seqan3::dna16sam Class Reference

A 16 letter DNA alphabet, containing all IUPAC symbols minus the gap and plus an equality sign ('='). More...

#include <seqan3/alphabet/nucleotide/dna16sam.hpp>

Inheritance diagram for seqan3::dna16sam:

Public Member Functions
Constructors, destructor and assignment
constexpr	dna16sam () noexcept=default
	Defaulted.
constexpr	dna16sam (dna16sam const &) noexcept=default
	Defaulted.
constexpr	dna16sam (dna16sam &&) noexcept=default
	Defaulted.
constexpr dna16sam &	operator= (dna16sam const &) noexcept=default
	Defaulted.
constexpr dna16sam &	operator= (dna16sam &&) noexcept=default
	Defaulted.
	~dna16sam () noexcept=default
	Defaulted.
Public Member Functions inherited from seqan3::nucleotide_base< dna16sam, 16 >
constexpr dna16sam	complement () const noexcept
	Return the complement of the letter.
constexpr	nucleotide_base (other_nucl_type const &other) noexcept
	Allow explicit construction from any other nucleotide type and convert via the character representation.
Public Member Functions inherited from seqan3::alphabet_base< derived_type, size, char_t >
constexpr	alphabet_base () noexcept=default
	Defaulted.
constexpr	alphabet_base (alphabet_base const &) noexcept=default
	Defaulted.
constexpr	alphabet_base (alphabet_base &&) noexcept=default
	Defaulted.
constexpr alphabet_base &	operator= (alphabet_base const &) noexcept=default
	Defaulted.
constexpr alphabet_base &	operator= (alphabet_base &&) noexcept=default
	Defaulted.
	~alphabet_base () noexcept=default
	Defaulted.
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).
constexpr derived_type &	assign_char (char_type const chr) noexcept
	Assign from a character, implicitly converts invalid characters.
constexpr derived_type &	assign_rank (rank_type const c) noexcept
	Assign from a numeric value.

Related Symbols
(Note that these are not member symbols.)
using	dna16sam_vector = std::vector< dna16sam >
	Alias for a std::vector of seqan3::dna16sam.

Additional Inherited Members
Static Public Member Functions inherited from seqan3::nucleotide_base< dna16sam, 16 >
static constexpr bool	char_is_valid (char_type const c) noexcept
	Validate whether a character value has a one-to-one mapping to an alphabet value.
Static Public Attributes inherited from seqan3::alphabet_base< derived_type, size, char_t >
static constexpr detail::min_viable_uint_t< size >	alphabet_size = size
	The size of the alphabet, i.e. the number of different values it can take.
Protected Types inherited from seqan3::alphabet_base< derived_type, size, char_t >
using	char_type = std::conditional_t< std::same_as< char_t, void >, char, char_t >
	The char representation; conditional needed to make semi alphabet definitions legal.
using	rank_type = detail::min_viable_uint_t< size - 1 >
	The type of the alphabet when represented as a number (e.g. via to_rank()).

Detailed Description

A 16 letter DNA alphabet, containing all IUPAC symbols minus the gap and plus an equality sign ('=').

The seqan3::dna16sam alphabet is the nucleotide alphabet used inside the SAM, BAM and CRAM formats. It has all the letters of the seqan3::dna15 alphabet and the extra alphabet character '=' which denotes a nucleotide character identical to the reference. Without the context of this reference sequence, no assumptions can be made about the actual value of '=' letter.

Note that you can assign 'U' as a character to dna16sam and it will silently be converted to 'T'. Lower case letters are accepted when assigning from char (just like seqan3::dna15) and unknown characters are silently converted to 'N'.

The complement is the same as for seqan3::dna15, with the addition that the complement of '=' is unknown and therefore set to 'N'.

// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
 
#include <seqan3/alphabet/nucleotide/dna16sam.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    seqan3::dna16sam letter{'A'_dna16sam};
 
    letter.assign_char('=');
    seqan3::debug_stream << letter << '\n'; // prints "="
 
    letter.assign_char('F');                // Unknown characters are implicitly converted to N.
    seqan3::debug_stream << letter << '\n'; // "N";
}

This entity is stable. Since version 3.1.

Friends And Related Symbol Documentation

dna16sam_vector

using dna16sam_vector = std::vector<dna16sam>

related

Alias for a std::vector of seqan3::dna16sam.

This entity is stable. Since version 3.1.

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

• dna16sam.hpp