cigar.hpp File Reference

Auxiliary functions for the SAM IO. More...

#include <algorithm>
#include <concepts>
#include <ranges>
#include <seqan3/std/charconv>
#include <sstream>
#include <seqan3/alignment/detail/pairwise_alignment_concept.hpp>
#include <seqan3/alphabet/cigar/cigar.hpp>
#include <seqan3/core/debug_stream/detail/to_string.hpp>
#include <seqan3/io/views/detail/take_until_view.hpp>
#include <seqan3/utility/char_operations/predicate.hpp>
#include <seqan3/utility/tuple/concept.hpp>
#include <seqan3/utility/views/single_pass_input.hpp>
#include <seqan3/utility/views/zip.hpp>

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Classes
struct	seqan3::detail::access_restrictor_fn
	A functor that always throws when calling operator() (needed for the alignment "dummy" sequence). More...
struct	seqan3::detail::view_equality_fn
	Comparator that is able two compare two views. More...

Namespaces
namespace	seqan3
	The main SeqAn3 namespace.
namespace	seqan3::detail
	The internal SeqAn3 namespace.

Functions
template<seqan3::aligned_sequence ref_seq_type, seqan3::aligned_sequence query_seq_type>
std::string	seqan3::detail::get_cigar_string (ref_seq_type &&ref_seq, query_seq_type &&query_seq, uint32_t const query_start_pos=0, uint32_t const query_end_pos=0, bool const extended_cigar=false)
	Transforms an alignment represented by two seqan3::aligned_sequence's into the corresponding cigar string.
std::string	seqan3::detail::get_cigar_string (std::vector< cigar > const &cigar_vector)
	Transforms a vector of cigar elements into a string representation.
constexpr std::vector< cigar >	seqan3::detail::parse_cigar (std::string_view const cigar_str)
	Parses a cigar string into a vector of operation-count pairs (e.g. (M, 3)).
void	seqan3::detail::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.

Detailed Description

Auxiliary functions for the SAM IO.

Author

Svenja Mehringer <svenja.mehringer AT fu-berlin.de>