69 template <
typename stream_type,
70 typename seq_legal_alph_type,
71 typename ref_seqs_type,
72 typename ref_ids_type,
73 typename stream_pos_type,
77 typename ref_seq_type,
79 typename ref_offset_type,
85 typename tag_dict_type,
86 typename e_value_type,
87 typename bit_score_type>
90 ref_seqs_type & ref_seqs,
92 stream_pos_type & position_buffer,
97 ref_seq_type & SEQAN3_DOXYGEN_ONLY(ref_seq),
99 ref_offset_type & ref_offset,
100 cigar_type & cigar_vector,
104 tag_dict_type & tag_dict,
105 e_value_type & SEQAN3_DOXYGEN_ONLY(e_value),
106 bit_score_type & SEQAN3_DOXYGEN_ONLY(bit_score));
108 template <
typename stream_type,
109 typename header_type,
112 typename ref_seq_type,
113 typename ref_id_type,
117 typename tag_dict_type>
120 [[maybe_unused]] header_type && header,
121 [[maybe_unused]] seq_type && seq,
122 [[maybe_unused]] qual_type && qual,
123 [[maybe_unused]] id_type &&
id,
124 [[maybe_unused]] int32_t
const offset,
125 [[maybe_unused]] ref_seq_type && SEQAN3_DOXYGEN_ONLY(ref_seq),
126 [[maybe_unused]] ref_id_type && ref_id,
128 [[maybe_unused]] cigar_type && cigar_vector,
129 [[maybe_unused]]
sam_flag const flag,
130 [[maybe_unused]] uint8_t
const mapq,
131 [[maybe_unused]] mate_type && mate,
132 [[maybe_unused]] tag_dict_type && tag_dict,
133 [[maybe_unused]]
double SEQAN3_DOXYGEN_ONLY(e_value),
134 [[maybe_unused]]
double SEQAN3_DOXYGEN_ONLY(bit_score));
137 template <
typename stream_t,
typename header_type>
174 ret[
static_cast<index_t
>(
'I')] = 1;
175 ret[
static_cast<index_t
>(
'D')] = 2;
176 ret[
static_cast<index_t
>(
'N')] = 3;
177 ret[
static_cast<index_t
>(
'S')] = 4;
178 ret[
static_cast<index_t
>(
'H')] = 5;
179 ret[
static_cast<index_t
>(
'P')] = 6;
180 ret[
static_cast<index_t
>(
'=')] = 7;
181 ret[
static_cast<index_t
>(
'X')] = 8;
189 static uint16_t
reg2bin(int32_t beg, int32_t end)
noexcept
192 if (beg >> 14 == end >> 14)
193 return ((1 << 15) - 1) / 7 + (beg >> 14);
194 if (beg >> 17 == end >> 17)
195 return ((1 << 12) - 1) / 7 + (beg >> 17);
196 if (beg >> 20 == end >> 20)
197 return ((1 << 9) - 1) / 7 + (beg >> 20);
198 if (beg >> 23 == end >> 23)
199 return ((1 << 6) - 1) / 7 + (beg >> 23);
200 if (beg >> 26 == end >> 26)
201 return ((1 << 3) - 1) / 7 + (beg >> 26);
211 template <
typename stream_view_type, std::
integral number_type>
222 template <
typename stream_view_type>
228 template <
typename stream_view_type,
typename value_type>
230 stream_view_type && stream_view,
231 value_type
const & SEQAN3_DOXYGEN_ONLY(value));
233 template <
typename stream_view_type>
236 template <
typename cigar_input_type>
243template <
typename stream_type,
244 typename seq_legal_alph_type,
245 typename ref_seqs_type,
246 typename ref_ids_type,
247 typename stream_pos_type,
250 typename offset_type,
251 typename ref_seq_type,
252 typename ref_id_type,
253 typename ref_offset_type,
259 typename tag_dict_type,
260 typename e_value_type,
261 typename bit_score_type>
265 ref_seqs_type & ref_seqs,
267 stream_pos_type & position_buffer,
271 offset_type & offset,
272 ref_seq_type & SEQAN3_DOXYGEN_ONLY(ref_seq),
273 ref_id_type & ref_id,
274 ref_offset_type & ref_offset,
275 cigar_type & cigar_vector,
279 tag_dict_type & tag_dict,
280 e_value_type & SEQAN3_DOXYGEN_ONLY(e_value),
281 bit_score_type & SEQAN3_DOXYGEN_ONLY(bit_score))
283 static_assert(detail::decays_to_ignore_v<ref_offset_type>
284 || detail::is_type_specialisation_of_v<ref_offset_type, std::optional>,
285 "The ref_offset must be a specialisation of std::optional.");
287 static_assert(detail::decays_to_ignore_v<mapq_type> || std::same_as<mapq_type, uint8_t>,
288 "The type of field::mapq must be uint8_t.");
290 static_assert(detail::decays_to_ignore_v<flag_type> || std::same_as<flag_type, sam_flag>,
291 "The type of field::flag must be seqan3::sam_flag.");
295 [[maybe_unused]] int32_t offset_tmp{};
296 [[maybe_unused]] int32_t ref_length{};
318 for (int32_t ref_idx = 0; ref_idx < n_ref; ++ref_idx)
330 if constexpr (detail::decays_to_ignore_v<ref_seqs_type>)
335 auto & reference_ids = header.
ref_ids();
341 header.
ref_dict.emplace(reference_ids.back(), reference_ids.size() - 1);
352 +
"' found in BAM file header (header.ref_ids():",
356 else if (id_it->second != ref_idx)
362 " does not correspond to the position ",
364 " in the header (header.ref_ids():",
368 else if (std::get<0>(header.
ref_id_info[id_it->second]) != l_ref)
370 throw format_error{
"Provided reference has unequal length as specified in the header."};
382 position_buffer = stream.tellg();
386 if (core.
refID >=
static_cast<int32_t
>(header.
ref_ids().size()) || core.
refID < -1)
390 "' is not in range of ",
391 "header.ref_ids(), which has size ",
395 else if (core.
refID > -1)
406 if constexpr (!detail::decays_to_ignore_v<mate_type>)
420 if constexpr (!detail::decays_to_ignore_v<id_type>)
428 if constexpr (!detail::decays_to_ignore_v<cigar_type>)
430 int32_t seq_length{};
432 int32_t soft_clipping_end{};
454 if constexpr (detail::decays_to_ignore_v<seq_type>)
456 auto skip_sequence_bytes = [&]()
463 skip_sequence_bytes();
467 using alph_t = std::ranges::range_value_t<
decltype(
seq)>;
468 constexpr auto from_dna16 = detail::convert_through_char_representation<dna16sam, alph_t>;
470 for (
auto [d1, d2] : seq_stream)
492 return static_cast<char>(chr + 33);
494 if constexpr (!detail::decays_to_ignore_v<qual_type>)
503 assert(remaining_bytes >= 0);
506 while (tags_view.size() > 0)
508 if constexpr (!detail::decays_to_ignore_v<tag_dict_type>)
516 if constexpr (!detail::decays_to_ignore_v<cigar_type>)
521 if (core.
l_seq != 0 && offset_tmp == core.
l_seq)
523 if constexpr (detail::decays_to_ignore_v<tag_dict_type> | detail::decays_to_ignore_v<seq_type>)
530 "N' suggests that the cigar string exceeded 65535 elements and was therefore ",
531 "stored in the optional field CG. You need to read in the field::tags and "
532 "field::seq in order to access this information.")};
536 auto it = tag_dict.
find(
"CG"_tag);
538 if (it == tag_dict.end())
540 "The cigar string '",
544 "N' suggests that the cigar string exceeded 65535 elements and was therefore ",
545 "stored in the optional field CG but this tag is not present in the given ",
549 int32_t seq_length{};
552 int32_t soft_clipping_end{};
561template <
typename stream_type,
562 typename header_type,
565 typename ref_seq_type,
566 typename ref_id_type,
570 typename tag_dict_type>
573 [[maybe_unused]] header_type && header,
574 [[maybe_unused]] seq_type && seq,
575 [[maybe_unused]] qual_type && qual,
576 [[maybe_unused]] id_type &&
id,
577 [[maybe_unused]] int32_t
const offset,
578 [[maybe_unused]] ref_seq_type && SEQAN3_DOXYGEN_ONLY(ref_seq),
579 [[maybe_unused]] ref_id_type && ref_id,
581 [[maybe_unused]] cigar_type && cigar_vector,
582 [[maybe_unused]]
sam_flag const flag,
583 [[maybe_unused]] uint8_t
const mapq,
584 [[maybe_unused]] mate_type && mate,
585 [[maybe_unused]] tag_dict_type && tag_dict,
586 [[maybe_unused]]
double SEQAN3_DOXYGEN_ONLY(e_value),
587 [[maybe_unused]]
double SEQAN3_DOXYGEN_ONLY(bit_score))
593 "The seq object must be a std::ranges::forward_range over "
594 "letters that model seqan3::alphabet.");
597 "The id object must be a std::ranges::forward_range over "
598 "letters that model seqan3::alphabet.");
601 "The ref_seq object must be a std::ranges::forward_range "
602 "over letters that model seqan3::alphabet.");
604 if constexpr (!detail::decays_to_ignore_v<ref_id_type>)
606 static_assert((std::ranges::forward_range<ref_id_type> || std::integral<std::remove_reference_t<ref_id_type>>
607 || detail::is_type_specialisation_of_v<std::remove_cvref_t<ref_id_type>,
std::optional>),
608 "The ref_id object must be a std::ranges::forward_range "
609 "over letters that model seqan3::alphabet or an integral or a std::optional<integral>.");
613 "The qual object must be a std::ranges::forward_range "
614 "over letters that model seqan3::alphabet.");
617 "The mate object must be a std::tuple of size 3 with "
618 "1) a std::ranges::forward_range with a value_type modelling seqan3::alphabet, "
619 "2) a std::integral or std::optional<std::integral>, and "
620 "3) a std::integral.");
623 ((std::ranges::forward_range<decltype(std::get<0>(
mate))>
625 || detail::is_type_specialisation_of_v<
627 std::optional>)&&(std::integral<std::remove_cvref_t<decltype(std::get<1>(
mate))>>
628 || detail::is_type_specialisation_of_v<
630 std::optional>)&&std::integral<std::remove_cvref_t<decltype(std::get<2>(
mate))>>),
631 "The mate object must be a std::tuple of size 3 with "
632 "1) a std::ranges::forward_range with a value_type modelling seqan3::alphabet, "
633 "2) a std::integral or std::optional<std::integral>, and "
634 "3) a std::integral.");
637 "The tag_dict object must be of type seqan3::sam_tag_dictionary.");
639 if constexpr (detail::decays_to_ignore_v<header_type>)
641 throw format_error{
"BAM can only be written with a header but you did not provide enough information! "
642 "You can either construct the output file with reference names and reference length "
643 "information and the header will be created for you, or you can access the `header` member "
669 int32_t ref_length{};
672 if (!std::ranges::empty(cigar_vector))
674 int32_t dummy_seq_length{};
675 for (
auto & [
count, operation] : cigar_vector)
679 if (cigar_vector.size() >= (1 << 16))
682 cigar_vector.resize(2);
683 cigar_vector[0] =
cigar{
static_cast<uint32_t
>(std::ranges::distance(
seq)),
'S'_cigar_operation};
684 cigar_vector[1] =
cigar{
static_cast<uint32_t
>(ref_length),
'N'_cigar_operation};
694 uint8_t read_name_size = std::min<uint8_t>(std::ranges::distance(
id), 254) + 1;
695 read_name_size +=
static_cast<uint8_t
>(read_name_size == 1);
703 static_cast<uint16_t
>(cigar_vector.size()),
705 static_cast<int32_t
>(std::ranges::distance(
seq)),
707 get<1>(
mate).value_or(-1),
710 auto check_and_assign_id_to = [&header]([[maybe_unused]]
auto & id_source, [[maybe_unused]]
auto & id_target)
714 if constexpr (!detail::decays_to_ignore_v<id_t>)
716 if constexpr (std::integral<id_t>)
718 id_target = id_source;
720 else if constexpr (detail::is_type_specialisation_of_v<id_t, std::optional>)
722 id_target = id_source.value_or(-1);
726 if (!std::ranges::empty(id_source))
730 if constexpr (std::ranges::contiguous_range<
decltype(id_source)>
731 && std::ranges::sized_range<
decltype(id_source)>
732 && std::ranges::borrowed_range<
decltype(id_source)>)
743 "The ref_id type is not convertible to the reference id information stored in the "
744 "reference dictionary of the header object.");
746 id_it = header.
ref_dict.find(id_source);
754 "not be found in BAM header ref_dict: ",
759 id_target = id_it->second;
766 check_and_assign_id_to(
ref_id, core.refID);
769 check_and_assign_id_to(get<0>(
mate), core.next_refID);
772 core.block_size =
sizeof(core) - 4 + core.l_read_name + core.n_cigar_op * 4
774 (core.l_seq + 1) / 2 +
776 tag_dict_binary_str.
size();
780 if (std::ranges::empty(
id))
787 for (
auto [cigar_count, op] : cigar_vector)
789 cigar_count = cigar_count << 4;
795 using alph_t = std::ranges::range_value_t<seq_type>;
796 constexpr auto to_dna16 = detail::convert_through_char_representation<alph_t, dna16sam>;
799 for (int32_t sidx = 0; sidx < ((core.l_seq & 1) ? core.l_seq - 1 : core.l_seq); ++sidx, ++sit)
804 stream_it =
static_cast<char>(compressed_chr);
808 stream_it =
static_cast<char>(
to_rank(to_dna16[
to_rank(*sit)]) << 4);
811 if (std::ranges::empty(
qual))
818 if (std::ranges::distance(
qual) != core.l_seq)
821 ". Got quality with size ",
822 std::ranges::distance(
qual),
829 return static_cast<char>(
to_rank(chr));
835 stream << tag_dict_binary_str;
840template <
typename stream_t,
typename header_type>
843 if constexpr (detail::decays_to_ignore_v<header_type>)
845 throw format_error{
"BAM can only be written with a header but you did not provide enough information! "
846 "You can either construct the output file with reference names and reference length "
847 "information and the header will be created for you, or you can access the `header` member "
859#if SEQAN3_COMPILER_IS_GCC && (__GNUC__ == 10)
860 int32_t
const l_text{
static_cast<int32_t
>(os.
str().size())};
862 int32_t
const l_text{
static_cast<int32_t
>(os.view().size())};
866#if SEQAN3_COMPILER_IS_GCC && (__GNUC__ == 10)
867 auto header_view = os.
str();
869 auto header_view = os.view();
873 assert(header.ref_ids().size() < (1ull << 32));
874 int32_t
const n_ref{
static_cast<int32_t
>(header.ref_ids().size())};
877 for (int32_t ridx = 0; ridx < n_ref; ++ridx)
879 assert(header.ref_ids()[ridx].size() + 1 < (1ull << 32));
880 int32_t
const l_name{
static_cast<int32_t
>(header.ref_ids()[ridx].size()) + 1};
886 std::ranges::copy_n(
reinterpret_cast<char *
>(&get<0>(header.ref_id_info[ridx])), 4, stream_it);
892template <
typename stream_view_type,
typename value_type>
894 stream_view_type && stream_view,
895 value_type
const & SEQAN3_DOXYGEN_ONLY(value))
905 if constexpr (std::integral<value_type>)
909 else if constexpr (std::same_as<value_type, float>)
915 constexpr bool always_false = std::is_same_v<value_type, void>;
916 static_assert(always_false,
"format_bam::read_sam_dict_vector: unsupported value_type");
921 variant = std::move(tmp_vector);
941template <
typename stream_view_type>
951 uint16_t tag =
static_cast<uint16_t
>(*it) << 8;
954 tag +=
static_cast<uint16_t
>(*it);
973 target[tag] =
static_cast<int32_t
>(tmp);
980 target[tag] =
static_cast<int32_t
>(tmp);
987 target[tag] =
static_cast<int32_t
>(tmp);
994 target[tag] =
static_cast<int32_t
>(tmp);
1001 target[tag] = std::move(tmp);
1008 target[tag] =
static_cast<int32_t
>(tmp);
1021 while (!is_char<'\0'>(*it))
1034 while (!is_char<'\0'>(*it))
1041 throw format_error{
"Hexadecimal tag has an uneven number of digits!"};
1049 target[tag] = byte_array;
1054 char array_value_type_id = *it;
1057 switch (array_value_type_id)
1082 "must be one of [cCsSiIf] but '",
1083 array_value_type_id,
1090 "SAM tag must be one of [A,i,Z,H,B,f] but '",
1110template <
typename cigar_input_type>
1114 char operation{
'\0'};
1116 int32_t ref_length{}, seq_length{};
1117 uint32_t operation_and_count{};
1118 constexpr char const * cigar_mapping =
"MIDNSHP=X*******";
1119 constexpr uint32_t cigar_mask = 0x0f;
1121 if (n_cigar_op == 0)
1122 return std::tuple{operations, ref_length, seq_length};
1126 while (n_cigar_op > 0)
1129 sizeof(operation_and_count),
1130 reinterpret_cast<char *
>(&operation_and_count));
1131 operation = cigar_mapping[operation_and_count & cigar_mask];
1132 count = operation_and_count >> 4;
1139 return std::tuple{operations, ref_length, seq_length};
1149 auto stream_variant_fn = [&result](
auto && arg)
1154 if constexpr (std::same_as<T, int32_t>)
1157 size_t const absolute_arg = std::abs(arg);
1159 bool const negative = arg < 0;
1160 n = n * n + 2 * negative;
1166 result[result.size() - 1] =
'C';
1167 result.append(
reinterpret_cast<char const *
>(&arg), 1);
1172 result[result.size() - 1] =
'S';
1173 result.append(
reinterpret_cast<char const *
>(&arg), 2);
1178 result[result.size() - 1] =
'c';
1179 int8_t tmp =
static_cast<int8_t
>(arg);
1180 result.append(
reinterpret_cast<char const *
>(&tmp), 1);
1185 result[result.size() - 1] =
's';
1186 int16_t tmp =
static_cast<int16_t
>(arg);
1187 result.append(
reinterpret_cast<char const *
>(&tmp), 2);
1192 result.append(
reinterpret_cast<char const *
>(&arg), 4);
1197 else if constexpr (std::same_as<T, std::string>)
1199 result.append(
reinterpret_cast<char const *
>(arg.data()), arg.size() + 1 );
1201 else if constexpr (!std::ranges::range<T>)
1203 result.append(
reinterpret_cast<char const *
>(&arg),
sizeof(arg));
1207 int32_t sz{
static_cast<int32_t
>(arg.size())};
1208 result.append(
reinterpret_cast<char *
>(&sz), 4);
1209 result.append(
reinterpret_cast<char const *
>(arg.data()),
1210 arg.size() *
sizeof(std::ranges::range_value_t<T>));
1214 for (
auto & [tag, variant] : tag_dict)
1216 result.push_back(
static_cast<char>(tag / 256));
1217 result.push_back(
static_cast<char>(tag % 256));
constexpr derived_type & assign_char(char_type const chr) noexcept
Assign from a character, implicitly converts invalid characters.
Definition: alphabet_base.hpp:163
constexpr derived_type & assign_rank(rank_type const c) noexcept
Assign from a numeric value.
Definition: alphabet_base.hpp:187
The seqan3::cigar semialphabet pairs a counter with a seqan3::cigar::operation letter.
Definition: alphabet/cigar/cigar.hpp:60
Functionally the same as std::ostreambuf_iterator, but offers writing a range more efficiently.
Definition: fast_ostreambuf_iterator.hpp:40
A 16 letter DNA alphabet, containing all IUPAC symbols minus the gap and plus an equality sign ('=')....
Definition: dna16sam.hpp:48
The actual implementation of seqan3::cigar::operation for documentation purposes only....
Definition: cigar_operation.hpp:48
The SAM tag dictionary class that stores all optional SAM fields.
Definition: sam_tag_dictionary.hpp:343
Provides seqan3::dna16sam.
T emplace_back(T... args)
Provides seqan3::detail::fast_ostreambuf_iterator.
constexpr auto to_rank
Return the rank representation of a (semi-)alphabet object.
Definition: alphabet/concept.hpp:155
constexpr void consume(rng_t &&rng)
Iterate over a range (consumes single-pass input ranges).
Definition: core/range/detail/misc.hpp:28
constexpr auto all
Returns a view that includes all elements of the range argument.
Definition: all_view.hpp:204
sam_flag
An enum flag that describes the properties of an aligned read (given as a SAM record).
Definition: sam_flag.hpp:76
constexpr std::tuple< std::vector< cigar >, int32_t, int32_t > parse_cigar(cigar_input_type &&cigar_input)
Parses a cigar string into a vector of operation-count pairs (e.g. (M, 3)).
Definition: io/sam_file/detail/cigar.hpp:94
std::string get_cigar_string(std::vector< cigar > const &cigar_vector)
Transforms a vector of cigar elements into a string representation.
Definition: io/sam_file/detail/cigar.hpp:128
constexpr char sam_tag_type_char_extra[12]
Each types SAM tag type extra char id. Index corresponds to the seqan3::detail::sam_tag_variant types...
Definition: sam_tag_dictionary.hpp:45
void update_alignment_lengths(int32_t &ref_length, int32_t &seq_length, char const cigar_operation, uint32_t const cigar_count)
Updates the sequence lengths by cigar_count depending on the cigar operation op.
Definition: io/sam_file/detail/cigar.hpp:51
constexpr char sam_tag_type_char[12]
Each SAM tag type char identifier. Index corresponds to the seqan3::detail::sam_tag_variant types.
Definition: sam_tag_dictionary.hpp:42
constexpr auto take_exactly_or_throw
A view adaptor that returns the first size elements from the underlying range and also exposes size i...
Definition: take_exactly_view.hpp:590
constexpr auto istreambuf
A view factory that returns a view over the stream buffer of an input stream.
Definition: istreambuf_view.hpp:107
@ flag
The alignment flag (bit information), uint16_t value.
@ ref_offset
Sequence (seqan3::field::ref_seq) relative start position (0-based), unsigned value.
@ 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.
@ ref_id
The identifier of the (reference) sequence that seqan3::field::seq was aligned to.
@ seq
The "sequence", usually a range of nucleotides or amino acids.
@ qual
The qualities, usually in Phred score notation.
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: type_list/traits.hpp:470
constexpr ptrdiff_t count
Count the occurrences of a type in a pack.
Definition: type_pack/traits.hpp:164
constexpr size_t size
The size of a type pack.
Definition: type_pack/traits.hpp:146
constexpr auto repeat_n
A view factory that repeats a given value n times.
Definition: repeat_n.hpp:91
The generic alphabet concept that covers most data types used in ranges.
Checks whether from can be implicityly converted to to.
Whether a type behaves like a tuple.
Auxiliary functions for the SAM IO.
Provides seqan3::detail::istreambuf.
std::string to_string(value_type &&... values)
Streams all parameters via the seqan3::debug_stream and returns a concatenated string.
Definition: to_string.hpp:29
The main SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29
Provides seqan3::debug_stream and related types.
Provides helper data structures for the seqan3::sam_file_output.
Provides the seqan3::sam_tag_dictionary class and auxiliaries.
Provides seqan3::views::slice.
The options type defines various option members that influence the behavior of all or some formats.
Definition: sam_file/output_options.hpp:26
Provides seqan3::views::take_exactly and seqan3::views::take_exactly_or_throw.