btllib::KmerBloomFilter Class Reference

#include <bloom_filter.hpp>

Public Member Functions
	KmerBloomFilter ()
	KmerBloomFilter (size_t bytes, unsigned hash_num, unsigned k)
	KmerBloomFilter (const std::string &path)
	KmerBloomFilter (const KmerBloomFilter &)=delete
	KmerBloomFilter (KmerBloomFilter &&)=delete
KmerBloomFilter &	operator= (const KmerBloomFilter &)=delete
KmerBloomFilter &	operator= (KmerBloomFilter &&)=delete
void	insert (const char *seq, size_t seq_len)
void	insert (const std::string &seq)
void	insert (const uint64_t *hashes)
void	insert (const std::vector< uint64_t > &hashes)
unsigned	contains (const char *seq, size_t seq_len) const
unsigned	contains (const std::string &seq) const
bool	contains (const uint64_t *hashes) const
bool	contains (const std::vector< uint64_t > &hashes) const
unsigned	contains_insert (const char *seq, size_t seq_len)
unsigned	contains_insert (const std::string &seq)
bool	contains_insert (const uint64_t *hashes)
bool	contains_insert (const std::vector< uint64_t > &hashes)
size_t	get_bytes () const
uint64_t	get_pop_cnt () const
double	get_occupancy () const
unsigned	get_hash_num () const
double	get_fpr () const
unsigned	get_k () const
const std::string &	get_hash_fn () const
BloomFilter &	get_bloom_filter ()
void	save (const std::string &path)

Static Public Member Functions
static bool	is_bloom_file (const std::string &path)

Friends
class	SeedBloomFilter

Detailed Description

Bloom filter data structure stores k-mers.

Constructor & Destructor Documentation

KmerBloomFilter() [1/3]

btllib::KmerBloomFilter::KmerBloomFilter ( )

inline

Construct a dummy Kmer Bloom filter (e.g. as a default argument).

KmerBloomFilter() [2/3]

btllib::KmerBloomFilter::KmerBloomFilter	(	size_t	bytes,
		unsigned	hash_num,
		unsigned	k
	)

Construct an empty Kmer Bloom filter of given size.

Parameters

bytes	Filter size in bytes.
hash_num	Number of hash values per element.
k	K-mer size.

KmerBloomFilter() [3/3]

btllib::KmerBloomFilter::KmerBloomFilter ( const std::string &  path )

explicit

Load a Kmer Bloom filter from a file.

Parameters

path	Filepath to load from.

Member Function Documentation

contains() [1/4]

unsigned btllib::KmerBloomFilter::contains	(	const char *	seq,
		size_t	seq_len
	)		const

Query the presence of k-mers of a sequence.

Parameters

seq	Sequence to k-merize.
seq_len	Length of seq.

Returns

The number of seq's k-mers found in the filter.

contains() [2/4]

unsigned btllib::KmerBloomFilter::contains ( const std::string &  seq ) const

inline

Query the presence of k-mers of a sequence.

Parameters

seq	Sequence to k-merize.

Returns

The number of seq's k-mers found in the filter.

contains() [3/4]

bool btllib::KmerBloomFilter::contains ( const std::vector< uint64_t > &  hashes ) const

inline

Check for the presence of an element's hash values.

Parameters

hashes

Integer vector of hash values.

contains() [4/4]

bool btllib::KmerBloomFilter::contains ( const uint64_t *  hashes ) const

inline

Check for the presence of an element's hash values.

Parameters

hashes

Integer array of hash values. Array size should equal the hash_num argument used when the Bloom filter was constructed.

contains_insert() [1/4]

unsigned btllib::KmerBloomFilter::contains_insert	(	const char *	seq,
		size_t	seq_len
	)

Query the presence of k-mers of a sequence and insert if missing.

Parameters

seq	Sequence to k-merize.
seq_len	Length of seq.

Returns

The number of seq's k-mers found in the filter before insertion.

contains_insert() [2/4]

unsigned btllib::KmerBloomFilter::contains_insert ( const std::string &  seq )

inline

Query the presence of k-mers of a sequence and insert if missing.

Parameters

seq	Sequence to k-merize.

Returns

The number of seq's k-mers found in the filter before insertion.

contains_insert() [3/4]

bool btllib::KmerBloomFilter::contains_insert ( const std::vector< uint64_t > &  hashes )

inline

Check for the presence of an element's hash values and insert if missing.

Parameters

hashes

Integer vector of hash values.

Returns

True if present before insertion, false otherwise.

contains_insert() [4/4]

bool btllib::KmerBloomFilter::contains_insert ( const uint64_t *  hashes )

inline

Check for the presence of an element's hash values and insert if missing.

Parameters

hashes

Integer array of hash values. Array size should equal the hash_num argument used when the Bloom filter was constructed.

Returns

True if present before insertion, false otherwise.

get_bloom_filter()

BloomFilter & btllib::KmerBloomFilter::get_bloom_filter ( )

inline

Get a reference to the underlying vanilla Bloom filter.

get_bytes()

size_t btllib::KmerBloomFilter::get_bytes ( ) const

inline

Get filter size in bytes.

get_fpr()

double btllib::KmerBloomFilter::get_fpr ( ) const

inline

Get the query false positive rate.

get_hash_fn()

const std::string & btllib::KmerBloomFilter::get_hash_fn ( ) const

inline

Get the name of the hash function used.

get_hash_num()

unsigned btllib::KmerBloomFilter::get_hash_num ( ) const

inline

Get the number of hash values per element.

get_k()

unsigned btllib::KmerBloomFilter::get_k ( ) const

inline

Get the k-mer size used.

get_occupancy()

double btllib::KmerBloomFilter::get_occupancy ( ) const

inline

Get the fraction of the filter occupied by 1 bits.

get_pop_cnt()

uint64_t btllib::KmerBloomFilter::get_pop_cnt ( ) const

inline

Get population count, i.e. the number of 1 bits in the filter.

insert() [1/4]

void btllib::KmerBloomFilter::insert	(	const char *	seq,
		size_t	seq_len
	)

Insert a sequence's k-mers into the filter.

Parameters

seq	Sequence to k-merize.
seq_len	Length of seq.

insert() [2/4]

void btllib::KmerBloomFilter::insert ( const std::string &  seq )

inline

Insert a sequence's k-mers into the filter.

Parameters

seq	Sequence to k-merize.

insert() [3/4]

void btllib::KmerBloomFilter::insert ( const std::vector< uint64_t > &  hashes )

inline

Insert an element's hash values.

Parameters

hashes

Integer vector of hash values.

insert() [4/4]

void btllib::KmerBloomFilter::insert ( const uint64_t *  hashes )

inline

Insert an element's hash values.

Parameters

hashes

Integer array of hash values. Array size should equal the hash_num argument used when the Bloom filter was constructed.

is_bloom_file()

static bool btllib::KmerBloomFilter::is_bloom_file ( const std::string &  path )

inlinestatic

Check whether the file at the given path is a saved Kmer Bloom filter.

Parameters

path	Filepath to check.

save()

void btllib::KmerBloomFilter::save

(

const std::string &

path

)

Save the Bloom filter to a file that can be loaded in the future.

Parameters

path	Filepath to store filter at.

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

• include/btllib/bloom_filter.hpp