| btllib
    | 
#include <counting_bloom_filter.hpp>
| Public Member Functions | |
| KmerCountingBloomFilter () | |
| KmerCountingBloomFilter (size_t bytes, unsigned hash_num, unsigned k) | |
| KmerCountingBloomFilter (const std::string &path) | |
| KmerCountingBloomFilter (const KmerCountingBloomFilter &)=delete | |
| KmerCountingBloomFilter (KmerCountingBloomFilter &&)=delete | |
| KmerCountingBloomFilter & | operator= (const KmerCountingBloomFilter &)=delete | 
| KmerCountingBloomFilter & | operator= (KmerCountingBloomFilter &&)=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) | 
| uint64_t | contains (const char *seq, size_t seq_len) const | 
| uint64_t | contains (const std::string &seq) const | 
| T | contains (const uint64_t *hashes) const | 
| T | contains (const std::vector< uint64_t > &hashes) const | 
| T | contains_insert (const char *seq, size_t seq_len) | 
| T | contains_insert (const std::string &seq) | 
| T | contains_insert (const uint64_t *hashes) | 
| T | contains_insert (const std::vector< uint64_t > &hashes) | 
| T | insert_contains (const char *seq, size_t seq_len) | 
| T | insert_contains (const std::string &seq) | 
| T | insert_contains (const uint64_t *hashes) | 
| T | insert_contains (const std::vector< uint64_t > &hashes) | 
| T | insert_thresh_contains (const char *seq, size_t seq_len, T threshold) | 
| T | insert_thresh_contains (const std::string &seq, const T threshold) | 
| T | insert_thresh_contains (const uint64_t *hashes, const T threshold) | 
| T | insert_thresh_contains (const std::vector< uint64_t > &hashes, const T threshold) | 
| T | contains_insert_thresh (const char *seq, size_t seq_len, T threshold) | 
| T | contains_insert_thresh (const std::string &seq, const T threshold) | 
| T | contains_insert_thresh (const uint64_t *hashes, const T threshold) | 
| T | contains_insert_thresh (const std::vector< uint64_t > &hashes, const T threshold) | 
| size_t | get_bytes () const | 
| uint64_t | get_pop_cnt (T threshold=1) const | 
| double | get_occupancy (T threshold=1) const | 
| unsigned | get_hash_num () const | 
| double | get_fpr (T threshold=1) const | 
| unsigned | get_k () const | 
| const std::string & | get_hash_fn () const | 
| CountingBloomFilter< T > & | get_counting_bloom_filter () | 
| void | save (const std::string &path) | 
| Static Public Member Functions | |
| static bool | is_bloom_file (const std::string &path) | 
Counting Bloom filter data structure that stores k-mers. Provides KmerCountingBloomFilter8, KmerCountingBloomFilter16, and KmerCountingBloomFilter32 classes with corresponding bit-size counters.
| 
 | inline | 
Construct a dummy k-mer Bloom filter (e.g. as a default argument).
| 
 | inline | 
Construct an empty k-mer Counting Bloom filter of given size.
| bytes | Filter size in bytes. | 
| hash_num | Number of hash values per element. | 
| k | K-mer size. | 
| 
 | inlineexplicit | 
Load a k-mer Counting Bloom filter from a file.
| path | Filepath to load from. | 
| 
 | inline | 
Query the counts of k-mers of a sequence.
| seq | Sequence to k-merize. | 
| seq_len | Length of seq. | 
| 
 | inline | 
Query the counts of k-mers of a sequence.
| seq | Sequence to k-merize. | 
| 
 | inline | 
Get a k-mer's count.
| hashes | Integer vector of k-mer's hash values. | 
| 
 | inline | 
Get a k-mer's count.
| hashes | Integer array of k-mer's hash values. Array size should equal the hash_num argument used when the Bloom filter was constructed. | 
| 
 | inline | 
Get the counts of a sequence's k-mers and then increment the counts.
| seq | Sequence to k-merize. | 
| seq_len | Length of seq. | 
| 
 | inline | 
Get the counts of a sequence's k-mers and then increment the counts.
| seq | Sequence to k-merize. | 
| 
 | inline | 
Get the count of a k-mer and then increment the count.
| hashes | Integer vector of the k-mer's hash values. | 
| 
 | inline | 
Get the count of a k-mer and then increment the count.
| hashes | Integer array of the k-mers's hash values. Array size should equal the hash_num argument used when the Bloom filter was constructed. | 
| 
 | inline | 
Get the counts of a sequence's k-mer's and then increment the counts if they are not above the threshold.
| seq | Sequence to k-merize. | 
| seq_len | Length of seq. | 
| threshold | The threshold. | 
| 
 | inline | 
Get the counts of a sequence's k-mer's and then increment the counts if they are not above the threshold.
| seq | Sequence to k-merize. | 
| threshold | The threshold. | 
| 
 | inline | 
Get the count of a k-mer and then increment the count if it's not above the threshold.
| hashes | Integer vector of the k-mer's hash values. | 
| threshold | The threshold. | 
| 
 | inline | 
Get the count of a k-mer and then increment the count if it's not above the threshold.
| hashes | Integer array of the k-mer's hash values. Array size should equal the hash_num argument used when the Bloom filter was constructed. | 
| threshold | The threshold. | 
| 
 | inline | 
Get filter size in bytes.
| 
 | inline | 
Get a reference to the underlying vanilla Counting Bloom filter.
| 
 | inline | 
Get the query false positive rate for elements with count >= threshold.
| threshold | The threshold. | 
| 
 | inline | 
Get the name of the hash function used.
| 
 | inline | 
Get the number of hash values per element.
| 
 | inline | 
Get the k-mer size used.
| 
 | inline | 
Get the fraction of the filter occupied by >0 counters.
| 
 | inline | 
Get population count, i.e. the number of counters >0 in the filter.
| 
 | inline | 
Insert a sequence's k-mers into the filter.
| seq | Sequence to k-merize. | 
| seq_len | Length of seq. | 
| 
 | inline | 
Insert a sequence's k-mers into the filter.
| seq | Sequence to k-merize. | 
| 
 | inline | 
Insert a k-mer into the filter.
| hashes | Integer vector of the k-mer's hash values. | 
| 
 | inline | 
Insert a k-mer into the filter.
| hashes | Integer array of the k-mer's hash values. Array size should equal the hash_num argument used when the Bloom filter was constructed. | 
| 
 | inline | 
Increment the counts of a sequence's k-mers and then return the counts.
| seq | Sequence to k-merize. | 
| seq_len | Length of seq. | 
| 
 | inline | 
Increment the counts of a sequence's k-mers and then return the counts.
| seq | Sequence to k-merize. | 
| 
 | inline | 
Increment a k-mer's count and then return the count.
| hashes | Integer vector of the k-mer's hash values. | 
| 
 | inline | 
Increment a k-mer's count and then return the count.
| hashes | Integer array of the k-mer's hash values. Array size should equal the hash_num argument used when the Bloom filter was constructed. | 
| 
 | inline | 
Increment the counts of a sequence's k-mers if they are not above the threshold and then return the counts.
| seq | Sequence to k-merize. | 
| seq_len | Length of seq. | 
| threshold | The threshold. | 
| 
 | inline | 
Increment the counts of a sequence's k-mers if they are not above the threshold and then return the counts.
| seq | Sequence to k-merize. | 
| threshold | The threshold. | 
| 
 | inline | 
Increment a k-mer's count if it's not above the threshold and then return the count.
| hashes | Integer array of the k-mer's hash values. Array size should equal the hash_num argument used when the Bloom filter was constructed. | 
| threshold | The threshold. | 
| 
 | inline | 
Increment a k-mer's count if it's not above the threshold and then return the count.
| hashes | Integer array of the k-mer's hash values. Array size should equal the hash_num argument used when the Bloom filter was constructed. | 
| threshold | The threshold. | 
| 
 | inlinestatic | 
Check whether the file at the given path is a saved k-mer counting Bloom filter.
| path | Filepath to check. | 
| 
 | inline | 
Save the Bloom filter to a file that can be loaded in the future.
| path | Filepath to store filter at. |