30namespace seqan3::detail
34struct view_equality_fn
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
51inline void update_alignment_lengths(int32_t & ref_length,
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;
75 throw format_error{
"Illegal cigar operation: " +
std::string{cigar_operation}};
97 uint32_t cigar_count{};
98 char const * ptr = cigar_str.
data();
99 char const *
const end = ptr + cigar_str.
size();
106 throw format_error{
"Corrupted cigar string."};
125 [&result](
auto & cig)
165template <seqan3::aligned_sequence ref_seq_type, seqan3::aligned_sequence query_seq_type>
167 query_seq_type && query_seq,
168 uint32_t
const query_start_pos = 0,
169 uint32_t
const query_end_pos = 0,
170 bool const extended_cigar =
false)
172 return get_cigar_string(
std::tie(
ref_seq, query_seq), query_start_pos, query_end_pos, extended_cigar);
177struct access_restrictor_fn
180 template <
typename chr_t>
181 [[noreturn]] chr_t operator()(chr_t)
const
183 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.
The actual implementation of seqan3::cigar::operation for documentation purposes only....
Definition: cigar_operation.hpp:48
constexpr auto assign_char_strictly_to
Assign a character to an alphabet object, throw if the character is not valid.
Definition: alphabet/concept.hpp:734
@ ref_seq
The (reference) "sequence" information, usually a range of nucleotides or amino acids.
Provides seqan3::detail::pairwise_alignment and seqan3::detail::writable_pairwise_alignment.
Provides character predicates for tokenisation.
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.