btllib::SeedNtHash Class Reference

#include <nthash_seed.hpp>

Public Member Functions
	SeedNtHash (const char *seq, size_t seq_len, const std::vector< std::string > &seeds, hashing_internals::NUM_HASHES_TYPE num_hashes_per_seed, hashing_internals::K_TYPE k, size_t pos=0)
	SeedNtHash (const std::string &seq, const std::vector< std::string > &seeds, hashing_internals::NUM_HASHES_TYPE num_hashes_per_seed, hashing_internals::K_TYPE k, size_t pos=0)
	SeedNtHash (const char *seq, size_t seq_len, const std::vector< std::vector< unsigned > > &seeds, hashing_internals::NUM_HASHES_TYPE num_hashes_per_seed, hashing_internals::K_TYPE k, size_t pos=0)
	SeedNtHash (const std::string &seq, const std::vector< std::vector< unsigned > > &seeds, hashing_internals::NUM_HASHES_TYPE num_hashes_per_seed, hashing_internals::K_TYPE k, size_t pos=0)
	SeedNtHash (const SeedNtHash &obj)
	SeedNtHash (SeedNtHash &&)=default
bool	roll ()
bool	roll_back ()
bool	peek ()
bool	peek_back ()
bool	peek (char char_in)
bool	peek_back (char char_in)
const uint64_t *	hashes () const
size_t	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

Spaced seed hashing.

Constructor & Destructor Documentation

SeedNtHash() [1/4]

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

inline

Construct an ntHash object for spaced seeds.

Parameters

seq	C-string of the sequence to be hashed
seq_len	Length of the sequence
seeds	Vector of spaced seed patterns as strings (1s as cares, 0s as don't cares, must be of size k)
num_hashes_per_seed	Number of hashes to generate per seed
k	K-mer size
pos	Position in seq to start hashing from

SeedNtHash() [2/4]

btllib::SeedNtHash::SeedNtHash ( const std::string & seq, const std::vector< std::string > & seeds, hashing_internals::NUM_HASHES_TYPE num_hashes_per_seed, hashing_internals::K_TYPE k, size_t pos = 0 )

inline

Construct an ntHash object for spaced seeds.

Parameters

seq	String of the sequence to be hashed
seeds	Vector of spaced seed patterns as strings (1s as cares, 0s as don't cares, must be of size k)
num_hashes_per_seed	Number of hashes to generate per seed
k	K-mer size
pos	Position in seq to start hashing from

SeedNtHash() [3/4]

btllib::SeedNtHash::SeedNtHash ( const char * seq, size_t seq_len, const std::vector< std::vector< unsigned > > & seeds, hashing_internals::NUM_HASHES_TYPE num_hashes_per_seed, hashing_internals::K_TYPE k, size_t pos = 0 )

inline

Construct an ntHash object for spaced seeds.

Parameters

seq	C-string of the sequence to be hashed
seq_len	Length of the sequence
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

SeedNtHash() [4/4]

btllib::SeedNtHash::SeedNtHash ( const std::string & seq, const std::vector< std::vector< unsigned > > & seeds, hashing_internals::NUM_HASHES_TYPE num_hashes_per_seed, hashing_internals::K_TYPE k, size_t pos = 0 )

inline

Construct an ntHash object for spaced seeds.

Parameters

seq	String of the sequence to be hashed
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::SeedNtHash::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::SeedNtHash::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::SeedNtHash::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::SeedNtHash::get_k ( ) const

inline

Get the length of the k-mers.

Returns

k

get_pos()

size_t btllib::SeedNtHash::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::SeedNtHash::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::SeedNtHash::hashes ( ) const

inline

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

Returns

Pointer to the hash array

peek() [1/2]

bool btllib::SeedNtHash::peek ( )

inline

Peeks the hash values as if roll() was called. Refer to NtHash::peek() for more information.

Returns

true on success and false otherwise.

peek() [2/2]

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

inline

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

Returns

true on success and false otherwise.

peek_back() [1/2]

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

inline

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

Returns

true on success and false otherwise.

roll()

bool btllib::SeedNtHash::roll ( )

inline

Calculate the next hash value. Refer to NtHash::roll() for more information.

Returns

true on success and false otherwise.

roll_back()

bool btllib::SeedNtHash::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/nthash_seed.hpp