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. More...

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. More...

constexpr rank_type	to_rank () const noexcept
	Return the letter's numeric value (rank in the alphabet). More...

constexpr derived_type &	assign_char (char_type const c) noexcept
	Assign from a character, implicitly converts invalid characters. More...

constexpr derived_type &	assign_rank (rank_type const c) noexcept
	Assign from a numeric value. More...

Private Types
using	base_t = nucleotide_base< dna3bs, 3 >
	The base class.

Private Attributes
friend	base_t
	Befriend seqan3::nucleotide_base.

Static Private Attributes
static constexpr std::array< rank_type, 256 >	char_to_rank
	Char to value conversion table.

static const std::array< dna3bs, alphabet_size >	complement_table
	The complement table. More...

static constexpr char_type	rank_to_char [alphabet_size]
	Value to char conversion table. More...

Related Functions
(Note that these are not member functions.)
using	dna3bs_vector = std::vector< dna3bs >
	Alias for an std::vector of seqan3::dna3bs.

Literals
constexpr dna3bs	operator""_dna3bs (char const c) noexcept
	The seqan3::dna3bs char literal. More...

dna3bs_vector	operator""_dna3bs (char const *s, std::size_t n)
	The seqan3::dna3bs string literal. More...

Related Functions inherited from semialphabet
template<cereal_output_archive archive_t, semialphabet alphabet_t>
alphabet_rank_t< alphabet_t >	save_minimal (archive_t const &, alphabet_t const &l)
	Save an alphabet letter to stream. More...

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. More...

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. More...

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. More...

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()). More...

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 dna4bs sequence will further reduce the alphabet to only 'T' and 'A', thereby loosing all information about 'G'. When working with bisulfite data, we recommend to create the reverse complement of the dna4/5/15 range first and convert to dna3bs later. This avoids simplifying the data by automatically setting 'A' as the complement of 'C'. As an example: The sequence 'ACGTGC' in dna4 would be 'ATGTGT' in dna3bs. The complement of this dna3bs sequence would be 'TATATA', however when complementing the dna4 sequence first and afterwards transforming it into 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 or use the function seqan3::dna3bs::assign_char().

#include <seqan3/alphabet/nucleotide/dna3bs.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using seqan3::operator""_dna3bs;
 
    seqan3::dna3bs my_letter{'A'_dna3bs};
 
    my_letter.assign_char('C'); // all C will be converted to T.
    if (my_letter.to_char() == 'T')
        seqan3::debug_stream << "yeah\n"; // "yeah";
 
    my_letter.assign_char('F'); // unknown characters are implicitly converted to A.
    if (my_letter.to_char() == 'A')
        seqan3::debug_stream << "yeah\n"; // "yeah";
 
    return 0;
}

Friends And Related Function Documentation

◆ operator""_dna3bs() [1/2]

dna3bs_vector operator""_dna3bs	(	char const *	s,
		std::size_t	n
	)

Returns: seqan3::dna3bs_vector

You can use this string literal to easily assign to dna3bs_vector:

#include <seqan3/alphabet/nucleotide/dna3bs.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using seqan3::operator""_dna3bs;
 
    seqan3::dna3bs_vector foo{"ACGTTA"_dna3bs}; // ATGTTA
    seqan3::dna3bs_vector bar = "ATGTTA"_dna3bs;
 
    if (foo == bar)
        seqan3::debug_stream << "yeah\n"; // "yeah";
 
    auto bax = "ACGTTA"_dna3bs;
 
    return 0;
}

◆ operator""_dna3bs() [2/2]

constexpr dna3bs operator""_dna3bs ( char const c )

Returns: seqan3::dna3bs

Member Data Documentation

◆ complement_table

constexpr std::array< dna3bs, dna3bs::alphabet_size > seqan3::dna3bs::complement_table

staticconstexprprivate

Initial value:

{
    'T'_dna3bs,    
    'T'_dna3bs,    
    'A'_dna3bs     
}

The complement table.

◆ rank_to_char

constexpr char_type seqan3::dna3bs::rank_to_char[alphabet_size]

staticconstexprprivate

Initial value:

{
        'A',
        'G',
        'T'
    }

Value to char conversion table.

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

seqan3/alphabet/nucleotide/dna3bs.hpp

Public Member Functions

Private Types

Private Attributes

Static Private Attributes

Related Functions