57template <detail::fields_specialisation selected_field_ids_ = fields<
field::seq,
68 detail::type_list_of_sam_file_output_formats valid_formats_ = type_list<format_sam, format_bam>,
69 typename ref_ids_type = ref_info_not_given>
99 "The field::offset is deprecated. It is already stored in the field::cigar as soft clipping (S) "
100 "at the front and not needed otherwise.");
103 "The seqan3::field::alignment was removed from the allowed fields for seqan3::sam_file_output. "
104 "Only seqan3::field::cigar is supported. seqan3::cigar_from_alignment on how to get a CIGAR string "
105 "from an alignment.");
110 for (
field f : selected_field_ids::as_array)
115 "You selected a field that is not valid for SAM files, "
116 "please refer to the documentation of "
117 "seqan3::sam_file_output::field_ids for the accepted values.");
161 assert(!
format.valueless_by_exception());
166 if constexpr (std::same_as<ref_ids_type, ref_info_not_given>)
205 ->open(filename, std::ios_base::out | std::ios::binary);
234 template <output_stream stream_type, sam_file_output_format file_format>
235 requires std::same_as<typename std::remove_reference_t<stream_type>::char_type,
stream_char_type>
237 file_format
const & SEQAN3_DOXYGEN_ONLY(format_tag),
241 format{detail::sam_file_output_format_exposer<file_format>{}}
243 static_assert(list_traits::contains<file_format, valid_formats>,
244 "You selected a format that is not in the valid_formats of this file.");
248 template <output_stream stream_type, sam_file_output_format file_format>
249 requires std::same_as<typename std::remove_reference_t<stream_type>::char_type, stream_char_type>
251 file_format
const & SEQAN3_DOXYGEN_ONLY(format_tag),
253 primary_stream{new stream_type{
std::move(stream)}, stream_deleter_default},
254 secondary_stream{&*primary_stream, stream_deleter_noop},
255 format{detail::sam_file_output_format_exposer<file_format>{}}
257 static_assert(list_traits::contains<file_format, valid_formats>,
258 "You selected a format that is not in the valid_formats of this file.");
291 template <
typename ref_
ids_type_, std::ranges::forward_range ref_lengths_type>
292 requires std::same_as<std::remove_reference_t<ref_ids_type_>, ref_ids_type>
294 ref_ids_type_ && ref_ids,
295 ref_lengths_type && ref_lengths,
300 initialise_header_information(std::forward<ref_ids_type_>(ref_ids),
301 std::forward<ref_lengths_type>(ref_lengths));
325 template <output_stream stream_type,
326 sam_file_output_format file_format,
327 typename ref_ids_type_,
328 std::ranges::forward_range ref_lengths_type>
329 requires std::same_as<std::remove_reference_t<ref_ids_type_>, ref_ids_type>
331 ref_ids_type_ && ref_ids,
332 ref_lengths_type && ref_lengths,
333 file_format
const & SEQAN3_DOXYGEN_ONLY(format_tag),
335 sam_file_output{
std::forward<stream_type>(stream), file_format{}, selected_field_ids{}}
337 initialise_header_information(std::forward<ref_ids_type_>(ref_ids),
338 std::forward<ref_lengths_type>(ref_lengths));
405 template <
typename record_t>
407 requires detail::record_like<record_t>
411 write_record(detail::get_or<field::header_ptr>(r,
nullptr),
416 detail::get_or<field::ref_id>(r, std::ignore),
419 detail::get_or<field::flag>(r, sam_flag::none),
420 detail::get_or<field::mapq>(r, 0u),
421 detail::get_or<field::mate>(r, default_mate_t{}),
423 detail::get_or<field::evalue>(r, 0u),
424 detail::get_or<field::bit_score>(r, 0u));
448 template <
typename tuple_t>
455 write_record(detail::get_or<selected_field_ids::index_of(field::header_ptr)>(t,
nullptr),
456 detail::get_or<selected_field_ids::index_of(field::seq)>(t,
std::string_view{}),
457 detail::get_or<selected_field_ids::index_of(field::qual)>(t,
std::string_view{}),
458 detail::get_or<selected_field_ids::index_of(field::id)>(t,
std::string_view{}),
459 detail::get_or<selected_field_ids::index_of(field::ref_seq)>(t,
std::string_view{}),
460 detail::get_or<selected_field_ids::index_of(field::ref_id)>(t, std::ignore),
463 detail::get_or<selected_field_ids::index_of(field::flag)>(t, sam_flag::none),
464 detail::get_or<selected_field_ids::index_of(field::mapq)>(t, 0u),
465 detail::get_or<selected_field_ids::index_of(field::mate)>(t, default_mate_t{}),
467 detail::get_or<selected_field_ids::index_of(field::evalue)>(t, 0u),
468 detail::get_or<selected_field_ids::index_of(field::bit_score)>(t, 0u));
494 template <
typename arg_t,
typename... arg_types>
495 requires (
sizeof...(arg_types) + 1 <= selected_field_ids::size)
522 template <
typename rng_t>
526 for (
auto &&
record : range)
559 template <
typename rng_t>
568 template <
typename rng_t>
585 return *secondary_stream;
601 if constexpr (std::same_as<ref_ids_type, ref_info_not_given>)
602 throw std::logic_error{
"Please construct your file with reference id and length information in order "
603 "to properly initialise the header before accessing it."};
611 bool header_has_been_written{
false};
651 template <
typename ref_
ids_type_,
typename ref_lengths_type>
654 assert(std::ranges::size(ref_ids) == std::ranges::size(ref_lengths));
656 header_ptr = std::make_unique<sam_file_header<ref_ids_type>>(std::forward<ref_ids_type_>(ref_ids));
658 for (int32_t idx = 0; idx < std::ranges::distance(
header_ptr->ref_ids()); ++idx)
660 header_ptr->ref_id_info.emplace_back(ref_lengths[idx],
"");
662 if constexpr (std::ranges::contiguous_range<std::ranges::range_reference_t<ref_ids_type_>>
663 && std::ranges::sized_range<std::ranges::range_reference_t<ref_ids_type_>>
664 && std::ranges::borrowed_range<std::ranges::range_reference_t<ref_ids_type_>>)
677 template <
typename record_header_ptr_t,
typename... pack_type>
678 void write_record(record_header_ptr_t && record_header_ptr, pack_type &&... remainder)
680 static_assert((
sizeof...(pack_type) == 13),
"Wrong parameter list passed to write_record.");
682 assert(!format.valueless_by_exception());
688 if constexpr (!std::same_as<record_header_ptr_t, std::nullptr_t>)
690 f.write_alignment_record(*secondary_stream,
693 std::forward<pack_type>(remainder)...);
695 else if constexpr (std::same_as<ref_ids_type, ref_info_not_given>)
697 f.write_alignment_record(*secondary_stream,
700 std::forward<pack_type>(remainder)...);
704 f.write_alignment_record(*secondary_stream,
707 std::forward<pack_type>(remainder)...);
712 header_has_been_written =
true;
727template <detail::fields_specialisation selected_field_
ids>
734template <output_stream stream_type,
743template <output_stream stream_type,
752template <output_stream stream_type, sam_file_output_format file_format>
759template <output_stream stream_type, sam_file_output_format file_format>
765 std::ranges::forward_range ref_ids_type,
766 std::ranges::forward_range ref_lengths_type>
773template <std::ranges::forward_range ref_
ids_type, std::ranges::forward_range ref_lengths_type>
780template <output_stream stream_type,
781 std::ranges::forward_range ref_ids_type,
782 std::ranges::forward_range ref_lengths_type,
789template <output_stream stream_type,
790 std::ranges::forward_range ref_ids_type,
791 std::ranges::forward_range ref_lengths_type,
798template <output_stream stream_type,
799 std::ranges::forward_range ref_ids_type,
800 std::ranges::forward_range ref_lengths_type,
802sam_file_output(stream_type &&, ref_ids_type &&, ref_lengths_type &&, file_format
const &)
808template <output_stream stream_type,
809 std::ranges::forward_range ref_ids_type,
810 std::ranges::forward_range ref_lengths_type,
812sam_file_output(stream_type &, ref_ids_type &&, ref_lengths_type &&, file_format
const &)
Output iterator necessary for providing a range-like interface in output file.
Definition out_file_iterator.hpp:44
A class for writing SAM files, both SAM and its binary representation BAM are supported.
Definition io/sam_file/output.hpp:71
sam_file_output(stream_type &, ref_ids_type &&, ref_lengths_type &&, file_format const &) -> sam_file_output< typename sam_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.
bool header_has_been_written
This is needed during deconstruction to know whether a header still needs to be written.
Definition io/sam_file/output.hpp:611
void const_reference
The const reference type (void).
Definition io/sam_file/output.hpp:129
void initialise_header_information(ref_ids_type_ &&ref_ids, ref_lengths_type &&ref_lengths)
Fill the header reference dictionary, with the given info.
Definition io/sam_file/output.hpp:652
friend sam_file_output operator|(rng_t &&range, sam_file_output &&f)
This is an overloaded member function, provided for convenience. It differs from the above function o...
Definition io/sam_file/output.hpp:569
sam_file_output(stream_type &, ref_ids_type &&, ref_lengths_type &&, file_format const &, selected_field_ids const &) -> sam_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.
sam_file_output(std::filesystem::path const &, ref_ids_type &&, ref_lengths_type &&) -> sam_file_output< typename sam_file_output<>::selected_field_ids, typename sam_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 size_type
The size type (void).
Definition io/sam_file/output.hpp:131
std::vector< char > stream_buffer
A larger (compared to stl default) stream buffer to use when reading from a file.
Definition io/sam_file/output.hpp:614
sam_file_output & operator=(rng_t &&range)
Write a range of records (or tuples) to the file.
Definition io/sam_file/output.hpp:523
friend iterator
Befriend iterator so it can access the buffers.
Definition io/sam_file/output.hpp:716
sam_file_output(sam_file_output const &)=delete
Copy construction is explicitly deleted, because you can't have multiple access to the same file.
sam_file_output()=delete
Default constructor is explicitly deleted, you need to give a stream or file name.
static void stream_deleter_noop(std::basic_ostream< stream_char_type > *)
Stream deleter that does nothing (no ownership assumed).
Definition io/sam_file/output.hpp:623
friend sam_file_output & operator|(rng_t &&range, sam_file_output &f)
Write a range of records (or tuples) to the file.
Definition io/sam_file/output.hpp:560
void emplace_back(arg_t &&arg, arg_types &&... args)
Write a record to the file by passing individual fields.
Definition io/sam_file/output.hpp:496
format_type format
The actual std::variant holding a pointer to the detected/selected format.
Definition io/sam_file/output.hpp:640
std::default_sentinel_t sentinel
The type returned by end().
Definition io/sam_file/output.hpp:139
char stream_char_type
Character type of the stream(s).
Definition io/sam_file/output.hpp:82
iterator begin() noexcept
Returns an iterator to current position in the file.
Definition io/sam_file/output.hpp:363
sentinel end() noexcept
Returns a sentinel for comparison with iterator.
Definition io/sam_file/output.hpp:382
sam_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 io/sam_file/output.hpp:293
~sam_file_output()
The destructor will write the header if it has not been written before.
Definition io/sam_file/output.hpp:156
sam_file_output(std::filesystem::path, selected_field_ids const &) -> sam_file_output< selected_field_ids, typename sam_file_output<>::valid_formats, ref_info_not_given >
Deduces selected_field_ids from input and sets sam_file_output::ref_ids_type to seqan3::detail::ref_i...
sam_file_output(stream_type &&, ref_ids_type &&, ref_lengths_type &&, file_format const &) -> sam_file_output< typename sam_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.
sam_file_output & operator=(sam_file_output &&)=default
Move assignment is defaulted.
std::unique_ptr< header_type > header_ptr
The file header object (will be set on construction).
Definition io/sam_file/output.hpp:648
selected_field_ids_ selected_field_ids
A seqan3::fields list with the fields selected for the record.
Definition io/sam_file/output.hpp:78
valid_formats_ valid_formats
A seqan3::type_list with the possible formats.
Definition io/sam_file/output.hpp:80
std::basic_ostream< stream_char_type > & get_stream()
Expose a reference to the secondary stream. [public, but not documented as part of the API].
Definition io/sam_file/output.hpp:583
sam_file_output & operator=(sam_file_output const &)=delete
Copy assignment is explicitly deleted, because you can't have multiple access to the same file.
sam_file_output(stream_type &&, ref_ids_type &&, ref_lengths_type &&, file_format const &, selected_field_ids const &) -> sam_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.
void reference
The reference type (void).
Definition io/sam_file/output.hpp:127
void write_record(record_header_ptr_t &&record_header_ptr, pack_type &&... remainder)
Write record to format.
Definition io/sam_file/output.hpp:678
sam_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 io/sam_file/output.hpp:236
void push_back(record_t &&r)
Write a seqan3::record to the file.
Definition io/sam_file/output.hpp:406
sam_file_output(stream_type &&, file_format const &) -> sam_file_output< typename sam_file_output<>::selected_field_ids, type_list< file_format >, ref_info_not_given >
Deduces the valid format from input and sets sam_file_output::ref_ids_type to seqan3::detail::ref_inf...
sam_file_output(std::filesystem::path filename, selected_field_ids const &fields_tag=selected_field_ids{})
Construct from filename.
Definition io/sam_file/output.hpp:199
static void stream_deleter_default(std::basic_ostream< stream_char_type > *ptr)
Stream deleter with default behaviour (ownership assumed).
Definition io/sam_file/output.hpp:626
stream_ptr_t secondary_stream
The secondary stream is a compression layer on the primary or just points to the primary (no compress...
Definition io/sam_file/output.hpp:634
sam_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 io/sam_file/output.hpp:330
void value_type
The value type (void).
Definition io/sam_file/output.hpp:125
sam_file_output_options options
The options are public and its members can be set directly.
Definition io/sam_file/output.hpp:578
sam_file_output(sam_file_output &&)=default
Move construction is defaulted.
sam_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 io/sam_file/output.hpp:250
sam_file_output(stream_type &, file_format const &, selected_field_ids const &) -> sam_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 sam_file_output::ref_ids_type to...
sam_file_output(stream_type &&, file_format const &, selected_field_ids const &) -> sam_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 sam_file_output::ref_ids_type to...
void push_back(tuple_t &&t)
Write a record in form of a std::tuple to the file.
Definition io/sam_file/output.hpp:449
stream_ptr_t primary_stream
The primary stream is the user provided stream or the file stream if constructed from filename.
Definition io/sam_file/output.hpp:632
auto & header()
Access the file's header.
Definition io/sam_file/output.hpp:599
sam_file_output(std::filesystem::path const &, ref_ids_type &&, ref_lengths_type &&, selected_field_ids const &) -> sam_file_output< selected_field_ids, typename sam_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.
typename detail::variant_from_tags< valid_formats, detail::sam_file_output_format_exposer >::type format_type
Type of the format, a std::variant over the valid_formats.
Definition io/sam_file/output.hpp:637
void const_iterator
The const iterator type is void, because files are not const-iterable.
Definition io/sam_file/output.hpp:137
sam_file_output(stream_type &, file_format const &) -> sam_file_output< typename sam_file_output<>::selected_field_ids, type_list< file_format >, ref_info_not_given >
Deduces the valid format from input and sets sam_file_output::ref_ids_type to seqan3::detail::ref_inf...
The SAM tag dictionary class that stores all optional SAM fields.
Definition sam_tag_dictionary.hpp:327
Auxiliary concept that checks whether a type is a specialisation of seqan3::fields.
Definition detail/record.hpp:32
Provides auxiliary data structures and functions for seqan3::record and seqan3::fields.
field
An enumerator for the fields used in file formats.
Definition record.hpp:60
void set_format(format_variant_type &format, std::filesystem::path const &file_name)
Sets the file format according to the file name extension.
Definition io/detail/misc.hpp:65
auto make_secondary_ostream(std::basic_ostream< char_t > &primary_stream, std::filesystem::path &filename) -> std::unique_ptr< std::basic_ostream< char_t >, std::function< void(std::basic_ostream< char_t > *)> >
Depending on the given filename/extension, create a compression stream or just forward the primary st...
Definition misc_output.hpp:40
@ flag
The alignment flag (bit information), uint16_t value.
@ ref_offset
Sequence (seqan3::field::ref_seq) relative start position (0-based), unsigned value.
@ 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.
@ 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::sam_file_header object storing header information.
@ ref_id
The identifier of the (reference) sequence that seqan3::field::seq was aligned to.
@ 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.
Whether a type behaves like a tuple.
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:26
SeqAn specific customisations in the standard namespace.
Provides the seqan3::detail::out_file_iterator class template.
Provides the seqan3::record template and the seqan3::field enum.
Provides seqan3::detail::record_like.
Provides seqan3::sam_file_output_options.
Provides helper data structures for the seqan3::sam_file_output.
A class template that holds a choice of seqan3::field.
Definition record.hpp:125
static constexpr bool contains(field f)
Whether a field is contained in the parameter pack.
Definition record.hpp:146
Thrown if there is an unspecified filesystem or stream error while opening, e.g. permission problem.
Definition io/exception.hpp:36
The class template that file records are based on; behaves like a std::tuple.
Definition record.hpp:190
Type tag which indicates that no reference information has been passed to the SAM file on constructio...
Definition sam_flag.hpp:21
The options type defines various option members that influence the behavior of all or some formats.
Definition sam_file/output_options.hpp:23
Type that contains multiple types.
Definition type_list.hpp:26
Provides traits for seqan3::type_list.
Provides seqan3::tuple_like.