SeqAn3 3.4.0-rc.1
The Modern C++ library for sequence analysis.
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io/sam_file/output.hpp
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1// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
2// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
3// SPDX-License-Identifier: BSD-3-Clause
4
10#pragma once
11
12#include <cassert>
13#include <filesystem>
14#include <fstream>
15#include <ranges>
16#include <string>
17#include <string_view>
18#include <variant>
19#include <vector>
20
23#include <seqan3/io/detail/record.hpp>
26#include <seqan3/io/record.hpp>
36
37namespace seqan3
38{
39
40// ----------------------------------------------------------------------------
41// sam_file_output
42// ----------------------------------------------------------------------------
43
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>
71{
72public:
78 using selected_field_ids = selected_field_ids_;
80 using valid_formats = valid_formats_;
82 using stream_char_type = char;
84
97
98 static_assert(!selected_field_ids::contains(field::offset),
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.");
101
102 static_assert(!selected_field_ids::contains(field::alignment),
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.");
106
107 static_assert(
108 []() constexpr
109 {
110 for (field f : selected_field_ids::as_array)
111 if (!field_ids::contains(f))
112 return false;
113 return true;
114 }(),
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.");
118
125 using value_type = void;
127 using reference = void;
129 using const_reference = void;
131 using size_type = void;
135 using iterator = detail::out_file_iterator<sam_file_output>;
137 using const_iterator = void;
139 using sentinel = std::default_sentinel_t;
141
146 sam_file_output() = delete;
157 {
158 if (header_has_been_written)
159 return;
160
161 assert(!format.valueless_by_exception());
162
164 [&](auto & f)
165 {
166 if constexpr (std::same_as<ref_ids_type, ref_info_not_given>)
167 f.write_header(*secondary_stream, options, std::ignore);
168 else
169 f.write_header(*secondary_stream, options, *header_ptr);
170 },
171 format);
172 }
173
200 selected_field_ids const & SEQAN3_DOXYGEN_ONLY(fields_tag) = selected_field_ids{}) :
201 primary_stream{new std::ofstream{}, stream_deleter_default}
202 {
203 primary_stream->rdbuf()->pubsetbuf(stream_buffer.data(), stream_buffer.size());
204 static_cast<std::basic_ofstream<char> *>(primary_stream.get())
205 ->open(filename, std::ios_base::out | std::ios::binary);
206
207 // open stream
208 if (!primary_stream->good())
209 throw file_open_error{"Could not open file " + filename.string() + " for writing."};
210
211 // possibly add intermediate compression stream
212 secondary_stream = detail::make_secondary_ostream(*primary_stream, filename);
213
214 // initialise format handler or throw if format is not found
215 detail::set_format(format, filename);
216 }
217
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>
236 sam_file_output(stream_type & stream,
237 file_format const & SEQAN3_DOXYGEN_ONLY(format_tag),
238 selected_field_ids const & SEQAN3_DOXYGEN_ONLY(fields_tag) = selected_field_ids{}) :
239 primary_stream{&stream, stream_deleter_noop},
240 secondary_stream{&stream, stream_deleter_noop},
241 format{detail::sam_file_output_format_exposer<file_format>{}}
242 {
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.");
245 }
246
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>
250 sam_file_output(stream_type && stream,
251 file_format const & SEQAN3_DOXYGEN_ONLY(format_tag),
252 selected_field_ids const & SEQAN3_DOXYGEN_ONLY(fields_tag) = selected_field_ids{}) :
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>{}}
256 {
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.");
259 }
260
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,
296 selected_field_ids const & SEQAN3_DOXYGEN_ONLY(fields_tag) = selected_field_ids{}) :
297 sam_file_output{filename, selected_field_ids{}}
298
299 {
300 initialise_header_information(std::forward<ref_ids_type_>(ref_ids),
301 std::forward<ref_lengths_type>(ref_lengths));
302 }
303
325 template <output_stream stream_type,
326 sam_file_output_format file_format,
327 typename ref_ids_type_, // generic type to capture lvalue references
328 std::ranges::forward_range ref_lengths_type>
329 requires std::same_as<std::remove_reference_t<ref_ids_type_>, ref_ids_type>
330 sam_file_output(stream_type && stream,
331 ref_ids_type_ && ref_ids,
332 ref_lengths_type && ref_lengths,
333 file_format const & SEQAN3_DOXYGEN_ONLY(format_tag),
334 selected_field_ids const & SEQAN3_DOXYGEN_ONLY(fields_tag) = selected_field_ids{}) :
335 sam_file_output{std::forward<stream_type>(stream), file_format{}, selected_field_ids{}}
336 {
337 initialise_header_information(std::forward<ref_ids_type_>(ref_ids),
338 std::forward<ref_lengths_type>(ref_lengths));
339 }
341
363 iterator begin() noexcept
364 {
365 return {*this};
366 }
367
382 sentinel end() noexcept
383 {
384 return {};
385 }
386
405 template <typename record_t>
406 void push_back(record_t && r)
407 requires detail::record_like<record_t>
408 {
409 using default_mate_t = std::tuple<std::string_view, std::optional<int32_t>, int32_t>;
410
411 write_record(detail::get_or<field::header_ptr>(r, nullptr),
412 detail::get_or<field::seq>(r, std::string_view{}),
413 detail::get_or<field::qual>(r, std::string_view{}),
414 detail::get_or<field::id>(r, std::string_view{}),
415 detail::get_or<field::ref_seq>(r, std::string_view{}),
416 detail::get_or<field::ref_id>(r, std::ignore),
417 detail::get_or<field::ref_offset>(r, std::optional<int32_t>{}),
418 detail::get_or<field::cigar>(r, std::vector<cigar>{}),
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{}),
422 detail::get_or<field::tags>(r, sam_tag_dictionary{}),
423 detail::get_or<field::evalue>(r, 0u),
424 detail::get_or<field::bit_score>(r, 0u));
425 }
426
448 template <typename tuple_t>
449 void push_back(tuple_t && t)
450 requires tuple_like<tuple_t> && (!detail::record_like<tuple_t>)
451 {
452 using default_mate_t = std::tuple<std::string_view, std::optional<int32_t>, int32_t>;
453
454 // index_of might return npos, but this will be handled well by get_or_ignore (and just return ignore)
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),
461 detail::get_or<selected_field_ids::index_of(field::ref_offset)>(t, std::optional<int32_t>{}),
462 detail::get_or<selected_field_ids::index_of(field::cigar)>(t, std::vector<cigar>{}),
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{}),
466 detail::get_or<selected_field_ids::index_of(field::tags)>(t, sam_tag_dictionary{}),
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));
469 }
470
494 template <typename arg_t, typename... arg_types>
495 requires (sizeof...(arg_types) + 1 <= selected_field_ids::size)
496 void emplace_back(arg_t && arg, arg_types &&... args)
497 {
498 push_back(std::tie(arg, args...));
499 }
500
522 template <typename rng_t>
523 sam_file_output & operator=(rng_t && range)
524 requires std::ranges::input_range<rng_t> && tuple_like<std::ranges::range_reference_t<rng_t>>
525 {
526 for (auto && record : range)
527 push_back(std::forward<decltype(record)>(record));
528 return *this;
529 }
530
559 template <typename rng_t>
560 friend sam_file_output & operator|(rng_t && range, sam_file_output & f)
561 requires std::ranges::input_range<rng_t> && tuple_like<std::ranges::range_reference_t<rng_t>>
562 {
563 f = range;
564 return f;
565 }
566
568 template <typename rng_t>
569 friend sam_file_output operator|(rng_t && range, sam_file_output && f)
570 requires std::ranges::input_range<rng_t> && tuple_like<std::ranges::range_reference_t<rng_t>>
571 {
572 f = range;
573 return std::move(f);
574 }
576
579
584 {
585 return *secondary_stream;
586 }
588
599 auto & header()
600 {
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."};
604
605 return *header_ptr;
606 }
607
608protected:
611 bool header_has_been_written{false};
612
614 std::vector<char> stream_buffer{std::vector<char>(1'000'000)};
615
623 static void stream_deleter_noop(std::basic_ostream<stream_char_type> *)
624 {}
626 static void stream_deleter_default(std::basic_ostream<stream_char_type> * ptr)
627 {
628 delete ptr;
629 }
630
632 stream_ptr_t primary_stream{nullptr, stream_deleter_noop};
634 stream_ptr_t secondary_stream{nullptr, stream_deleter_noop};
635
637 using format_type = typename detail::variant_from_tags<valid_formats, detail::sam_file_output_format_exposer>::type;
638
640 format_type format;
642
644 using header_type = sam_file_header<
646
649
651 template <typename ref_ids_type_, typename ref_lengths_type>
652 void initialise_header_information(ref_ids_type_ && ref_ids, ref_lengths_type && ref_lengths)
653 {
654 assert(std::ranges::size(ref_ids) == std::ranges::size(ref_lengths));
655
656 header_ptr = std::make_unique<sam_file_header<ref_ids_type>>(std::forward<ref_ids_type_>(ref_ids));
657
658 for (int32_t idx = 0; idx < std::ranges::distance(header_ptr->ref_ids()); ++idx)
659 {
660 header_ptr->ref_id_info.emplace_back(ref_lengths[idx], "");
661
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_>>)
665 {
666 auto && id = header_ptr->ref_ids()[idx];
667 header_ptr->ref_dict[std::span{std::ranges::data(id), std::ranges::size(id)}] = idx;
668 }
669 else
670 {
671 header_ptr->ref_dict[header_ptr->ref_ids()[idx]] = idx;
672 }
673 }
674 }
675
677 template <typename record_header_ptr_t, typename... pack_type>
678 void write_record(record_header_ptr_t && record_header_ptr, pack_type &&... remainder)
679 {
680 static_assert((sizeof...(pack_type) == 13), "Wrong parameter list passed to write_record.");
681
682 assert(!format.valueless_by_exception());
683
685 [&](auto & f)
686 {
687 // use header from record if explicitly given, e.g. file_output = file_input
688 if constexpr (!std::same_as<record_header_ptr_t, std::nullptr_t>)
689 {
690 f.write_alignment_record(*secondary_stream,
691 options,
692 *record_header_ptr,
693 std::forward<pack_type>(remainder)...);
694 }
695 else if constexpr (std::same_as<ref_ids_type, ref_info_not_given>)
696 {
697 f.write_alignment_record(*secondary_stream,
698 options,
699 std::ignore,
700 std::forward<pack_type>(remainder)...);
701 }
702 else
703 {
704 f.write_alignment_record(*secondary_stream,
705 options,
706 *header_ptr,
707 std::forward<pack_type>(remainder)...);
708 }
709 },
710 format);
711
712 header_has_been_written = true; // when writing a record, the header is written automatically
713 }
714
716 friend iterator;
717};
718
727template <detail::fields_specialisation selected_field_ids>
730
734template <output_stream stream_type,
735 sam_file_output_format file_format,
736 detail::fields_specialisation selected_field_ids>
737sam_file_output(stream_type &&, file_format const &, selected_field_ids const &)
739
743template <output_stream stream_type,
744 sam_file_output_format file_format,
745 detail::fields_specialisation selected_field_ids>
746sam_file_output(stream_type &, file_format const &, selected_field_ids const &)
748
752template <output_stream stream_type, sam_file_output_format file_format>
753sam_file_output(stream_type &&, file_format const &)
755
759template <output_stream stream_type, sam_file_output_format file_format>
760sam_file_output(stream_type &, file_format const &)
762
764template <detail::fields_specialisation selected_field_ids,
765 std::ranges::forward_range ref_ids_type,
766 std::ranges::forward_range ref_lengths_type>
767sam_file_output(std::filesystem::path const &, ref_ids_type &&, ref_lengths_type &&, selected_field_ids const &)
771
773template <std::ranges::forward_range ref_ids_type, std::ranges::forward_range ref_lengths_type>
774sam_file_output(std::filesystem::path const &, ref_ids_type &&, ref_lengths_type &&)
778
780template <output_stream stream_type,
781 std::ranges::forward_range ref_ids_type,
782 std::ranges::forward_range ref_lengths_type,
783 sam_file_output_format file_format,
784 detail::fields_specialisation selected_field_ids>
785sam_file_output(stream_type &&, ref_ids_type &&, ref_lengths_type &&, file_format const &, selected_field_ids const &)
787
789template <output_stream stream_type,
790 std::ranges::forward_range ref_ids_type,
791 std::ranges::forward_range ref_lengths_type,
792 sam_file_output_format file_format,
793 detail::fields_specialisation selected_field_ids>
794sam_file_output(stream_type &, ref_ids_type &&, ref_lengths_type &&, file_format const &, selected_field_ids const &)
796
798template <output_stream stream_type,
799 std::ranges::forward_range ref_ids_type,
800 std::ranges::forward_range ref_lengths_type,
801 sam_file_output_format file_format>
802sam_file_output(stream_type &&, ref_ids_type &&, ref_lengths_type &&, file_format const &)
806
808template <output_stream stream_type,
809 std::ranges::forward_range ref_ids_type,
810 std::ranges::forward_range ref_lengths_type,
811 sam_file_output_format file_format>
812sam_file_output(stream_type &, ref_ids_type &&, ref_lengths_type &&, file_format const &)
817
818} // namespace seqan3
The generic concept for alignment file out formats.
Definition sam_file/output_format_concept.hpp:125
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.
void const_reference
The const reference type (void).
Definition io/sam_file/output.hpp:129
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
sam_file_output & operator=(rng_t &&range)
Write a range of records (or tuples) to the file.
Definition io/sam_file/output.hpp:523
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.
detail::out_file_iterator< sam_file_output > iterator
The iterator type of this view (an output iterator).
Definition io/sam_file/output.hpp:135
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
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.
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
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
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
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
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.
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
T data(T... args)
Provides the seqan3::format_bam.
Provides the seqan3::format_sam.
T format(T... args)
T forward(T... args)
T get(T... args)
field
An enumerator for the fields used in file formats.
Definition record.hpp:60
@ 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.
Provides the seqan3::sam_file_header class.
Whether a type behaves like a tuple.
Provides exceptions used in the I/O module.
Stream concepts.
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_format and auxiliary classes.
Provides seqan3::sam_file_output_options.
Provides helper data structures for the seqan3::sam_file_output.
T size(T... args)
A class template that holds a choice of seqan3::field.
Definition record.hpp:125
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
T tie(T... args)
Provides traits for seqan3::type_list.
Provides seqan3::tuple_like.
T visit(T... args)
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