btllib::BiHashDirectional Class Reference

#include <bihash_kmer_directional.hpp>

Public Member Functions
	BiHashDirectional (const char *seq, size_t seq_len, hashing_internals::NUM_HASHES_TYPE num_hashes, hashing_internals::K_TYPE k, std::string conversion_type, size_t pos=0)
	BiHashDirectional (const std::string &seq, hashing_internals::NUM_HASHES_TYPE num_hashes, hashing_internals::K_TYPE k, std::string conversion_type, size_t pos=0)
	BiHashDirectional (const BiHashDirectional &obj)
	BiHashDirectional (BiHashDirectional &&)=default
bool	roll ()
bool	roll_back ()
bool	peek ()
bool	peek_back ()
bool	peek (char char_in)
bool	peek_back (char char_in)
bool	is_methylated ()
bool	is_forward_higher () const
void	sub (const std::vector< unsigned > &positions, const std::vector< unsigned char > &new_bases)
const uint64_t *	hashes () const
size_t	get_pos () const
hashing_internals::NUM_HASHES_TYPE	get_hash_num () const
hashing_internals::K_TYPE	get_k () const
uint64_t	get_forward_hash () const
uint64_t	get_reverse_hash () const

Detailed Description

Directional BI-seq k-mer hashing.

Constructor & Destructor Documentation

BiHashDirectional() [1/2]

btllib::BiHashDirectional::BiHashDirectional ( const char * seq, size_t seq_len, hashing_internals::NUM_HASHES_TYPE num_hashes, hashing_internals::K_TYPE k, std::string conversion_type, size_t pos = 0 )

inline

Construct an ntHash object for k-mers.

Parameters

seq	C-string containing sequence data
seq_len	Length of the sequence
num_hashes	Number of hashes to generate per k-mer
k	K-mer size
conversion_type	Bisulfite conversion mode ("CT" or "GA"), used to determine how bases are interpreted during hashing.
pos	Position in the sequence to start hashing from

BiHashDirectional() [2/2]

btllib::BiHashDirectional::BiHashDirectional ( const std::string & seq, hashing_internals::NUM_HASHES_TYPE num_hashes, hashing_internals::K_TYPE k, std::string conversion_type, size_t pos = 0 )

inline

Construct an BiHash object for k-mers.

Parameters

seq	Sequence string
num_hashes	Number of hashes to produce per k-mer
k	K-mer size
conversion_type	Bisulfite conversion mode ("CT" or "GA"), used to determine how bases are interpreted during hashing.
pos	Position in sequence to start hashing from

Member Function Documentation

get_forward_hash()

uint64_t btllib::BiHashDirectional::get_forward_hash ( ) const

inline

Get the hash value of the forward strand.

Returns

Forward hash value

get_hash_num()

hashing_internals::NUM_HASHES_TYPE btllib::BiHashDirectional::get_hash_num ( ) const

inline

Get the number of hashes generated per k-mer.

Returns

Number of hashes per k-mer

get_k()

hashing_internals::K_TYPE btllib::BiHashDirectional::get_k ( ) const

inline

Get the length of the k-mers.

Returns

k

get_pos()

size_t btllib::BiHashDirectional::get_pos ( ) const

inline

Get the position of last hashed k-mer or the k-mer to be hashed if roll() has never been called on this BiHash object.

Returns

Position of the most recently hashed k-mer's first base-pair

get_reverse_hash()

uint64_t btllib::BiHashDirectional::get_reverse_hash ( ) const

inline

Get the hash value of the reverse strand.

Returns

Reverse-complement hash value

hashes()

const uint64_t * btllib::BiHashDirectional::hashes ( ) const

inline

Get the array of current canonical hash values (length = get_hash_num())

Returns

Pointer to the hash array

is_forward_higher()

bool btllib::BiHashDirectional::is_forward_higher ( ) const

inline

Check if the forward hash is higher than the reverse hash.

Returns

true if forward hash > reverse hash, false otherwise

is_methylated()

bool btllib::BiHashDirectional::is_methylated ( )

inline

Check if the k-mer center position is methylated based on conversion type. For CT conversion, methylation corresponds to a cytosine ('C'/'c'). For GA conversion, methylation corresponds to a guanine ('G'/'g').

Returns

true if the base at the methylation index indicates methylation, false otherwise.

peek() [1/2]

bool btllib::BiHashDirectional::peek ( )

inline

Peeks the hash values as if roll() was called (without advancing the BiHash object. The peeked hash values can be obtained through the hashes() method.

Returns

true on success and false otherwise

peek() [2/2]

bool btllib::BiHashDirectional::peek ( char char_in )

inline

Peeks the hash values as if roll() was called for char_in (without advancing the BiHash object. The peeked hash values can be obtained through the hashes() method.

Returns

true on success and false otherwise

peek_back() [1/2]

bool btllib::BiHashDirectional::peek_back ( )

inline

Like peek(), but as if roll_back() was called.

Returns

true on success and false otherwise

peek_back() [2/2]

bool btllib::BiHashDirectional::peek_back ( char char_in )

inline

Like peek(), but as if roll_back on char_in was called.

Returns

true on success and false otherwise

roll()

bool btllib::BiHashDirectional::roll ( )

inline

Calculate the hash values of current k-mer and advance to the next k-mer. BiHash advances one nucleotide at a time until it finds a k-mer with valid characters (ACGTU) and skips over those with invalid characters (non-ACGTU, including N). This method must be called before hashes() is accessed, for the first and every subiequent hashed kmer. get_pos() may be called at any time to obtain the position of last hashed k-mer or the k-mer to be hashed if roll() has never been called on this BiHash object. It is important to note that the number of roll() calls is NOT necessarily equal to get_pos(), if there are N's or invalid characters in the hashed sequence.

Returns

true on success and false otherwise

roll_back()

bool btllib::BiHashDirectional::roll_back ( )

inline

Like the roll() function, but advance backwards.

Returns

true on success and false otherwise

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

• include/btllib/bihash_kmer_directional.hpp