37 template <std::ranges::forward_range rng1_type, std::ranges::forward_range rng2_type>
38 constexpr bool operator()(rng1_type && rng1, rng2_type && rng2)
const
53 char const cigar_operation,
54 uint32_t
const cigar_count)
56 switch (cigar_operation)
61 ref_length += cigar_count, seq_length += cigar_count;
65 ref_length += cigar_count;
68 seq_length += cigar_count;
93template <
typename cigar_input_type>
98 char cigar_operation{};
99 uint32_t cigar_count{};
100 int32_t ref_length{}, seq_length{};
114 throw format_error{
"Corrupted cigar string encountered"};
120 return {operations, ref_length, seq_length};
132 [&result](
auto & cig)
172template <seqan3::aligned_sequence ref_seq_type, seqan3::aligned_sequence query_seq_type>
174 query_seq_type && query_seq,
175 uint32_t
const query_start_pos = 0,
176 uint32_t
const query_end_pos = 0,
177 bool const extended_cigar =
false)
187 template <
typename chr_t>
190 throw std::logic_error{
"Access is not allowed because there is no sequence information."};
Provides the seqan3::cigar alphabet.
The <charconv> header from C++17's standard library.
constexpr derived_type & assign_char(char_type const chr) noexcept
Assign from a character, implicitly converts invalid characters.
Definition: alphabet_base.hpp:163
The actual implementation of seqan3::cigar::operation for documentation purposes only....
Definition: cigar_operation.hpp:48
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
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 auto take_until_or_throw
A view adaptor that returns elements from the underlying range until the functor evaluates to true (t...
Definition: take_until_view.hpp:574
@ ref_seq
The (reference) "sequence" information, usually a range of nucleotides or amino acids.
constexpr auto is_digit
Checks whether c is a digital character.
Definition: predicate.hpp:262
constexpr auto single_pass_input
A view adapter that decays most of the range properties and adds single pass behavior.
Definition: single_pass_input.hpp:348
The internal SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29
Provides seqan3::detail::pairwise_alignment and seqan3::detail::writable_pairwise_alignment.
Provides character predicates for tokenisation.
A functor that always throws when calling operator() (needed for the alignment "dummy" sequence).
Definition: io/sam_file/detail/cigar.hpp:185
chr_t operator()(chr_t) const
Always throws a std::logic_error when called.
Definition: io/sam_file/detail/cigar.hpp:188
Comparator that is able two compare two views.
Definition: io/sam_file/detail/cigar.hpp:35
constexpr bool operator()(rng1_type &&rng1, rng2_type &&rng2) const
Compares to ranges by delegating to std::ranges::equal.
Definition: io/sam_file/detail/cigar.hpp:38
Provides seqan3::views::take_until and seqan3::views::take_until_or_throw.
Auxiliary for pretty printing of exception messages.
Provides seqan3::tuple_like.
Provides seqan3::views::zip.