#include <bloom_filter.hpp>
Bloom filter data structure that stores spaced seed k-mers. 
◆ SeedBloomFilter() [1/3]
  
  | 
        
          | btllib::SeedBloomFilter::SeedBloomFilter | ( |  | ) |  |  | inline | 
 
Construct a dummy Seed Bloom filter (e.g. as a default argument). 
 
 
◆ SeedBloomFilter() [2/3]
      
        
          | btllib::SeedBloomFilter::SeedBloomFilter | ( | size_t | bytes, | 
        
          |  |  | unsigned | k, | 
        
          |  |  | const std::vector< std::string > & | seeds, | 
        
          |  |  | unsigned | hash_num_per_seed | 
        
          |  | ) |  |  | 
      
 
Construct an empty Seed Bloom filter of given size.
- Parameters
- 
  
    | bytes | Filter size in bytes. |  | k | K-mer size. |  | seeds | A vector of spaced seeds in string format. 0s indicate ignored and 1s indicate relevant bases. |  
 
 
 
◆ SeedBloomFilter() [3/3]
  
  | 
        
          | btllib::SeedBloomFilter::SeedBloomFilter | ( | const std::string & | path | ) |  |  | explicit | 
 
Load a Seed Bloom filter from a file.
- Parameters
- 
  
    | path | Filepath to load from. |  
 
 
 
◆ contains() [1/4]
      
        
          | std::vector< std::vector< unsigned > > btllib::SeedBloomFilter::contains | ( | const char * | seq, | 
        
          |  |  | size_t | seq_len | 
        
          |  | ) |  | const | 
      
 
Query the presence of spaced seed k-mers of a sequence.
- Parameters
- 
  
    | seq | Sequence to k-merize. |  | seq_len | Length of seq. |  
 
- Returns
- A vector indicating which seeds had a hit for every k-mer. The indices of the outer vector are indices of seq k-mers. The indices of inner vector are indices of spaced seeds hit for that k-mer. 
 
 
◆ contains() [2/4]
  
  | 
        
          | std::vector< std::vector< unsigned > > btllib::SeedBloomFilter::contains | ( | const std::string & | seq | ) | const |  | inline | 
 
Query the presence of spaced seed k-mers of a sequence.
- Parameters
- 
  
  
- Returns
- A vector indicating which seeds had a hit for every k-mer. The indices of the outer vector are indices of seq k-mers. The indices of inner vector are indices of spaced seeds hit for that k-mer. 
 
 
◆ contains() [3/4]
  
  | 
        
          | bool btllib::SeedBloomFilter::contains | ( | const std::vector< uint64_t > & | hashes | ) | const |  | inline | 
 
Check for the presence of an element's hash values. A single spaced seed is an element here.
- Parameters
- 
  
    | hashes | Integer vector of hash values. |  
 
 
 
◆ contains() [4/4]
  
  | 
        
          | bool btllib::SeedBloomFilter::contains | ( | const uint64_t * | hashes | ) | const |  | inline | 
 
Check for the presence of an element's hash values. A single spaced seed is an element here.
- Parameters
- 
  
    | hashes | Integer array of hash values. Array size should equal the hash_num_per_seed argument used when the Bloom filter was constructed. |  
 
 
 
◆ contains_insert() [1/4]
      
        
          | std::vector< std::vector< unsigned > > btllib::SeedBloomFilter::contains_insert | ( | const char * | seq, | 
        
          |  |  | size_t | seq_len | 
        
          |  | ) |  |  | 
      
 
Query the presence of spaced seed k-mers of a sequence and insert if missing.
- Parameters
- 
  
    | seq | Sequence to k-merize. |  | seq_len | Length of seq. |  
 
- Returns
- A vector indicating which seeds had a hit for every k-mer before insertion. The indices of the outer vector are indices of seq k-mers. The indices of inner vector are indices of spaced seeds hit for that k-mer. 
 
 
◆ contains_insert() [2/4]
  
  | 
        
          | std::vector< std::vector< unsigned > > btllib::SeedBloomFilter::contains_insert | ( | const std::string & | seq | ) |  |  | inline | 
 
Query the presence of spaced seed k-mers of a sequence and insert if missing.
- Parameters
- 
  
  
- Returns
- A vector indicating which seeds had a hit for every k-mer before insertion. The indices of the outer vector are indices of seq k-mers. The indices of inner vector are indices of spaced seeds hit for that k-mer. 
 
 
◆ contains_insert() [3/4]
  
  | 
        
          | bool btllib::SeedBloomFilter::contains_insert | ( | const std::vector< uint64_t > & | hashes | ) |  |  | inline | 
 
Check for the presence of an element's hash values and insert if missing. A single spaced seed is an element here.
- Parameters
- 
  
    | hashes | Integer vector of hash values. |  
 
- Returns
- True if present before insertion, false otherwise. 
 
 
◆ contains_insert() [4/4]
  
  | 
        
          | bool btllib::SeedBloomFilter::contains_insert | ( | const uint64_t * | hashes | ) |  |  | inline | 
 
Check for the presence of an element's hash values and insert if missing. A single spaced seed is an element here.
- Parameters
- 
  
    | hashes | Integer array of hash values. Array size should equal the hash_num_per_seed argument used when the Bloom filter was constructed. |  
 
- Returns
- True if present before insertion, false otherwise. 
 
 
◆ get_bytes()
  
  | 
        
          | size_t btllib::SeedBloomFilter::get_bytes | ( |  | ) | const |  | inline | 
 
Get filter size in bytes. 
 
 
◆ get_fpr()
      
        
          | double btllib::SeedBloomFilter::get_fpr | ( |  | ) | const | 
      
 
Get the false positive rate of at least one seed falsely reporting a hit per k-mer. 
 
 
◆ get_hash_fn()
  
  | 
        
          | const std::string & btllib::SeedBloomFilter::get_hash_fn | ( |  | ) | const |  | inline | 
 
Get the name of the hash function used. 
 
 
◆ get_hash_num()
  
  | 
        
          | unsigned btllib::SeedBloomFilter::get_hash_num | ( |  | ) | const |  | inline | 
 
Get the number of hash values per element, i.e. seed. 
 
 
◆ get_hash_num_per_seed()
  
  | 
        
          | unsigned btllib::SeedBloomFilter::get_hash_num_per_seed | ( |  | ) | const |  | inline | 
 
Get the number of hash values per element, i.e. seed. 
 
 
◆ get_k()
  
  | 
        
          | unsigned btllib::SeedBloomFilter::get_k | ( |  | ) | const |  | inline | 
 
 
◆ get_kmer_bloom_filter()
Get a reference to the underlying Kmer Bloom filter. 
 
 
◆ get_occupancy()
  
  | 
        
          | double btllib::SeedBloomFilter::get_occupancy | ( |  | ) | const |  | inline | 
 
Get the fraction of the filter occupied by 1 bits. 
 
 
◆ get_parsed_seeds()
  
  | 
        
          | const std::vector< SpacedSeed > & btllib::SeedBloomFilter::get_parsed_seeds | ( |  | ) | const |  | inline | 
 
Get the seeds used in parsed format. Parsed format is a vector of indices of 0s in the seed. 
 
 
◆ get_pop_cnt()
  
  | 
        
          | uint64_t btllib::SeedBloomFilter::get_pop_cnt | ( |  | ) | const |  | inline | 
 
Get population count, i.e. the number of 1 bits in the filter. 
 
 
◆ get_seeds()
  
  | 
        
          | const std::vector< std::string > & btllib::SeedBloomFilter::get_seeds | ( |  | ) | const |  | inline | 
 
Get the seeds used in string format. 
 
 
◆ get_total_hash_num()
  
  | 
        
          | unsigned btllib::SeedBloomFilter::get_total_hash_num | ( |  | ) | const |  | inline | 
 
Get the number of hash values per k-mer, i.e. total number of hash values for all seeds. 
 
 
◆ insert() [1/4]
      
        
          | void btllib::SeedBloomFilter::insert | ( | const char * | seq, | 
        
          |  |  | size_t | seq_len | 
        
          |  | ) |  |  | 
      
 
Insert a sequence's spaced seed k-mers into the filter.
- Parameters
- 
  
    | seq | Sequence to k-merize. |  | seq_len | Length of seq. |  
 
 
 
◆ insert() [2/4]
  
  | 
        
          | void btllib::SeedBloomFilter::insert | ( | const std::string & | seq | ) |  |  | inline | 
 
Insert a sequence's spaced seed k-mers into the filter.
- Parameters
- 
  
  
 
 
◆ insert() [3/4]
  
  | 
        
          | void btllib::SeedBloomFilter::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::SeedBloomFilter::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()
  
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          | static bool btllib::SeedBloomFilter::is_bloom_file | ( | const std::string & | path | ) |  |  | inlinestatic | 
 
Check whether the file at the given path is a saved Seed Bloom filter.
- Parameters
- 
  
  
 
 
◆ save()
      
        
          | void btllib::SeedBloomFilter::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. |  
 
 
 
The documentation for this class was generated from the following file: