80template <
typename reference_type,
typename sequence_type>
82 reference_type
const & reference,
84 sequence_type
const & query)
87 throw std::logic_error{
"An empty CIGAR is not a valid alignment representation."};
93 uint32_t query_length{0};
114 throw std::logic_error{
"The CIGAR string indicates a reference length of at least "
116 +
", but the supplied reference sequence is only of size"
163 throw std::logic_error{
"The CIGAR string indicates a query/read sequence length of "
165 +
", but the supplied query/read sequence is of size"
227template <
typename reference_type,
typename sequence_type>
231 sequence_type
const & query)
Includes the aligned_sequence and the related insert_gap and erase_gap functions to enable stl contai...
Provides the seqan3::cigar alphabet.
A "pretty printer" for most SeqAn data structures and related types.
Definition debug_stream_type.hpp:79
A gap decorator allows the annotation of sequences with gap symbols while leaving the underlying sequ...
Definition gap_decorator.hpp:78
Provides seqan3::gap_decorator.
auto alignment_from_cigar(std::vector< cigar > const &cigar_vector, reference_type const &reference, uint32_t const zero_based_reference_start_position, sequence_type const &query)
Construct an alignment from a CIGAR string and the corresponding sequences.
Definition alignment_from_cigar.hpp:81
@ alignment
The (pairwise) alignment stored in an object that models seqan3::detail::pairwise_alignment.
constexpr auto slice
A view adaptor that returns a half-open interval on the underlying range.
Definition slice.hpp:175
Auxiliary functions for the SAM IO.
The main SeqAn3 namespace.
Definition aligned_sequence_concept.hpp:26
Provides seqan3::views::slice.