32 #include <seqan3/io/detail/record.hpp>
144 template <detail::fields_specialisation selected_field_ids_ =
161 detail::type_list_of_alignment_file_output_formats valid_formats_ = type_list<format_sam, format_bam>,
162 typename ref_ids_type = ref_info_not_given>
196 static_assert([] () constexpr
198 for (
field f : selected_field_ids::as_array)
199 if (!field_ids::contains(f))
203 "You selected a field that is not valid for alignment files, "
204 "please refer to the documentation of "
205 "seqan3::alignment_file_output::field_ids for the accepted values.");
223 using iterator = detail::out_file_iterator<alignment_file_output>;
275 primary_stream->rdbuf()->pubsetbuf(stream_buffer.
data(), stream_buffer.
size());
277 std::ios_base::out | std::ios::binary);
280 if (!primary_stream->good())
281 throw file_open_error{
"Could not open file " + filename.
string() +
" for writing."};
284 secondary_stream = detail::make_secondary_ostream(*primary_stream, filename);
287 detail::set_format(format, filename);
306 template <output_stream stream_type, alignment_file_output_format file_format>
308 requires std::same_as<typename std::remove_reference_t<stream_type>::char_type,
stream_char_type>
311 file_format
const & SEQAN3_DOXYGEN_ONLY(format_tag),
313 primary_stream{&stream, stream_deleter_noop},
314 secondary_stream{&stream, stream_deleter_noop},
315 format{detail::alignment_file_output_format_exposer<file_format>{}}
317 static_assert(list_traits::contains<file_format, valid_formats>,
318 "You selected a format that is not in the valid_formats of this file.");
322 template <output_stream stream_type, alignment_file_output_format file_format>
324 requires std::same_as<typename std::remove_reference_t<stream_type>::char_type,
stream_char_type>
327 file_format
const & SEQAN3_DOXYGEN_ONLY(format_tag),
329 primary_stream{
new stream_type{
std::move(stream)}, stream_deleter_default},
330 secondary_stream{&*primary_stream, stream_deleter_noop},
331 format{detail::alignment_file_output_format_exposer<file_format>{}}
333 static_assert(list_traits::contains<file_format, valid_formats>,
334 "You selected a format that is not in the valid_formats of this file.");
367 template <
typename ref_
ids_type_, std::ranges::forward_range ref_lengths_type>
369 requires std::same_as<std::remove_reference_t<ref_ids_type_>, ref_ids_type>
372 ref_ids_type_ && ref_ids,
373 ref_lengths_type && ref_lengths,
378 initialise_header_information(ref_ids, ref_lengths);
402 template <output_stream stream_type,
404 typename ref_ids_type_,
405 std::ranges::forward_range ref_lengths_type>
407 requires std::same_as<std::remove_reference_t<ref_ids_type_>, ref_ids_type>
410 ref_ids_type_ && ref_ids,
411 ref_lengths_type && ref_lengths,
412 file_format
const & SEQAN3_DOXYGEN_ONLY(format_tag),
416 initialise_header_information(ref_ids, ref_lengths);
483 template <
typename record_t>
486 requires detail::record_like<record_t>
492 write_record(detail::get_or<field::header_ptr>(r,
nullptr),
496 detail::get_or<field::offset>(r, 0u),
498 detail::get_or<field::ref_id>(r, std::ignore),
500 detail::get_or<field::alignment>(r, default_align_t{}),
503 detail::get_or<field::mapq>(r, 0u),
504 detail::get_or<field::mate>(r, default_mate_t{}),
506 detail::get_or<field::evalue>(r, 0u),
507 detail::get_or<field::bit_score>(r, 0u));
531 template <
typename tuple_t>
541 write_record(detail::get_or<selected_field_ids::index_of(
field::header_ptr)>(t,
nullptr),
545 detail::get_or<selected_field_ids::index_of(
field::offset)>(t, 0u),
547 detail::get_or<selected_field_ids::index_of(
field::ref_id)>(t, std::ignore),
549 detail::get_or<selected_field_ids::index_of(
field::alignment)>(t, default_align_t{}),
552 detail::get_or<selected_field_ids::index_of(
field::mapq)>(t, 0u),
553 detail::get_or<selected_field_ids::index_of(
field::mate)>(t, default_mate_t{}),
555 detail::get_or<selected_field_ids::index_of(
field::evalue)>(t, 0u),
582 template <
typename arg_t,
typename ...arg_types>
609 template <
typename rng_t>
615 for (
auto &&
record : range)
648 template <
typename rng_t>
659 template <
typename rng_t>
678 return *secondary_stream;
694 if constexpr (std::same_as<ref_ids_type, ref_info_not_given>)
695 throw std::logic_error{
"Please construct your file with reference id and length information in order "
696 "to properly initialise the header before accessing it."};
718 stream_ptr_t primary_stream{
nullptr, stream_deleter_noop};
720 stream_ptr_t secondary_stream{
nullptr, stream_deleter_noop};
723 using format_type =
typename detail::variant_from_tags<
valid_formats,
724 detail::alignment_file_output_format_exposer>::type;
731 using header_type = alignment_file_header<std::conditional_t<std::same_as<ref_ids_type, ref_info_not_given>,
739 template <
typename ref_
ids_type_,
typename ref_lengths_type>
740 void initialise_header_information(ref_ids_type_ && ref_ids, ref_lengths_type && ref_lengths)
744 header_ptr = std::make_unique<alignment_file_header<ref_ids_type>>(std::forward<ref_ids_type_>(ref_ids));
746 for (int32_t idx = 0; idx < std::ranges::distance(ref_ids); ++idx)
748 header_ptr->ref_id_info.emplace_back(ref_lengths[idx],
"");
750 if constexpr (std::ranges::contiguous_range<std::ranges::range_reference_t<ref_ids_type_>> &&
751 std::ranges::sized_range<std::ranges::range_reference_t<ref_ids_type_>> &&
752 std::ranges::borrowed_range<std::ranges::range_reference_t<ref_ids_type_>>)
765 template <
typename record_header_ptr_t,
typename ...pack_type>
766 void write_record(record_header_ptr_t && record_header_ptr, pack_type && ...remainder)
768 static_assert((
sizeof...(pack_type) == 15),
"Wrong parameter list passed to write_record.");
770 assert(!
format.valueless_by_exception());
775 if constexpr (!std::same_as<record_header_ptr_t, std::nullptr_t>)
777 f.write_alignment_record(*secondary_stream,
780 std::forward<pack_type>(remainder)...);
782 else if constexpr (std::same_as<ref_ids_type, ref_info_not_given>)
784 f.write_alignment_record(*secondary_stream,
787 std::forward<pack_type>(remainder)...);
791 f.write_alignment_record(*secondary_stream,
794 std::forward<pack_type>(remainder)...);
811 template <detail::fields_specialisation selected_field_
ids>
820 template <output_stream stream_type,
831 template <output_stream stream_type,
842 template <output_stream stream_type,
852 template <output_stream stream_type,
861 std::ranges::forward_range ref_ids_type,
862 std::ranges::forward_range ref_lengths_type>
872 template <std::ranges::forward_range ref_ids_type,
873 std::ranges::forward_range ref_lengths_type>
882 template <output_stream stream_type,
883 std::ranges::forward_range ref_ids_type,
884 std::ranges::forward_range ref_lengths_type,
897 template <output_stream stream_type,
898 std::ranges::forward_range ref_ids_type,
899 std::ranges::forward_range ref_lengths_type,
912 template <output_stream stream_type,
913 std::ranges::forward_range ref_ids_type,
914 std::ranges::forward_range ref_lengths_type,
925 template <output_stream stream_type,
926 std::ranges::forward_range ref_ids_type,
927 std::ranges::forward_range ref_lengths_type,
Provides seqan3::alignment_file_output_options.
A class for writing alignment files, e.g. SAM, BAL, BLAST, ...
Definition: output.hpp:164
alignment_file_output_options options
The options are public and its members can be set directly.
Definition: output.hpp:671
void value_type
The value type (void).
Definition: output.hpp:213
alignment_file_output & operator=(rng_t &&range)
Write a range of records (or tuples) to the file.
Definition: output.hpp:610
sentinel end() noexcept
Returns a sentinel for comparison with iterator.
Definition: output.hpp:460
alignment_file_output(stream_type &&, file_format const &) -> alignment_file_output< typename alignment_file_output<>::selected_field_ids, type_list< file_format >, ref_info_not_given >
Deduces the valid format from input and sets alignment_file_output::ref_ids_type to seqan3::detail::r...
alignment_file_output(std::filesystem::path, selected_field_ids const &) -> alignment_file_output< selected_field_ids, typename alignment_file_output<>::valid_formats, ref_info_not_given >
Deduces selected_field_ids from input and sets alignment_file_output::ref_ids_type to seqan3::detail:...
alignment_file_output & operator=(alignment_file_output &&)=default
Move assignment is defaulted.
void push_back(record_t &&r)
Write a seqan3::record to the file.
Definition: output.hpp:484
void size_type
The size type (void).
Definition: output.hpp:219
alignment_file_output(stream_type &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: output.hpp:310
alignment_file_output(stream_type &, file_format const &, selected_field_ids const &) -> alignment_file_output< selected_field_ids, type_list< file_format >, ref_info_not_given >
Deduces selected_field_ids, and the valid format from input and sets alignment_file_output::ref_ids_t...
alignment_file_output(stream_type &&stream, ref_ids_type_ &&ref_ids, ref_lengths_type &&ref_lengths, file_format const &format_tag, selected_field_ids const &fields_tag=selected_field_ids{})
Construct from an existing stream and with specified format.
Definition: output.hpp:409
alignment_file_output(alignment_file_output &&)=default
Move construction is defaulted.
void const_reference
The const reference type (void).
Definition: output.hpp:217
void push_back(tuple_t &&t)
Write a record in form of a std::tuple to the file.
Definition: output.hpp:532
alignment_file_output(std::filesystem::path filename, selected_field_ids const &fields_tag=selected_field_ids{})
Construct from filename.
Definition: output.hpp:271
alignment_file_output(stream_type &, file_format const &) -> alignment_file_output< typename alignment_file_output<>::selected_field_ids, type_list< file_format >, ref_info_not_given >
Deduces the valid format from input and sets alignment_file_output::ref_ids_type to seqan3::detail::r...
alignment_file_output(std::filesystem::path const &filename, ref_ids_type_ &&ref_ids, ref_lengths_type &&ref_lengths, selected_field_ids const &fields_tag=selected_field_ids{})
Construct from filename.
Definition: output.hpp:371
std::default_sentinel_t sentinel
The type returned by end().
Definition: output.hpp:227
iterator begin() noexcept
Returns an iterator to current position in the file.
Definition: output.hpp:441
alignment_file_output(stream_type &&, ref_ids_type &&, ref_lengths_type &&, file_format const &, selected_field_ids const &) -> alignment_file_output< selected_field_ids, type_list< file_format >, std::remove_reference_t< ref_ids_type >>
Deduces selected_field_ids, the valid format, and the ref_ids_type from input.
alignment_file_output(stream_type &, ref_ids_type &&, ref_lengths_type &&, file_format const &) -> alignment_file_output< typename alignment_file_output<>::selected_field_ids, type_list< file_format >, std::remove_reference_t< ref_ids_type >>
Deduces the valid format, and the ref_ids_type from input. selected_field_ids set to the default.
alignment_file_output & operator=(alignment_file_output const &)=delete
Copy assignment is explicitly deleted, because you can't have multiple access to the same file.
void const_iterator
The const iterator type is void, because files are not const-iterable.
Definition: output.hpp:225
selected_field_ids_ selected_field_ids
A seqan3::fields list with the fields selected for the record.
Definition: output.hpp:171
alignment_file_output()=delete
Default constructor is explicitly deleted, you need to give a stream or file name.
char stream_char_type
Character type of the stream(s).
Definition: output.hpp:175
alignment_file_output(stream_type &&, ref_ids_type &&, ref_lengths_type &&, file_format const &) -> alignment_file_output< typename alignment_file_output<>::selected_field_ids, type_list< file_format >, std::remove_reference_t< ref_ids_type >>
Deduces the valid format, and the ref_ids_type from input. selected_field_ids set to the default.
alignment_file_output(std::filesystem::path const &, ref_ids_type &&, ref_lengths_type &&, selected_field_ids const &) -> alignment_file_output< selected_field_ids, typename alignment_file_output<>::valid_formats, std::remove_reference_t< ref_ids_type >>
Deduces selected_field_ids and ref_ids_type from input. valid_formats is set to the default.
valid_formats_ valid_formats
A seqan3::type_list with the possible formats.
Definition: output.hpp:173
void reference
The reference type (void).
Definition: output.hpp:215
~alignment_file_output()=default
Destructor is defaulted.
auto & header()
Access the file's header.
Definition: output.hpp:692
detail::out_file_iterator< alignment_file_output > iterator
The iterator type of this view (an output iterator).
Definition: output.hpp:223
alignment_file_output(stream_type &&, file_format const &, selected_field_ids const &) -> alignment_file_output< selected_field_ids, type_list< file_format >, ref_info_not_given >
Deduces selected_field_ids, and the valid format from input and sets alignment_file_output::ref_ids_t...
friend alignment_file_output operator|(rng_t &&range, alignment_file_output &&f)
This is an overloaded member function, provided for convenience. It differs from the above function o...
Definition: output.hpp:660
friend alignment_file_output & operator|(rng_t &&range, alignment_file_output &f)
Write a range of records (or tuples) to the file.
Definition: output.hpp:649
alignment_file_output(stream_type &&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: output.hpp:326
alignment_file_output(std::filesystem::path const &, ref_ids_type &&, ref_lengths_type &&) -> alignment_file_output< typename alignment_file_output<>::selected_field_ids, typename alignment_file_output<>::valid_formats, std::remove_reference_t< ref_ids_type >>
Deduces ref_ids_type from input. Valid formats, and selected_field_ids are set to the default.
void emplace_back(arg_t &&arg, arg_types &&... args)
Write a record to the file by passing individual fields.
Definition: output.hpp:583
alignment_file_output(alignment_file_output const &)=delete
Copy construction is explicitly deleted, because you can't have multiple access to the same file.
alignment_file_output(stream_type &, ref_ids_type &&, ref_lengths_type &&, file_format const &, selected_field_ids const &) -> alignment_file_output< selected_field_ids, type_list< file_format >, std::remove_reference_t< ref_ids_type >>
Deduces selected_field_ids, the valid format, and the ref_ids_type from input.
The SAM tag dictionary class that stores all optional SAM fields.
Definition: sam_tag_dictionary.hpp:326
This header includes C++17 filesystem support and imports it into namespace std::filesystem (independ...
@ none
None of the flags below are set.
field
An enumerator for the fields used in file formats.
Definition: record.hpp:62
@ flag
The alignment flag (bit information), uint16_t value.
@ ref_offset
Sequence (seqan3::field::ref_seq) relative start position (0-based), unsigned value.
@ ref_seq
The (reference) "sequence" information, usually a range of nucleotides or amino acids.
@ alignment
The (pairwise) alignment stored in an object that models seqan3::detail::pairwise_alignment.
@ cigar
The cigar vector (std::vector<seqan3::cigar>) representing the alignment in SAM/BAM format.
@ mapq
The mapping quality of the seqan3::field::seq alignment, usually a Phred-scaled score.
@ bit_score
The bit score (statistical significance indicator), unsigned value.
@ offset
Sequence (seqan3::field::seq) relative start position (0-based), unsigned value.
@ mate
The mate pair information given as a std::tuple of reference name, offset and template length.
@ header_ptr
A pointer to the seqan3::alignment_file_header object storing header information.
@ ref_id
The identifier of the (reference) sequence that seqan3::field::seq was aligned to.
@ evalue
The e-value (length normalized bit score), double value.
@ id
The identifier, usually a string.
@ tags
The optional tags in the SAM format, stored in a dictionary.
@ seq
The "sequence", usually a range of nucleotides or amino acids.
@ qual
The qualities, usually in Phred score notation.
meta::list< types... > type_list
Type that contains multiple types, an alias for meta::list.
Definition: type_list.hpp:31
constexpr size_t size
The size of a type pack.
Definition: traits.hpp:150
auto const move
A view that turns lvalue-references into rvalue-references.
Definition: move.hpp:70
Whether a type behaves like a tuple.
Provides helper data structures for the seqan3::alignment_file_output.
Provides exceptions used in the I/O module.
Provides various utility functions required only for output.
The main SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29
Provides the seqan3::detail::out_file_iterator class template.
Adaptations of concepts from the Ranges TS.
Provides the seqan3::record template and the seqan3::field enum.
Provides seqan3::detail::record_like.
The options type defines various option members that influence the behavior of all or some formats.
Definition: output_options.hpp:23
A class template that holds a choice of seqan3::field.
Definition: record.hpp:163
The class template that file records are based on; behaves like an std::tuple.
Definition: record.hpp:223
Type tag which indicates that no reference information has been passed to the alignment file on const...
Definition: misc.hpp:23
Provides seqan3::tuple_like.
Provides traits for seqan3::type_list.