22 #include <seqan3/alphabet/detail/convert.hpp>
85 template <
typename stream_type,
86 typename seq_legal_alph_type,
87 typename ref_seqs_type,
88 typename ref_ids_type,
92 typename ref_seq_type,
94 typename ref_offset_type,
101 typename tag_dict_type,
102 typename e_value_type,
103 typename bit_score_type>
106 ref_seqs_type & ref_seqs,
111 offset_type & offset,
112 ref_seq_type & SEQAN3_DOXYGEN_ONLY(ref_seq),
113 ref_id_type & ref_id,
114 ref_offset_type & ref_offset,
116 cigar_type & cigar_vector,
120 tag_dict_type & tag_dict,
121 e_value_type & SEQAN3_DOXYGEN_ONLY(e_value),
122 bit_score_type & SEQAN3_DOXYGEN_ONLY(bit_score));
124 template <
typename stream_type,
125 typename header_type,
128 typename ref_seq_type,
129 typename ref_id_type,
134 typename tag_dict_type>
137 [[maybe_unused]] header_type && header,
138 [[maybe_unused]] seq_type && seq,
139 [[maybe_unused]] qual_type && qual,
140 [[maybe_unused]] id_type &&
id,
141 [[maybe_unused]] int32_t
const offset,
142 [[maybe_unused]] ref_seq_type && SEQAN3_DOXYGEN_ONLY(ref_seq),
143 [[maybe_unused]] ref_id_type && ref_id,
145 [[maybe_unused]] align_type && align,
146 [[maybe_unused]] cigar_type && cigar_vector,
147 [[maybe_unused]]
sam_flag const flag,
148 [[maybe_unused]] uint8_t
const mapq,
149 [[maybe_unused]] mate_type && mate,
150 [[maybe_unused]] tag_dict_type && tag_dict,
151 [[maybe_unused]]
double SEQAN3_DOXYGEN_ONLY(e_value),
152 [[maybe_unused]]
double SEQAN3_DOXYGEN_ONLY(bit_score));
156 bool header_was_read{
false};
162 struct alignment_record_core
167 uint32_t l_read_name:8;
170 uint32_t n_cigar_op:16;
188 ret[
static_cast<index_t
>(
'I')] = 1;
189 ret[
static_cast<index_t
>(
'D')] = 2;
190 ret[
static_cast<index_t
>(
'N')] = 3;
191 ret[
static_cast<index_t
>(
'S')] = 4;
192 ret[
static_cast<index_t
>(
'H')] = 5;
193 ret[
static_cast<index_t
>(
'P')] = 6;
194 ret[
static_cast<index_t
>(
'=')] = 7;
195 ret[
static_cast<index_t
>(
'X')] = 8;
202 static uint16_t reg2bin(int32_t beg, int32_t end) noexcept
205 if (beg >> 14 == end >> 14)
return ((1 << 15) - 1) / 7 + (beg >> 14);
206 if (beg >> 17 == end >> 17)
return ((1 << 12) - 1) / 7 + (beg >> 17);
207 if (beg >> 20 == end >> 20)
return ((1 << 9) - 1) / 7 + (beg >> 20);
208 if (beg >> 23 == end >> 23)
return ((1 << 6) - 1) / 7 + (beg >> 23);
209 if (beg >> 26 == end >> 26)
return ((1 << 3) - 1) / 7 + (beg >> 26);
213 using format_sam_base::read_field;
221 template <
typename stream_view_type, std::
integral number_type>
222 void read_field(stream_view_type && stream_view, number_type & target)
224 std::ranges::copy_n(std::ranges::begin(stream_view),
sizeof(target),
reinterpret_cast<char *
>(&target));
232 template <
typename stream_view_type>
233 void read_field(stream_view_type && stream_view,
float & target)
235 std::ranges::copy_n(std::ranges::begin(stream_view),
sizeof(int32_t),
reinterpret_cast<char *
>(&target));
248 template <
typename stream_view_type,
typename optional_value_type>
251 optional_value_type tmp;
252 read_field(std::forward<stream_view_type>(stream_view), tmp);
256 template <
typename stream_view_type,
typename value_type>
258 stream_view_type && stream_view,
259 value_type
const & SEQAN3_DOXYGEN_ONLY(value));
261 template <
typename stream_view_type>
262 void read_field(stream_view_type && stream_view, sam_tag_dictionary & target);
264 template <
typename cigar_input_type>
265 auto parse_binary_cigar(cigar_input_type && cigar_input, uint16_t n_cigar_op)
const;
267 static std::string get_tag_dict_str(sam_tag_dictionary
const & tag_dict);
271 template <
typename stream_type,
272 typename seq_legal_alph_type,
273 typename ref_seqs_type,
274 typename ref_ids_type,
277 typename offset_type,
278 typename ref_seq_type,
279 typename ref_id_type,
280 typename ref_offset_type,
287 typename tag_dict_type,
288 typename e_value_type,
289 typename bit_score_type>
292 ref_seqs_type & ref_seqs,
297 offset_type & offset,
298 ref_seq_type & SEQAN3_DOXYGEN_ONLY(ref_seq),
299 ref_id_type & ref_id,
300 ref_offset_type & ref_offset,
302 cigar_type & cigar_vector,
306 tag_dict_type & tag_dict,
307 e_value_type & SEQAN3_DOXYGEN_ONLY(e_value),
308 bit_score_type & SEQAN3_DOXYGEN_ONLY(bit_score))
310 static_assert(detail::decays_to_ignore_v<ref_offset_type> ||
311 detail::is_type_specialisation_of_v<ref_offset_type, std::optional>,
312 "The ref_offset must be a specialisation of std::optional.");
314 static_assert(detail::decays_to_ignore_v<mapq_type> || std::same_as<mapq_type, uint8_t>,
315 "The type of field::mapq must be uint8_t.");
317 static_assert(detail::decays_to_ignore_v<flag_type> || std::same_as<flag_type, sam_flag>,
318 "The type of field::flag must be seqan3::sam_flag.");
323 [[maybe_unused]] int32_t offset_tmp{};
324 [[maybe_unused]] int32_t soft_clipping_end{};
326 [[maybe_unused]] int32_t ref_length{0}, seq_length{0};
330 if (!header_was_read)
337 read_field(stream_view, tmp32);
343 read_field(stream_view, n_ref);
345 for (int32_t ref_idx = 0; ref_idx < n_ref; ++ref_idx)
347 read_field(stream_view, tmp32);
349 string_buffer.
resize(tmp32 - 1);
350 std::ranges::copy_n(std::ranges::begin(stream_view), tmp32 - 1, string_buffer.
data());
351 std::ranges::next(std::ranges::begin(stream_view));
353 read_field(stream_view, tmp32);
355 auto id_it = header.
ref_dict.find(string_buffer);
360 throw format_error{detail::to_string(
"Unknown reference name '" + string_buffer +
361 "' found in BAM file header (header.ref_ids():",
364 else if (id_it->second != ref_idx)
366 throw format_error{detail::to_string(
"Reference id '", string_buffer,
"' at position ", ref_idx,
367 " does not correspond to the position ", id_it->second,
368 " in the header (header.ref_ids():", header.
ref_ids(),
").")};
370 else if (std::get<0>(header.
ref_id_info[id_it->second]) != tmp32)
372 throw format_error{
"Provided reference has unequal length as specified in the header."};
376 header_was_read =
true;
378 if (std::ranges::begin(stream_view) == std::ranges::end(stream_view))
384 alignment_record_core core;
387 if (core.refID >=
static_cast<int32_t
>(header.
ref_ids().size()) || core.refID < -1)
389 throw format_error{detail::to_string(
"Reference id index '", core.refID,
"' is not in range of ",
390 "header.ref_ids(), which has size ", header.
ref_ids().size(),
".")};
392 else if (core.refID > -1)
403 if constexpr (!detail::decays_to_ignore_v<mate_type>)
405 if (core.next_refID > -1)
406 get<0>(
mate) = core.next_refID;
408 if (core.next_pos > -1)
409 get<1>(
mate) = core.next_pos;
411 get<2>(
mate) = core.tlen;
417 std::ranges::next(std::ranges::begin(stream_view));
421 if constexpr (!detail::decays_to_ignore_v<align_type> || !detail::decays_to_ignore_v<cigar_type>)
423 std::tie(tmp_cigar_vector, ref_length, seq_length) = parse_binary_cigar(stream_view, core.n_cigar_op);
424 transfer_soft_clipping_to(tmp_cigar_vector, offset_tmp, soft_clipping_end);
438 auto seq_stream = stream_view
446 if constexpr (detail::decays_to_ignore_v<seq_type>)
448 auto skip_sequence_bytes = [&] ()
450 detail::consume(seq_stream);
452 std::ranges::next(std::ranges::begin(stream_view));
455 if constexpr (!detail::decays_to_ignore_v<align_type>)
458 "If you want to read ALIGNMENT but not SEQ, the alignment"
459 " object must store a sequence container at the second (query) position.");
461 if (!tmp_cigar_vector.empty())
463 assert(core.l_seq == (seq_length + offset_tmp + soft_clipping_end));
464 using alph_t = std::ranges::range_value_t<decltype(get<1>(align))>;
465 constexpr
auto from_dna16 = detail::convert_through_char_representation<alph_t, sam_dna16>;
467 get<1>(align).reserve(seq_length);
469 auto tmp_iter = std::ranges::begin(seq_stream);
470 std::ranges::advance(tmp_iter, offset_tmp / 2);
474 get<1>(align).push_back(from_dna16[
to_rank(get<1>(*tmp_iter))]);
479 for (
size_t i = (seq_length / 2); i > 0; --i)
481 get<1>(align).push_back(from_dna16[
to_rank(get<0>(*tmp_iter))]);
482 get<1>(align).push_back(from_dna16[
to_rank(get<1>(*tmp_iter))]);
488 get<1>(align).push_back(from_dna16[
to_rank(get<0>(*tmp_iter))]);
493 std::ranges::advance(tmp_iter, (soft_clipping_end + !(seq_length & 1)) / 2);
497 skip_sequence_bytes();
503 skip_sequence_bytes();
508 using alph_t = std::ranges::range_value_t<decltype(
seq)>;
509 constexpr
auto from_dna16 = detail::convert_through_char_representation<alph_t, sam_dna16>;
511 for (
auto [d1, d2] : seq_stream)
521 std::ranges::next(std::ranges::begin(stream_view));
524 if constexpr (!detail::decays_to_ignore_v<align_type>)
526 assign_unaligned(get<1>(align),
527 seq |
views::slice(
static_cast<std::ranges::range_difference_t<seq_type>
>(offset_tmp),
528 std::ranges::distance(
seq) - soft_clipping_end));
540 int32_t remaining_bytes = core.block_size - (
sizeof(alignment_record_core) - 4) -
541 core.l_read_name - core.n_cigar_op * 4 - (core.l_seq + 1) / 2 - core.l_seq;
542 assert(remaining_bytes >= 0);
545 while (tags_view.size() > 0)
546 read_field(tags_view, tag_dict);
550 if constexpr (!detail::decays_to_ignore_v<align_type> || !detail::decays_to_ignore_v<cigar_type>)
555 if (core.l_seq != 0 && offset_tmp == core.l_seq)
557 if constexpr (detail::decays_to_ignore_v<tag_dict_type> | detail::decays_to_ignore_v<seq_type>)
559 throw format_error{detail::to_string(
"The cigar string '", offset_tmp,
"S", ref_length,
560 "N' suggests that the cigar string exceeded 65535 elements and was therefore ",
561 "stored in the optional field CG. You need to read in the field::tags and "
562 "field::seq in order to access this information.")};
566 auto it = tag_dict.find(
"CG"_tag);
568 if (it == tag_dict.end())
569 throw format_error{detail::to_string(
"The cigar string '", offset_tmp,
"S", ref_length,
570 "N' suggests that the cigar string exceeded 65535 elements and was therefore ",
571 "stored in the optional field CG but this tag is not present in the given ",
574 auto cigar_view = std::views::all(std::get<std::string>(it->second));
575 std::tie(tmp_cigar_vector, ref_length, seq_length) = parse_cigar(cigar_view);
576 offset_tmp = soft_clipping_end = 0;
577 transfer_soft_clipping_to(tmp_cigar_vector, offset_tmp, soft_clipping_end);
580 if constexpr (!detail::decays_to_ignore_v<align_type>)
582 assign_unaligned(get<1>(align),
583 seq |
views::slice(
static_cast<std::ranges::range_difference_t<seq_type>
>(offset_tmp),
584 std::ranges::distance(
seq) - soft_clipping_end));
591 if constexpr (!detail::decays_to_ignore_v<align_type>)
592 construct_alignment(align, tmp_cigar_vector, core.refID, ref_seqs, core.pos, ref_length);
594 if constexpr (!detail::decays_to_ignore_v<cigar_type>)
595 std::swap(cigar_vector, tmp_cigar_vector);
599 template <
typename stream_type,
600 typename header_type,
603 typename ref_seq_type,
604 typename ref_id_type,
609 typename tag_dict_type>
612 [[maybe_unused]] header_type && header,
613 [[maybe_unused]] seq_type && seq,
614 [[maybe_unused]] qual_type && qual,
615 [[maybe_unused]] id_type &&
id,
616 [[maybe_unused]] int32_t
const offset,
617 [[maybe_unused]] ref_seq_type && SEQAN3_DOXYGEN_ONLY(ref_seq),
618 [[maybe_unused]] ref_id_type && ref_id,
620 [[maybe_unused]] align_type && align,
621 [[maybe_unused]] cigar_type && cigar_vector,
622 [[maybe_unused]]
sam_flag const flag,
623 [[maybe_unused]] uint8_t
const mapq,
624 [[maybe_unused]] mate_type && mate,
625 [[maybe_unused]] tag_dict_type && tag_dict,
626 [[maybe_unused]]
double SEQAN3_DOXYGEN_ONLY(e_value),
627 [[maybe_unused]]
double SEQAN3_DOXYGEN_ONLY(bit_score))
632 static_assert((std::ranges::forward_range<seq_type> &&
633 alphabet<std::ranges::range_reference_t<seq_type>>),
634 "The seq object must be a std::ranges::forward_range over "
635 "letters that model seqan3::alphabet.");
637 static_assert((std::ranges::forward_range<id_type> &&
638 alphabet<std::ranges::range_reference_t<id_type>>),
639 "The id object must be a std::ranges::forward_range over "
640 "letters that model seqan3::alphabet.");
642 static_assert((std::ranges::forward_range<ref_seq_type> &&
643 alphabet<std::ranges::range_reference_t<ref_seq_type>>),
644 "The ref_seq object must be a std::ranges::forward_range "
645 "over letters that model seqan3::alphabet.");
647 if constexpr (!detail::decays_to_ignore_v<ref_id_type>)
649 static_assert((std::ranges::forward_range<ref_id_type> ||
652 "The ref_id object must be a std::ranges::forward_range "
653 "over letters that model seqan3::alphabet or an integral or a std::optional<integral>.");
657 "The align object must be a std::pair of two ranges whose "
658 "value_type is comparable to seqan3::gap");
661 std::equality_comparable_with<
gap, std::ranges::range_reference_t<decltype(std::get<0>(align))>> &&
662 std::equality_comparable_with<
gap, std::ranges::range_reference_t<decltype(std::get<1>(align))>>),
663 "The align object must be a std::pair of two ranges whose "
664 "value_type is comparable to seqan3::gap");
666 static_assert((std::ranges::forward_range<qual_type> &&
667 alphabet<std::ranges::range_reference_t<qual_type>>),
668 "The qual object must be a std::ranges::forward_range "
669 "over letters that model seqan3::alphabet.");
672 "The mate object must be a std::tuple of size 3 with "
673 "1) a std::ranges::forward_range with a value_type modelling seqan3::alphabet, "
674 "2) a std::integral or std::optional<std::integral>, and "
675 "3) a std::integral.");
677 static_assert(((std::ranges::forward_range<decltype(std::get<0>(
mate))> ||
683 "The mate object must be a std::tuple of size 3 with "
684 "1) a std::ranges::forward_range with a value_type modelling seqan3::alphabet, "
685 "2) a std::integral or std::optional<std::integral>, and "
686 "3) a std::integral.");
689 "The tag_dict object must be of type seqan3::sam_tag_dictionary.");
691 if constexpr (detail::decays_to_ignore_v<header_type>)
693 throw format_error{
"BAM can only be written with a header but you did not provide enough information! "
694 "You can either construct the output file with ref_ids and ref_seqs information and "
695 "the header will be created for you, or you can access the `header` member directly."};
706 detail::fast_ostreambuf_iterator stream_it{*stream.rdbuf()};
711 if (!header_was_written)
715 write_header(os, options, header);
716 int32_t l_text{
static_cast<int32_t
>(os.
str().size())};
717 std::ranges::copy_n(
reinterpret_cast<char *
>(&l_text), 4, stream_it);
721 int32_t n_ref{
static_cast<int32_t
>(header.
ref_ids().size())};
722 std::ranges::copy_n(
reinterpret_cast<char *
>(&n_ref), 4, stream_it);
724 for (int32_t ridx = 0; ridx < n_ref; ++ridx)
726 int32_t l_name{
static_cast<int32_t
>(header.
ref_ids()[ridx].size()) + 1};
727 std::ranges::copy_n(
reinterpret_cast<char *
>(&l_name), 4, stream_it);
729 std::ranges::copy(header.
ref_ids()[ridx].begin(), header.
ref_ids()[ridx].end(), stream_it);
732 std::ranges::copy_n(
reinterpret_cast<char *
>(&get<0>(header.
ref_id_info[ridx])), 4, stream_it);
735 header_was_written =
true;
741 int32_t ref_length{};
745 if (!std::ranges::empty(cigar_vector))
747 int32_t dummy_seq_length{};
748 for (
auto & [
count, operation] : cigar_vector)
749 update_alignment_lengths(ref_length, dummy_seq_length, operation.to_char(),
count);
751 else if (!std::ranges::empty(get<0>(align)) && !std::ranges::empty(get<1>(align)))
753 ref_length = std::ranges::distance(get<1>(align));
759 int32_t off_end{
static_cast<int32_t
>(std::ranges::distance(
seq)) -
offset};
761 for (
auto chr : get<1>(align))
765 off_end -= ref_length;
766 cigar_vector = detail::get_cigar_vector(align,
offset, off_end);
769 if (cigar_vector.size() >= (1 << 16))
771 tag_dict[
"CG"_tag] = detail::get_cigar_string(cigar_vector);
772 cigar_vector.resize(2);
773 cigar_vector[0] =
cigar{
static_cast<uint32_t
>(std::ranges::distance(
seq)),
'S'_cigar_operation};
774 cigar_vector[1] =
cigar{
static_cast<uint32_t
>(std::ranges::distance(get<1>(align))),
'N'_cigar_operation};
777 std::string tag_dict_binary_str = get_tag_dict_str(tag_dict);
784 uint8_t read_name_size = std::min<uint8_t>(std::ranges::distance(
id), 254) + 1;
785 read_name_size +=
static_cast<uint8_t
>(read_name_size == 1);
787 alignment_record_core core
795 static_cast<uint16_t
>(cigar_vector.size()),
797 static_cast<int32_t
>(std::ranges::distance(
seq)),
799 get<1>(
mate).value_or(-1),
803 auto check_and_assign_id_to = [&header] ([[maybe_unused]]
auto & id_source,
804 [[maybe_unused]]
auto & id_target)
808 if constexpr (!detail::decays_to_ignore_v<id_t>)
810 if constexpr (std::integral<id_t>)
812 id_target = id_source;
814 else if constexpr (detail::is_type_specialisation_of_v<id_t, std::optional>)
816 id_target = id_source.value_or(-1);
820 if (!std::ranges::empty(id_source))
824 if constexpr (std::ranges::contiguous_range<decltype(id_source)> &&
825 std::ranges::sized_range<decltype(id_source)> &&
826 std::ranges::borrowed_range<decltype(id_source)>)
836 "The ref_id type is not convertible to the reference id information stored in the "
837 "reference dictionary of the header object.");
839 id_it = header.
ref_dict.find(id_source);
844 throw format_error{detail::to_string(
"Unknown reference name '", id_source,
"' could "
845 "not be found in BAM header ref_dict: ",
849 id_target = id_it->second;
856 check_and_assign_id_to(
ref_id, core.refID);
859 check_and_assign_id_to(get<0>(
mate), core.next_refID);
862 core.block_size =
sizeof(core) - 4 +
864 core.n_cigar_op * 4 +
865 (core.l_seq + 1) / 2 +
867 tag_dict_binary_str.
size();
869 std::ranges::copy_n(
reinterpret_cast<char *
>(&core),
sizeof(core), stream_it);
871 if (std::ranges::empty(
id))
874 std::ranges::copy_n(std::ranges::begin(
id), core.l_read_name - 1, stream_it);
878 for (
auto [cigar_count, op] : cigar_vector)
880 cigar_count = cigar_count << 4;
881 cigar_count |=
static_cast<int32_t
>(char_to_sam_rank[op.to_char()]);
882 std::ranges::copy_n(
reinterpret_cast<char *
>(&cigar_count), 4, stream_it);
886 using alph_t = std::ranges::range_value_t<seq_type>;
887 constexpr
auto to_dna16 = detail::convert_through_char_representation<sam_dna16, alph_t>;
889 auto sit = std::ranges::begin(
seq);
890 for (int32_t sidx = 0; sidx < ((core.l_seq & 1) ? core.l_seq - 1 : core.l_seq); ++sidx, ++sit)
895 stream_it =
static_cast<char>(compressed_chr);
899 stream_it =
static_cast<char>(
to_rank(to_dna16[
to_rank(*sit)]) << 4);
902 if (std::ranges::empty(
qual))
905 std::ranges::copy_n(v.begin(), core.l_seq, stream_it);
909 if (std::ranges::distance(
qual) != core.l_seq)
910 throw format_error{detail::to_string(
"Expected quality of same length as sequence with size ",
911 core.l_seq,
". Got quality with size ",
912 std::ranges::distance(
qual),
" instead.")};
915 std::ranges::copy_n(v.begin(), core.l_seq, stream_it);
919 stream << tag_dict_binary_str;
924 template <
typename stream_view_type,
typename value_type>
926 stream_view_type && stream_view,
927 value_type const & SEQAN3_DOXYGEN_ONLY(value))
930 read_field(stream_view,
count);
937 read_field(stream_view, tmp);
961 template <
typename stream_view_type>
962 inline void format_bam::read_field(stream_view_type && stream_view, sam_tag_dictionary & target)
971 uint16_t tag =
static_cast<uint16_t
>(*it) << 8;
974 tag +=
static_cast<uint16_t
>(*it);
992 read_field(stream_view, tmp);
993 target[tag] =
static_cast<int32_t
>(tmp);
999 read_field(stream_view, tmp);
1000 target[tag] =
static_cast<int32_t
>(tmp);
1006 read_field(stream_view, tmp);
1007 target[tag] =
static_cast<int32_t
>(tmp);
1013 read_field(stream_view, tmp);
1014 target[tag] =
static_cast<int32_t
>(tmp);
1020 read_field(stream_view, tmp);
1027 read_field(stream_view, tmp);
1028 target[tag] =
static_cast<int32_t
>(tmp);
1034 read_field(stream_view, tmp);
1040 string_buffer.
clear();
1041 while (!is_char<'\0'>(*it))
1047 target[tag] = string_buffer;
1054 while (!is_char<'\0'>(*it))
1056 string_buffer.
clear();
1061 throw format_error{
"Hexadecimal tag has an uneven number of digits!"};
1065 read_field(string_buffer, value);
1069 target[tag] = byte_array;
1074 char array_value_type_id = *it;
1077 switch (array_value_type_id)
1080 read_sam_dict_vector(target[tag], stream_view, int8_t{});
1083 read_sam_dict_vector(target[tag], stream_view, uint8_t{});
1086 read_sam_dict_vector(target[tag], stream_view, int16_t{});
1089 read_sam_dict_vector(target[tag], stream_view, uint16_t{});
1092 read_sam_dict_vector(target[tag], stream_view, int32_t{});
1095 read_sam_dict_vector(target[tag], stream_view, uint32_t{});
1098 read_sam_dict_vector(target[tag], stream_view,
float{});
1101 throw format_error{detail::to_string(
"The first character in the numerical id of a SAM tag ",
1102 "must be one of [cCsSiIf] but '", array_value_type_id,
"' was given.")};
1107 throw format_error{detail::to_string(
"The second character in the numerical id of a "
1108 "SAM tag must be one of [A,i,Z,H,B,f] but '", type_id,
"' was given.")};
1126 template <
typename cigar_input_type>
1127 inline auto format_bam::parse_binary_cigar(cigar_input_type && cigar_input, uint16_t n_cigar_op)
const
1130 char operation{
'\0'};
1132 int32_t ref_length{}, seq_length{};
1133 uint32_t operation_and_count{};
1134 constexpr
char const * cigar_mapping =
"MIDNSHP=X*******";
1135 constexpr uint32_t cigar_mask = 0x0f;
1137 if (n_cigar_op == 0)
1138 return std::tuple{operations, ref_length, seq_length};
1142 while (n_cigar_op > 0)
1144 std::ranges::copy_n(std::ranges::begin(cigar_input),
1145 sizeof(operation_and_count),
1146 reinterpret_cast<char*
>(&operation_and_count));
1147 operation = cigar_mapping[operation_and_count & cigar_mask];
1148 count = operation_and_count >> 4;
1150 update_alignment_lengths(ref_length, seq_length, operation,
count);
1155 return std::tuple{operations, ref_length, seq_length};
1161 inline std::string format_bam::get_tag_dict_str(sam_tag_dictionary
const & tag_dict)
1165 auto stream_variant_fn = [&result] (
auto && arg)
1170 if constexpr (std::same_as<T, int32_t>)
1173 size_t const absolute_arg = std::abs(arg);
1175 bool const negative = arg < 0;
1176 n = n * n + 2 * negative;
1182 result[result.size() - 1] =
'C';
1183 result.append(
reinterpret_cast<char const *
>(&arg), 1);
1188 result[result.size() - 1] =
'S';
1189 result.append(
reinterpret_cast<char const *
>(&arg), 2);
1194 result[result.size() - 1] =
'c';
1195 int8_t tmp =
static_cast<int8_t
>(arg);
1196 result.append(
reinterpret_cast<char const *
>(&tmp), 1);
1201 result[result.size() - 1] =
's';
1202 int16_t tmp =
static_cast<int16_t
>(arg);
1203 result.append(
reinterpret_cast<char const *
>(&tmp), 2);
1208 result.append(
reinterpret_cast<char const *
>(&arg), 4);
1213 else if constexpr (std::same_as<T, std::string>)
1215 result.append(
reinterpret_cast<char const *
>(arg.data()), arg.size() + 1);
1217 else if constexpr (!std::ranges::range<T>)
1219 result.append(
reinterpret_cast<char const *
>(&arg),
sizeof(arg));
1223 int32_t sz{
static_cast<int32_t
>(arg.size())};
1224 result.append(
reinterpret_cast<char *
>(&sz), 4);
1225 result.append(
reinterpret_cast<char const *
>(arg.data()),
1226 arg.size() *
sizeof(std::ranges::range_value_t<T>));
1230 for (
auto & [tag, variant] : tag_dict)
1232 result.push_back(
static_cast<char>(tag / 256));
1233 result.push_back(
static_cast<char>(tag % 256));
1235 result.push_back(detail::sam_tag_type_char[variant.
index()]);
1237 if (!is_char<'\0'>(detail::sam_tag_type_char_extra[variant.
index()]))
1238 result.push_back(detail::sam_tag_type_char_extra[variant.
index()]);
Provides the C++20 <bit> header if it is not already available.
constexpr derived_type & assign_char(char_type const c) noexcept
Assign from a character, implicitly converts invalid characters.
Definition: alphabet_base.hpp:159
constexpr derived_type & assign_rank(rank_type const c) noexcept
Assign from a numeric value.
Definition: alphabet_base.hpp:186
The seqan3::cigar semialphabet pairs a counter with a seqan3::cigar::operation letter.
Definition: cigar.hpp:59
exposition_only::cigar_operation operation
The (extended) cigar operation alphabet of M,D,I,H,N,P,S,X,=.
Definition: cigar.hpp:98
The alphabet of a gap character '-'.
Definition: gap.hpp:37
A 16 letter DNA alphabet, containing all IUPAC symbols minus the gap and plus an equality sign ('=').
Definition: sam_dna16.hpp:46
The SAM tag dictionary class that stores all optional SAM fields.
Definition: sam_tag_dictionary.hpp:326
Provides various transformation traits used by the range module.
Auxiliary for pretty printing of exception messages.
Provides seqan3::debug_stream and related types.
Provides type traits for working with templates.
Provides concepts for core language types and relations that don't have concepts in C++20 (yet).
Provides seqan3::detail::fast_ostreambuf_iterator.
constexpr auto to_rank
Return the rank representation of a (semi-)alphabet object.
Definition: concept.hpp:146
constexpr T bit_ceil(T x) noexcept
Calculates the smallest integral power of two that is not smaller than x.
Definition: bit:133
constexpr int countr_zero(T x) noexcept
Returns the number of consecutive 0 bits in the value of x, starting from the least significant bit (...
Definition: bit:199
sam_flag
An enum flag that describes the properties of an aligned read (given as a SAM record).
Definition: sam_flag.hpp:73
@ 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: traits.hpp:434
constexpr ptrdiff_t count
Count the occurrences of a type in a pack.
Definition: traits.hpp:168
constexpr size_t size
The size of a type pack.
Definition: traits.hpp:150
constexpr auto slice
A view adaptor that returns a half-open interval on the underlying range.
Definition: slice.hpp:141
constexpr auto istreambuf
A view factory that returns a view over the stream buffer of an input stream.
Definition: istreambuf.hpp:114
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.hpp:91
constexpr auto repeat_n
A view factory that repeats a given value n times.
Definition: repeat_n.hpp:94
auto const move
A view that turns lvalue-references into rvalue-references.
Definition: move.hpp:70
Provides seqan3::detail::ignore_output_iterator for writing to null stream.
The generic alphabet concept that covers most data types used in ranges.
Resolves to std::ranges::implicitly_convertible_to<type1, type2>(). <dl class="no-api">This entity i...
A more refined container concept than seqan3::container.
Whether a type behaves like a tuple.
Provides various utility functions.
Auxiliary functions for the alignment IO.
Provides seqan3::views::istreambuf.
The main SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29
Provides various utility functions.
Adaptations of concepts from the Ranges TS.
Provides seqan3::sam_dna16.
Provides seqan3::sam_file_output_options.
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: output_options.hpp:23
Exposes the value_type of another type.
Definition: pre.hpp:58
Provides seqan3::views::take_exactly and seqan3::views::take_exactly_or_throw.
Provides seqan3::views::take_until and seqan3::views::take_until_or_throw.
Provides character predicates for tokenisation.
Provides seqan3::tuple_like.