The three letter reduced DNA alphabet for bisulfite sequencing mode (A,G,T(=C)). More...

#include <seqan3/alphabet/nucleotide/dna3bs.hpp>

Inheritance diagram for seqan3::dna3bs:

Public Member Functions
Constructors, destructor and assignment
constexpr	dna3bs () noexcept=default
	Defaulted.

constexpr	dna3bs (dna3bs const &) noexcept=default
	Defaulted.

constexpr	dna3bs (dna3bs &&) noexcept=default
	Defaulted.

constexpr dna3bs &	operator= (dna3bs const &) noexcept=default
	Defaulted.

constexpr dna3bs &	operator= (dna3bs &&) noexcept=default
	Defaulted.

	~dna3bs () noexcept=default
	Defaulted.

Public Member Functions inherited from seqan3::nucleotide_base< dna3bs, 3 >
constexpr dna3bs	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	dna3bs_vector = std::vector< dna3bs >
	Alias for a std::vector of seqan3::dna3bs.

Additional Inherited Members
Static Public Member Functions inherited from seqan3::nucleotide_base< dna3bs, 3 >
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

The three letter reduced DNA alphabet for bisulfite sequencing mode (A,G,T(=C)).

This alphabet represents a reduced version that can be used when dealing with bisulfite-converted data. All 'C's are converted to a 'T' in order to allow comparison of normal sequences with bisulfite-converted sequences. For completeness, this nucleotide alphabet has a complement table, however, it is not recommended to use it when dealing with bisulfite data because the complement of T is ambiguous in reads from bisulfite sequencing. A 'T' can represent a true thymidine or an unmethylated 'C' that was converted into a 'T'. Therefore, complementing a seqan3::dna3bs sequence will further reduce the alphabet to only 'T' and 'A', thereby losing all information about 'G'. When working with bisulfite data, we recommend to create the reverse complement of the seqan3::dna4 / seqan3::dna5 / seqan3::dna15 range first and convert to seqan3::dna3bs later. This avoids simplifying the data by automatically setting 'A' as the complement of 'C'. As an example: The sequence 'ACGTGC' in seqan3::dna4 would be 'ATGTGT' in seqan3::dna3bs. The complement of this seqan3::dna3bs sequence would be 'TATATA', however when complementing the seqan3::dna4 sequence first and afterwards transforming it into seqan3::dna3bs, it would be 'TGTATG' which preserves more information from the original sequence.

Like most alphabets, this alphabet cannot be initialised directly from its character representation. Instead initialise/assign from the character literal 'A'_dna3bs or use the function seqan3::dna3bs::assign_char().

// 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/dna3bs.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    seqan3::dna3bs letter{'A'_dna3bs};
 
    letter.assign_char('C');                // All C will be converted to T.
    seqan3::debug_stream << letter << '\n'; // prints "T"
 
    letter.assign_char('F');                // Unknown characters are implicitly converted to A.
    seqan3::debug_stream << letter << '\n'; // prints "A"
}

See also: https://en.wikipedia.org/wiki/Bisulfite_sequencing

This entity is stable. Since version 3.1.

Friends And Related Symbol Documentation

◆ dna3bs_vector

using dna3bs_vector = std::vector<dna3bs>

This entity is stable. Since version 3.1.

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

dna3bs.hpp

Public Member Functions

Related Symbols

Additional Inherited Members

Detailed Description

Friends And Related Symbol Documentation

◆ dna3bs_vector