bio::alphabet::cigar_op Class Reference

The cigar operation alphabet.. More...

#include <bio/alphabet/cigar/cigar_op.hpp>

Inheritance diagram for bio::alphabet::cigar_op:

Public Member Functions
Constructors, destructor and assignment
constexpr	cigar_op () noexcept=default
	Defaulted.
constexpr	cigar_op (cigar_op const &) noexcept=default
	Defaulted.
constexpr	cigar_op (cigar_op &&) noexcept=default
	Defaulted.
constexpr cigar_op &	operator= (cigar_op const &) noexcept=default
	Defaulted.
constexpr cigar_op &	operator= (cigar_op &&) noexcept=default
	Defaulted.
	~cigar_op () noexcept=default
Read functions
constexpr char_type	to_char () const noexcept
	Return the letter as a character of char_type.
constexpr rank_type	to_rank () const noexcept
	Return the letter's numeric value (rank in the alphabet).
Write functions
constexpr cigar_op &	assign_char (char_type const c) noexcept
	Assign from a character, implicitly converts invalid characters.
constexpr cigar_op &	assign_rank (rank_type const c) noexcept
	Assign from a numeric value.

Static Public Attributes
static constexpr size_t	alphabet_size
	The size of the alphabet, i.e. the number of different values it can take.

Protected Types
Member types
using	char_type = std::conditional_t< std::same_as< char, void >, char, char >
	The char representation; conditional needed to make semi alphabet definitions legal.
using	rank_type = meta::detail::min_viable_uint_t< size - 1 >
	The type of the alphabet when represented as a number (e.g. via to_rank()).

Related Functions
(Note that these are not member functions.)
Literals
consteval cigar_op	operator""_cigar_op (char const c)
	The bio::alphabet::cigar_op char literal.

Detailed Description

The cigar operation alphabet.

.

The main purpose of the bio::alphabet::cigar_op alphabet is to be used in the bio::alphabet::cigar composition, where a cigar operation is paired with a count value.

Op	Rank	Description	Consumes query	Consumes reference
M	0	alignment match (can be a sequence match or mismatch)	yes	yes
I	1	insertion to the reference	yes	no
D	2	deletion from the reference	no	yes
N	3	skipped region from the reference	no	yes
S	4	soft clipping (clipped sequences present in SEQ)	yes	no
H	5	hard clipping (clipped sequences NOT present in SEQ)	no	no
P	6	padding (silent deletion from padded reference)	no	no
=	7	sequence match	yes	yes
X	8	sequence mismatch	yes	yes
B	9	?	?	?

This table is reproduced from the SAM standard. The B operation is used internally and not documented.

Example

#include <bio/alphabet/cigar/cigar_op.hpp>
#include <bio/alphabet/fmt.hpp>
 
using namespace bio::alphabet::literals;
 
int main()
{
    // Initialise a bio::alphabet::cigar_op:
    bio::alphabet::cigar_op match{'M'_cigar_op};
 
    // you can print cigar_op values:
    fmt::print("{}\n", match); // M
}

Constructor & Destructor Documentation

~cigar_op()

bio::alphabet::cigar_op::~cigar_op ( )

defaultnoexcept

Defaulted.

Member Function Documentation

assign_char()

constexpr cigar_op & bio::alphabet::base< cigar_op , size, char >::assign_char ( char_type const  c )

inlineconstexprnoexceptinherited

Assign from a character, implicitly converts invalid characters.

Parameters

c	The character to be assigned.

Provides an implementation for bio::alphabet::assign_char_to, required to model bio::alphabet::alphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

assign_rank()

constexpr cigar_op & bio::alphabet::base< cigar_op , size, char >::assign_rank ( rank_type const  c )

inlineconstexprnoexceptinherited

Assign from a numeric value.

Parameters

c	The rank to be assigned.

Provides an implementation for bio::alphabet::assign_rank_to, required to model bio::alphabet::semialphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

to_char()

constexpr char_type bio::alphabet::base< cigar_op , size, char >::to_char ( ) const

inlineconstexprnoexceptinherited

Return the letter as a character of char_type.

Provides an implementation for bio::alphabet::to_char, required to model bio::alphabet::alphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

to_rank()

constexpr rank_type bio::alphabet::base< cigar_op , size, char >::to_rank ( ) const

inlineconstexprnoexceptinherited

Return the letter's numeric value (rank in the alphabet).

Provides an implementation for bio::alphabet::to_rank, required to model bio::alphabet::semialphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

Friends And Related Function Documentation

operator""_cigar_op()

consteval cigar_op operator""_cigar_op ( char const  c )

related

The bio::alphabet::cigar_op char literal.

Returns

bio::alphabet::cigar_op

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The documentation for this class was generated from the following file:

• bio/alphabet/cigar/cigar_op.hpp