btllib::BlindSeedNtHash Class Reference

#include <nthash_seed.hpp>

Public Member Functions
	BlindSeedNtHash (const char *seq, const std::vector< std::string > &seeds, hashing_internals::NUM_HASHES_TYPE num_hashes_per_seed, hashing_internals::K_TYPE k, long pos=0)
	BlindSeedNtHash (const BlindSeedNtHash &seed_nthash)
	BlindSeedNtHash (BlindSeedNtHash &&)=default
void	roll (char char_in)
void	roll_back (char char_in)
const uint64_t *	hashes () const
long	get_pos () const
unsigned	get_hash_num () const
hashing_internals::NUM_HASHES_TYPE	get_hash_num_per_seed () 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 SeedNtHash class, but instead of rolling on a predefined sequence, BlindSeedNtHash needs to be fed the new character on each roll.

Constructor & Destructor Documentation

BlindSeedNtHash()

btllib::BlindSeedNtHash::BlindSeedNtHash ( const char * seq, const std::vector< std::string > & seeds, hashing_internals::NUM_HASHES_TYPE num_hashes_per_seed, hashing_internals::K_TYPE k, long pos = 0 )

inline

Construct an ntHash object for hashing spaced seeds on-the-fly.

Parameters

seq	C-string of the data. Only the first k characters will be used, starting from pos.
seeds	Vector of parsed spaced seed patterns (vectors of don't care positions)
num_hashes_per_seed	Number of hashes to generate per seed
k	K-mer size
pos	Position in seq to start hashing from

Member Function Documentation

get_forward_hash()

uint64_t * btllib::BlindSeedNtHash::get_forward_hash ( ) const

inline

Get the hash values of the forward strand.

Returns

Array of forward hash value arrays for each seed

get_hash_num()

unsigned btllib::BlindSeedNtHash::get_hash_num ( ) const

inline

Get the length of the hash array.

Returns

Number of seeds times get_hash_num_per_seed()

get_hash_num_per_seed()

hashing_internals::NUM_HASHES_TYPE btllib::BlindSeedNtHash::get_hash_num_per_seed ( ) const

inline

Get the number of hashes generated per seed.

Returns

Number of hashes per seed

get_k()

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

inline

Get the length of the k-mers.

Returns

k

get_pos()

long btllib::BlindSeedNtHash::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::BlindSeedNtHash::get_reverse_hash ( ) const

inline

Get the hash values of the reverse strand.

Returns

Array of reverse-complement hash value arrays for each seed

hashes()

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

inline

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

Returns

Pointer to the hash array

roll()

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

inline

Like the NtHash::roll() function, but instead of advancing in the sequence BlindSeedNtHash object was constructed on, the provided character char_in is used as the next base.

roll_back()

void btllib::BlindSeedNtHash::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_seed.hpp