Kmer Class Reference

Interface to store and manipulate k-mers. More...

Public Member Functions
	Kmer ()
	Constructor (initialize a k-mer with 'A' k times).
	Kmer (const Kmer &o)
	Copy constructor (copy a k-mer). More...
	Kmer (const char *s)
	Constructor. More...
Kmer &	operator= (const Kmer &o)
	Copy assignment operator (copy a k-mer). More...
void	set_deleted ()
	Set a k-mer as "deleted".
void	set_empty ()
	Set a k-mer as "empty".
bool	isDeleted () const
	Check whether a k-mer is "deleted". More...
bool	isEmpty () const
	Check whether a k-mer is "empty". More...
bool	operator== (const Kmer &o) const
	Equality comparison operator. More...
bool	operator!= (const Kmer &o) const
	Inequality comparison operator. More...
uint64_t	hash (const uint64_t seed=0) const
	Get the hash of a k-mer. More...
Kmer	twin () const
	Get the reverse-complement of a k-mer. More...
Kmer	rep () const
	Get the canonical k-mer (lexicographically smallest between a k-mer and its reverse-complement). More...
Kmer	forwardBase (const char b) const
	Get a new k-mer which is the shift of the current k-mer of one base on the left with one new character on the right. More...
Kmer	backwardBase (const char b) const
	Get a new k-mer which is the shift of the current k-mer of one base on the right with one new character on the left. More...
void	selfForwardBase (const char b)
	Shift the current k-mer of one base on the left with one new character on the right. More...
char	getChar (const size_t offset) const
	Get the character at a given position in a k-mer. More...
bool	setChar (const size_t offset, const char b)
	Set a character at a given position in a k-mer. More...
void	toString (char *s) const
	Get the string of a k-mer. More...
std::string	toString () const
	Get the string of a k-mer. More...
bool	write (std::ostream &stream_out) const
	Write a k-mer (binary) to a stream. More...
bool	read (std::istream &stream_in)
	Read a k-mer (binary) from a stream. More...

Static Public Member Functions
static void	set_k (const unsigned int _k)
	Set the length of k-mers. More...

Detailed Description

Interface to store and manipulate k-mers.

The default maximum supported k-mer size is 31. To work with larger k, you must replace the macro defined MAX_KMER_SIZE with a larger number which is a multiple of 32. For such a number K, the available maximum supported k-mer size will be K-1. For example, if MAX_KMER_SIZE is defined as 64, the maximum k allowed is 63. Keep in mind that increasing MAX_KMER_SIZE increases memory usage (k=31 uses 8 bytes of memory per k-mer while k=63 uses 16 bytes of memory per k-mer).

Constructor & Destructor Documentation

Kmer() [1/2]

Kmer::Kmer

(

const Kmer &

o

)

Copy constructor (copy a k-mer).

After the call to this function, the same k-mer exists twice in memory.

Parameters

o	is a constant reference to the k-mer to copy

Kmer() [2/2]

Kmer::Kmer ( const char *  s )

explicit

Constructor.

Initialize a k-mer from a string of characters.

Parameters

s	is a constant pointer to an array of characters. The array of characters must contain valid DNA characters ('A', 'C', 'G', 'T') and be of length at least k.

Member Function Documentation

backwardBase()

Kmer Kmer::backwardBase

(

const char

b

)

const

Get a new k-mer which is the shift of the current k-mer of one base on the right with one new character on the left.

For a k-mer km of length k, km.backwardBase(b) = b + km[0..k-2].

Parameters

b	is a new character to add on the left of the shifted k-mer (as a first character). It must be either 'A', 'C', 'G' or 'T'.

Returns

a new k-mer which is the shifted k-mer.

forwardBase()

Kmer Kmer::forwardBase

(

const char

b

)

const

Get a new k-mer which is the shift of the current k-mer of one base on the left with one new character on the right.

For a k-mer km of length k, km.forwardBase(b) = km[1..k-1] + b.

Parameters

b	is a new character to add on the right of the shifted k-mer (as a last character). It must be either 'A', 'C', 'G' or 'T'.

Returns

a new k-mer which is the shifted k-mer.

getChar()

char Kmer::getChar

(

const size_t

offset

)

const

Get the character at a given position in a k-mer.

Parameters

offset

is the position of the character to get in the k-mer.

Returns

the character to get in the k-mer

hash()

uint64_t Kmer::hash ( const uint64_t  seed = 0 ) const

inline

Get the hash of a k-mer.

Parameters

seed	is a seed number for the hash function (0 by default).

Returns

a hash of the k-mer.

isDeleted()

bool Kmer::isDeleted ( ) const

inline

Check whether a k-mer is "deleted".

Returns

a boolean indicating if the k-mer is "deleted" (true) or not (false).

isEmpty()

bool Kmer::isEmpty ( ) const

inline

Check whether a k-mer is "empty".

Returns

a boolean indicating if the k-mer is "empty" (true) or not (false).

operator!=()

bool Kmer::operator!=

(

const Kmer &

o

)

const

Inequality comparison operator.

Parameters

o	is a constant reference to the k-mer to compare to.

Returns

a boolean indicating if two k-mers are the different (true), including their "empty" and "deleted" flags, or not (false).

operator=()

Kmer& Kmer::operator=

(

const Kmer &

o

)

Copy assignment operator (copy a k-mer).

After the call to this function, the same k-mer exists twice in memory.

Parameters

o	is a constant reference to the k-mer to copy

operator==()

bool Kmer::operator==

(

const Kmer &

o

)

const

Equality comparison operator.

Parameters

o	is a constant reference to the k-mer to compare to.

Returns

a boolean indicating if two k-mers are the same (true), including their "empty" and "deleted" flags, or not (false).

read()

bool Kmer::read

(

std::istream &

stream_in

)

Read a k-mer (binary) from a stream.

The stream must be opened prior to this function call and it won't be closed by this function.

Parameters

stream_in

is an in stream from which the k-mer must be read. The stream must be opened prior to this function call and it won't be closed by this function.

Returns

a boolean indicating if the reading was successful (true) or not.

rep()

Kmer Kmer::rep

(

)

const

Get the canonical k-mer (lexicographically smallest between a k-mer and its reverse-complement).

Returns

a new k-mer which is the canonical k-mer.

selfForwardBase()

void Kmer::selfForwardBase

(

const char

b

)

Shift the current k-mer of one base on the left with one new character on the right.

Parameters

b	is a new character to add on the right (as a last character) after shifting the current k-mer. It must be either 'A', 'C', 'G' or 'T'.

set_k()

static void Kmer::set_k ( const unsigned int  _k )

static

Set the length of k-mers.

After this function call, all Kmer functions considers _k to be the k-mer length.

Parameters

_k	is the k-mer length to set.

setChar()

bool Kmer::setChar	(	const size_t	offset,
		const char	b
	)

Set a character at a given position in a k-mer.

Parameters

offset	is the position of the character to set in the k-mer.
b	is the character to set. It must be either 'A', 'C', 'G' or 'T'.

Returns

a boolean indicating if the character was succesfully set. The boolean will be equal to false if offset > k-mer length or if the character to set is not 'A', 'C', 'G' or 'T'.

toString() [1/2]

std::string Kmer::toString

(

)

const

Get the string of a k-mer.

Returns

the string of a k-mer.

toString() [2/2]

void Kmer::toString

(

char *

s

)

const

Get the string of a k-mer.

Parameters

s	is a pointer to an array of characters that will be set with the string of a k-mer.

twin()

Kmer Kmer::twin

(

)

const

Get the reverse-complement of a k-mer.

Returns

a new k-mer which is the reverse-complement.

write()

bool Kmer::write

(

std::ostream &

stream_out

)

const

Write a k-mer (binary) to a stream.

The stream must be opened prior to this function call and it won't be closed by this function.

Parameters

stream_out

is an out stream to which the k-mer must be written to. The stream must be opened prior to this function call and it won't be closed by this function.

Returns

a boolean indicating if the writing was successful (true) or not.

---

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

• src/Kmer.hpp