input.hpp:427

seqan3::sam_file_input::init_by_filename
void init_by_filename(std::filesystem::path filename)
Definition: input.hpp:830

seqan3::sam_file_input::front
reference front() noexcept
Return the record we are currently at in the file.
Definition: input.hpp:793

seqan3::sam_file_input::reference_sequences_ptr
traits_type::ref_sequences const  * reference_sequences_ptr
A pointer to the reference sequence information if given on construction.
Definition: input.hpp:899

seqan3::sam_file_input::sam_file_input
sam_file_input(stream_type &stream, file_format const &, selected_field_ids const &) -> sam_file_input< typename sam_file_input<>::traits_type, selected_field_ids, type_list< file_format > >
Deduce selected fields, file_format, and default the rest.

seqan3::sam_record< detail::select_types_with_ids_t< field_types, field_ids, selected_field_ids >, selected_field_ids >

seqan3::sam_tag_dictionary
The SAM tag dictionary class that stores all optional SAM fields.
Definition: sam_tag_dictionary.hpp:334

concepts
The Concepts library.

std::conditional_t

record.hpp
Provides auxiliary data structures and functions for seqan3::record and seqan3::fields.

dna15.hpp
Provides seqan3::dna15, container aliases and string literals.

dna5.hpp
Provides seqan3::dna5, container aliases and string literals.

filesystem
This header includes C++17 filesystem support and imports it into namespace std::filesystem (independ...

format_bam.hpp
Provides the seqan3::format_bam.

format_sam.hpp
Provides the seqan3::format_sam.

fstream

std::function

gap_decorator.hpp
Provides seqan3::gap_decorator.

std::unique_ptr::get
T get(T... args)

seqan3::sam_flag
sam_flag
An enum flag that describes the properties of an aligned read (given as a SAM record).
Definition: sam_flag.hpp:74

seqan3::detail::type_list_of_sam_file_input_formats
SEQAN3_CONCEPT type_list_of_sam_file_input_formats
Auxiliary concept that checks whether a type is a seqan3::type_list and all types meet seqan3::sam_fi...
Definition: input_format_concept.hpp:246

seqan3::field
field
An enumerator for the fields used in file formats.
Definition: record.hpp:63

seqan3::detail::set_format
void set_format(format_variant_type &format, std::filesystem::path const &file_name)
Sets the file format according to the file name extension.
Definition: misc.hpp:67

seqan3::detail::make_secondary_istream
auto make_secondary_istream(std::basic_istream< char_t > &primary_stream, std::filesystem::path &filename) -> std::unique_ptr< std::basic_istream< char_t >, std::function< void(std::basic_istream< char_t > *)> >
Depending on the magic bytes of the given stream, return a decompression stream or forward the primar...
Definition: misc_input.hpp:81

seqan3::detail::fields_specialisation
SEQAN3_CONCEPT fields_specialisation
Auxiliary concept that checks whether a type is a specialisation of seqan3::fields.
Definition: record.hpp:35

seqan3::field::flag
@ flag
The alignment flag (bit information), uint16_t value.

seqan3::field::ref_offset
@ ref_offset
Sequence (seqan3::field::ref_seq) relative start position (0-based), unsigned value.

seqan3::field::alignment
@ alignment
The (pairwise) alignment stored in an object that models seqan3::detail::pairwise_alignment.

seqan3::field::cigar
@ cigar
The cigar vector (std::vector<seqan3::cigar>) representing the alignment in SAM/BAM format.

seqan3::field::mapq
@ mapq
The mapping quality of the seqan3::field::seq alignment, usually a Phred-scaled score.

seqan3::field::offset
@ offset
Sequence (seqan3::field::seq) relative start position (0-based), unsigned value.

seqan3::field::mate
@ mate
The mate pair information given as a std::tuple of reference name, offset and template length.

seqan3::field::header_ptr
@ header_ptr
A pointer to the seqan3::sam_file_header object storing header information.

seqan3::field::ref_id
@ ref_id
The identifier of the (reference) sequence that seqan3::field::seq was aligned to.

seqan3::field::id
@ id
The identifier, usually a string.

seqan3::field::tags
@ tags
The optional tags in the SAM format, stored in a dictionary.

seqan3::field::seq
@ seq
The "sequence", usually a range of nucleotides or amino acids.

seqan3::field::qual
@ qual
The qualities, usually in Phred score notation.

seqan3::list_traits::contains
constexpr bool contains
Whether a type occurs in a type list or not.
Definition: traits.hpp:231

seqan3::list_traits::transform
decltype(detail::transform< trait_t >(list_t{})) transform
Apply a transformation trait to every type in the list and return a seqan3::type_list of the results.
Definition: traits.hpp:471

seqan3::pack_traits::size
constexpr size_t size
The size of a type pack.
Definition: traits.hpp:151

seqan3::views::slice
constexpr auto slice
A view adaptor that returns a half-open interval on the underlying range.
Definition: slice.hpp:183

seqan3::views::repeat_n
constexpr auto repeat_n
A view factory that repeats a given value n times.
Definition: repeat_n.hpp:91

in_file_iterator.hpp
Provides the seqan3::detail::in_file_iterator class template.

alphabet
The generic alphabet concept that covers most data types used in ranges.

explicitly_convertible_to
Resolves to std::ranges::explicitly_convertible_to<type1, type2>().  <dl class="no-api">This entity i...

sam_file_input_format
The generic concept for alignment file input formats.

sam_file_input_traits
The requirements a traits_type for seqan3::sam_file_input must meet.

sequence_container
A more refined container concept than seqan3::container.

writable_alphabet
Refines seqan3::alphabet and adds assignability.

writable_quality_alphabet
A concept that indicates whether a writable alphabet represents quality scores.

exception.hpp
Provides exceptions used in the I/O module.

concept.hpp
Stream concepts.

std::istreambuf_iterator

std::make_signed_t

misc_input.hpp
Provides various utility functions required only for input.

seqan3
The main SeqAn3 namespace.
Definition: cigar_operation_table.hpp:2

std::optional

std::filesystem::path

phred42.hpp
Provides seqan3::phred42 quality scores.

qualified.hpp
Provides quality alphabet composites.

ranges
Adaptations of concepts from the Ranges TS.

std::remove_reference_t

repeat_n.hpp
Provides seqan3::views::repeat_n.

input_format_concept.hpp
Provides seqan3::sam_file_input_format and auxiliary classes.

record.hpp
Provides seqan3::sam_record.

sam_flag.hpp
Provides helper data structures for the seqan3::sam_file_output.

slice.hpp
Provides seqan3::views::slice.

std::span

string

seqan3::detail::lazy
An empty type whose only purpose is to hold an uninstantiated template plus its arguments.
Definition: lazy_conditional.hpp:33

seqan3::detail::sam_file_input_format_exposer
Internal class used to expose the actual format interface to read alignment records from the file.
Definition: input_format_concept.hpp:46

seqan3::detail::variant_from_tags
Base class to deduce the std::variant type from format tags.
Definition: misc.hpp:30

seqan3::fields
A class template that holds a choice of seqan3::field.
Definition: record.hpp:128

seqan3::fields::contains
static constexpr bool contains(field f)
Whether a field is contained in the parameter pack.
Definition: record.hpp:149

seqan3::file_open_error
Thrown if there is an unspecified filesystem or stream error while opening, e.g. permission problem.
Definition: exception.hpp:39

seqan3::record::clear
void clear() noexcept(noexcept(std::apply(expander, std::declval< record & >())))
Clears containers that provide .clear() and (re-)initialises all other elements with = {}.
Definition: record.hpp:235

seqan3::sam_file_input_default_traits
The default traits for seqan3::sam_file_input.
Definition: input.hpp:184

seqan3::sam_file_input_default_traits::ref_ids
ref_ids_t ref_ids
The type of the reference identifiers is deduced on construction.
Definition: input.hpp:215

seqan3::sam_file_input_default_traits::ref_sequences
ref_sequences_t ref_sequences
The type of the reference sequences is deduced on construction.
Definition: input.hpp:212

seqan3::sam_file_input_options
The options type defines various option members that influence the behaviour of all or some formats.
Definition: input_options.hpp:24

seqan3::type_list
Type that contains multiple types.
Definition: type_list.hpp:29

transformation_trait_or.hpp
Provides seqan3::detail::transformation_trait_or.

std::tuple

traits.hpp
Provides traits for seqan3::type_list.

std::unique_ptr

concept.hpp
Provides seqan3::tuple_like.

variant

vector

std::visit
T visit(T... args)