33 #include <seqan3/io/detail/record.hpp> 169 template <detail::Fields selected_field_ids_ =
185 detail::TypeListOfAlignmentFileOutputFormats valid_formats_ = type_list<format_sam, format_bam>,
186 Char stream_char_type_ = char,
187 typename ref_ids_type = ref_info_not_given>
220 static_assert([] () constexpr
222 for (
field f : selected_field_ids::as_array)
223 if (!field_ids::contains(f))
227 "You selected a field that is not valid for alignment files, " 228 "please refer to the documentation of " 229 "seqan3::alignment_file_output::field_ids for the accepted values.");
247 using iterator = detail::out_file_iterator<alignment_file_output>;
297 primary_stream{
new std::ofstream{filename, std::ios_base::out | std::ios::binary}, stream_deleter_default}
300 if (!primary_stream->good())
304 secondary_stream = detail::make_secondary_ostream(*primary_stream, filename);
307 detail::set_format(format, filename);
326 template <OStream2 stream_type, AlignmentFileOutputFormat file_format>
328 file_format
const & SEQAN3_DOXYGEN_ONLY(format_tag),
330 primary_stream{&stream, stream_deleter_noop},
331 secondary_stream{&stream, stream_deleter_noop},
332 format{detail::alignment_file_output_format<file_format>{}}
334 static_assert(meta::in<valid_formats, file_format>::value,
335 "You selected a format that is not in the valid_formats of this file.");
339 template <OStream2 stream_type, AlignmentFileOutputFormat file_format>
341 file_format
const & SEQAN3_DOXYGEN_ONLY(format_tag),
343 primary_stream{
new stream_type{std::move(stream)}, stream_deleter_default},
344 secondary_stream{&*primary_stream, stream_deleter_noop},
345 format{detail::alignment_file_output_format<file_format>{}}
347 static_assert(meta::in<valid_formats, file_format>::value,
348 "You selected a format that is not in the valid_formats of this file.");
381 template <
typename ref_
ids_type_, std::ranges::ForwardRange ref_lengths_type>
386 ref_ids_type_ && ref_ids,
387 ref_lengths_type && ref_lengths,
394 header_ptr = std::make_unique<alignment_file_header<ref_ids_type>>(std::forward<ref_ids_type_>(ref_ids));
399 header_ptr->ref_id_info.push_back({ref_lengths[idx],
""});
400 header_ptr->ref_dict[(header_ptr->ref_ids()[idx])] = idx;
425 template <OStream2 stream_type,
427 typename ref_ids_type_,
430 requires std::Same<std::remove_reference_t<ref_ids_type_>, ref_ids_type>
433 ref_ids_type_ && ref_ids,
434 ref_lengths_type && ref_lengths,
435 file_format
const & SEQAN3_DOXYGEN_ONLY(format_tag),
441 header_ptr = std::make_unique<alignment_file_header<ref_ids_type>>(std::forward<ref_ids_type_>(ref_ids));
446 header_ptr->ref_id_info.emplace_back(ref_lengths[idx],
"");
447 header_ptr->ref_dict[header_ptr->ref_ids()[idx]] = idx;
515 template <
typename record_t>
519 requires { requires detail::is_type_specialisation_of_v<remove_cvref_t<record_t>,
record>; }
525 write_record(detail::get_or<field::HEADER_PTR>(r,
nullptr),
529 detail::get_or<field::OFFSET>(r, 0u),
531 detail::get_or<field::REF_ID>(r, std::ignore),
533 detail::get_or<field::ALIGNMENT>(r, default_align_t{}),
534 detail::get_or<field::FLAG>(r, 0u),
535 detail::get_or<field::MAPQ>(r, 0u),
536 detail::get_or<field::MATE>(r, default_mate_t{}),
538 detail::get_or<field::EVALUE>(r, 0u),
539 detail::get_or<field::BIT_SCORE>(r, 0u));
563 template <
typename tuple_t>
573 write_record(detail::get_or<selected_field_ids::index_of(field::HEADER_PTR)>(t,
nullptr),
574 detail::get_or<selected_field_ids::index_of(field::SEQ)>(t,
std::string_view{}),
575 detail::get_or<selected_field_ids::index_of(field::QUAL)>(t,
std::string_view{}),
576 detail::get_or<selected_field_ids::index_of(field::ID)>(t,
std::string_view{}),
577 detail::get_or<selected_field_ids::index_of(field::OFFSET)>(t, 0u),
578 detail::get_or<selected_field_ids::index_of(field::REF_SEQ)>(t,
std::string_view{}),
579 detail::get_or<selected_field_ids::index_of(field::REF_ID)>(t, std::ignore),
581 detail::get_or<selected_field_ids::index_of(field::ALIGNMENT)>(t, default_align_t{}),
582 detail::get_or<selected_field_ids::index_of(field::FLAG)>(t, 0u),
583 detail::get_or<selected_field_ids::index_of(field::MAPQ)>(t, 0u),
584 detail::get_or<selected_field_ids::index_of(field::MATE)>(t, default_mate_t{}),
586 detail::get_or<selected_field_ids::index_of(field::EVALUE)>(t, 0u),
587 detail::get_or<selected_field_ids::index_of(field::BIT_SCORE)>(t, 0u));
613 template <
typename arg_t,
typename ... arg_types>
640 template <
typename rng_t>
646 for (
auto &&
record : range)
679 template <
typename rng_t>
690 template <
typename rng_t>
709 return *secondary_stream;
726 throw std::logic_error{
"Please construct your file with reference id and length information in order " 727 "to properly initialise the header before accessing it."};
747 stream_ptr_t primary_stream{
nullptr, stream_deleter_noop};
749 stream_ptr_t secondary_stream{
nullptr, stream_deleter_noop};
752 using format_type =
typename detail::variant_from_tags<valid_formats, detail::alignment_file_output_format>::type;
767 template <
typename record_header_ptr_t,
typename ...pack_type>
768 void write_record(record_header_ptr_t && record_header_ptr, pack_type && ...remainder)
770 static_assert((
sizeof...(pack_type) == 14),
"Wrong parameter list passed to write_record.");
772 assert(!format.valueless_by_exception());
778 f.write(*secondary_stream, options, *record_header_ptr, std::forward<pack_type>(remainder)...);
780 f.write(*secondary_stream, options, std::ignore, std::forward<pack_type>(remainder)...);
782 f.write(*secondary_stream, options, *header_ptr, std::forward<pack_type>(remainder)...);
798 template <detail::Fields selected_field_
ids>
808 template <OStream2 stream_type,
810 detail::Fields selected_field_ids>
820 template <OStream2 stream_type,
822 detail::Fields selected_field_ids>
825 type_list<file_format>,
826 typename std::remove_reference_t<stream_type>::char_type,
832 template <OStream2 stream_type,
836 type_list<file_format>,
837 typename std::remove_reference_t<stream_type>::char_type,
843 template <OStream2 stream_type,
847 type_list<file_format>,
848 typename std::remove_reference_t<stream_type>::char_type,
858 selected_field_ids
const &)
860 typename alignment_file_output<>::valid_formats,
861 typename alignment_file_output<>::stream_char_type,
871 typename alignment_file_output<>::valid_formats,
872 typename alignment_file_output<>::stream_char_type,
873 std::remove_reference_t<ref_ids_type>>;
876 template <OStream2 stream_type,
880 detail::Fields selected_field_ids>
885 selected_field_ids
const &)
887 type_list<file_format>,
888 typename std::remove_reference_t<stream_type>::char_type,
889 std::remove_reference_t<ref_ids_type>>;
892 template <OStream2 stream_type,
896 detail::Fields selected_field_ids>
901 selected_field_ids
const &)
903 type_list<file_format>,
904 typename std::remove_reference_t<stream_type>::char_type,
905 std::remove_reference_t<ref_ids_type>>;
908 template <OStream2 stream_type,
917 type_list<file_format>,
918 typename std::remove_reference_t<stream_type>::char_type,
919 std::remove_reference_t<ref_ids_type>>;
922 template <OStream2 stream_type,
931 type_list<file_format>,
932 typename std::remove_reference_t<stream_type>::char_type,
933 std::remove_reference_t<ref_ids_type>>;
detail::out_file_iterator< alignment_file_output > iterator
The iterator type of this view (an output iterator).
Definition: output.hpp:247
The (reference) "sequence" information, usually a range of nucleotides or amino acids.
The "sequence", usually a range of nucleotides or amino acids.
void emplace_back(arg_t &&arg, arg_types &&... args)
Write a record to the file by passing individual fields.
Definition: output.hpp:614
~alignment_file_output()=default
Destructor is defaulted.
Provides exceptions used in the I/O module.
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...
valid_formats_ valid_formats
A seqan3::type_list with the possible formats.
Definition: output.hpp:198
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:327
The (pairwise) alignment stored in an seqan3::alignment object.
The alignment flag (bit information), uint16_t value.
auto & header()
Access the file's header.
Definition: output.hpp:723
The class template that file records are based on; behaves like an std::tuple.
Definition: record.hpp:187
Provides various utility functions required only for output.
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:385
Provides seqan3::type_list and auxiliary type traits.
void const_reference
The const reference type (void).
Definition: output.hpp:241
alignment_file_output(std::filesystem::path filename, selected_field_ids const &fields_tag=selected_field_ids{})
Construct from filename.
Definition: output.hpp:295
sentinel end() noexcept
Returns a sentinel for comparison with iterator.
Definition: output.hpp:492
alignment_file_output(stream_type &&stream, file_format const &format_tag, selected_field_ids const &fields_tag=selected_field_ids{})
Definition: output.hpp:340
::ranges::size size
Alias for ranges::size. Obtains the size of a range whose size can be calculated in constant time...
Definition: ranges:189
The main SeqAn3 namespace.
The qualities, usually in phred-score notation.
The e-value (length normalized bit score), double value.
Provides seqan3::alignment_file_output_options.
Sequence (REF_SEQ) relative start position (0-based), unsigned value.
selected_field_ids_ selected_field_ids
A seqan3::fields list with the fields selected for the record.
Definition: output.hpp:196
Thrown if there is an unspecified filesystem or stream error while opening, e.g. permission problem...
Definition: exception.hpp:39
A class template that holds a choice of seqan3::field.
Definition: record.hpp:127
A class for writing alignment files, e.g. SAM, BAL, BLAST, ...
Definition: output.hpp:188
iterator begin() noexcept
Returns an iterator to current position in the file.
Definition: output.hpp:473
Provides seqan3::TupleLike.
std::ranges::default_sentinel_t sentinel
The type returned by end().
Definition: output.hpp:251
alignment_file_output & operator=(rng_t &&range)
Write a range of records (or tuples) to the file.
Definition: output.hpp:641
Provides the seqan3::record template and the seqan3::field enum.
Sequence (SEQ) relative start position (0-based), unsigned value.
void push_back(record_t &&r)
Write a seqan3::record to the file.
Definition: output.hpp:516
The identifier, usually a string.
void size_type
The size type (void).
Definition: output.hpp:243
void value_type
The value type (void).
Definition: output.hpp:237
Adaptations of concepts from the Ranges TS.
The mate pair information given as a std::tuple of reference name, offset and template length...
The identifier of the (reference) sequence that SEQ was aligned to.
The concept std::Same<T, U> is satisfied if and only if T and U denote the same type.
Specifies requirements of a Range type for which begin returns a type that models std::ForwardIterato...
The options type defines various option members that influence the behavior of all or some formats...
Definition: output_options.hpp:22
Whether a type behaves like a tuple.
A pointer to the seqan3::alignment_file_header object storing header information. ...
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:432
void push_back(tuple_t &&t)
Write a record in form of a std::tuple to the file.
Definition: output.hpp:564
Provides helper data structures for the seqan3::alignment_file_output.
alignment_file_output_options options
The options are public and its members can be set directly.
Definition: output.hpp:702
Provides various type traits on generic types.
Provides the seqan3::detail::out_file_iterator class template.
void reference
The reference type (void).
Definition: output.hpp:239
friend alignment_file_output operator|(rng_t &&range, alignment_file_output &&f)
Definition: output.hpp:691
void const_iterator
The const iterator type is void, because files are not const-iterable.
Definition: output.hpp:249
::ranges::default_sentinel_t default_sentinel_t
Alias for ranges::default_sentinel_t. Type of ranges::default_sentinel.
Definition: iterator:351
meta::list< types... > type_list
Type that contains multiple types, an alias for meta::list.
Definition: type_list.hpp:27
Type tag which indicates that no reference information has been passed to the alignment file on const...
Definition: misc.hpp:21
field
An enumerator for the fields used in file formats.Some of the fields are shared between formats...
Definition: record.hpp:63
The optional tags in the SAM format, stored in a dictionary.
alignment_file_output()=delete
Default constructor is explicitly deleted, you need to give a stream or file name.
The bit score (statistical significance indicator), unsigned value.
stream_char_type_ stream_char_type
Character type of the stream(s), usually char.
Definition: output.hpp:200
The mapping quality of the SEQ alignment, usually a ohred-scaled score.
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:680
The SAM tag dictionary class that stores all optional SAM fields.
Definition: sam_tag_dictionary.hpp:324
This header includes C++17 filesystem support and imports it into namespace seqan3::filesystem (indep...