btllib
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btllib::NtHash Class Reference

Public Member Functions

 NtHash (const char *seq, size_t seq_len, unsigned hash_num, unsigned k, size_t pos=0)
 
 NtHash (const std::string &seq, unsigned hash_num, unsigned k, size_t pos=0)
 
 NtHash (const NtHash &nthash)
 
 NtHash (NtHash &&)=default
 
bool roll ()
 
bool roll_back ()
 
bool peek ()
 
bool peek_back ()
 
bool peek (char char_in)
 
bool peek_back (char char_in)
 
void sub (const std::vector< unsigned > &positions, const std::vector< unsigned char > &new_bases)
 
const uint64_t * hashes () const
 
size_t get_pos () const
 
bool forward () const
 
unsigned get_hash_num () const
 
unsigned get_k () const
 
uint64_t get_forward_hash () const
 
uint64_t get_reverse_hash () const
 
void change_seq (const std::string &new_seq, size_t new_pos=0)
 

Friends

class SeedNtHash
 

Constructor & Destructor Documentation

◆ NtHash() [1/2]

btllib::NtHash::NtHash ( const char *  seq,
size_t  seq_len,
unsigned  hash_num,
unsigned  k,
size_t  pos = 0 
)

Constructor.

Parameters
seqC string of DNA sequence to be hashed.
seq_lenLength of seq.
hash_numNumber of hashes to produce per k-mer.
kK-mer size.
posPosition in seq to start hashing from.

◆ NtHash() [2/2]

btllib::NtHash::NtHash ( const std::string &  seq,
unsigned  hash_num,
unsigned  k,
size_t  pos = 0 
)

Constructor.

Parameters
seqString of DNA sequence to be hashed.
hash_numNumber of hashes to produce per k-mer.
kK-mer size.
posPosition in seq to start hashing from.

Member Function Documentation

◆ get_pos()

size_t btllib::NtHash::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.

◆ peek() [1/2]

bool btllib::NtHash::peek ( )

Peeks the hash values as if roll() was called (without advancing the NtHash object. The peeked hash values can be obtained through the hashes() method.

Returns
true on success and false otherwise.

◆ peek() [2/2]

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

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

Returns
true on success and false otherwise.

◆ peek_back() [1/2]

bool btllib::NtHash::peek_back ( )

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

Returns
true on success and false otherwise.

◆ peek_back() [2/2]

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

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

Returns
true on success and false otherwise.

◆ roll()

bool btllib::NtHash::roll ( )

Calculate the hash values of current k-mer and advance to the next k-mer. NtHash advances one nucleotide at a time until it finds a k-mer with valid characters (ACTG) and skips over those with invalid characters (non-ACTG, including N). This method must be called before hashes() is accessed, for the first and every subsequent hashed kmer. get_pos() may be called at any time to obtain the position of last hashed k-mer or the k-mer to be hashed if roll() has never been called on this NtHash object. It is important to note that the number of roll() calls is NOT necessarily equal to get_pos(), if there are N or invalid characters in the hashed sequence.

Returns
true on success and false otherwise.

◆ roll_back()

bool btllib::NtHash::roll_back ( )

Like the roll() function, but advance backwards.

Returns
true on success and false otherwise.

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