btllib::BlindNtHash Class Reference

#include <nthash_kmer.hpp>

Public Member Functions
	BlindNtHash (const std::string &seq, hashing_internals::NUM_HASHES_TYPE num_hashes, hashing_internals::K_TYPE k, long pos=0)
	BlindNtHash (const BlindNtHash &obj)
	BlindNtHash (BlindNtHash &&)=default
void	roll (char char_in)
void	roll_back (char char_in)
void	peek (char char_in)
void	peek_back (char char_in)
const uint64_t *	hashes () const
long	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

Similar to the NtHash class, but instead of rolling on a predefined sequence, BlindNtHash needs to be fed the new character on each roll. This is useful when traversing an implicit de Bruijn Graph, as we need to query all bases to know the possible extensions.

Constructor & Destructor Documentation

BlindNtHash()

btllib::BlindNtHash::BlindNtHash ( const std::string & seq, hashing_internals::NUM_HASHES_TYPE num_hashes, hashing_internals::K_TYPE k, long pos = 0 )

inline

Construct an ntHash object for hashing k-mers on-the-fly.

Parameters

seq	Sequence data. Only the first k characters will be used, starting from pos.
hash_num	Number of hashes to generate per k-mer
k	K-mer size
pos	Position in sequence to start hashing from

Member Function Documentation

get_forward_hash()

uint64_t btllib::BlindNtHash::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::BlindNtHash::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::BlindNtHash::get_k ( ) const

inline

Get the length of the k-mers.

Returns

k

get_pos()

long btllib::BlindNtHash::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 NtHash object.

Returns

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

get_reverse_hash()

uint64_t btllib::BlindNtHash::get_reverse_hash ( ) const

inline

Get the hash value of the reverse strand.

Returns

Reverse-complement hash value

hashes()

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

inline

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

Returns

Pointer to the hash array

peek()

void btllib::BlindNtHash::peek ( char char_in )

inline

Like NtHash::peek(), but as if roll(char char_in) was called.

peek_back()

void btllib::BlindNtHash::peek_back ( char char_in )

inline

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

roll()

void btllib::BlindNtHash::roll ( char char_in )

inline

Like the NtHash::roll() function, but instead of advancing in the sequence BlindNtHash object was constructed on, the provided character char_in is used as the next base. Useful if you want to query for possible paths in an implicit de Bruijn graph graph.

roll_back()

void btllib::BlindNtHash::roll_back ( char char_in )

inline

Like the roll(char char_in) function, but advance backwards.

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

• include/btllib/nthash_kmer.hpp