Child class of Digester that defines a minimizer as a kmer whose hash is equal to some target value after being modded. Parameters without a description are the same as the parameters in the Digester parent class. They are simply passed up to the parent constructor. More...
#include <mod_minimizer.hpp>
Inheritance diagram for digest::ModMin< P >:
Public Member Functions | |
| ModMin (const char *seq, size_t len, unsigned k, uint32_t mod, uint32_t congruence=0, size_t start=0, MinimizedHashType minimized_h=MinimizedHashType::CANON) | |
| ModMin (const std::string &seq, unsigned k, uint32_t mod, uint32_t congruence=0, size_t start=0, MinimizedHashType minimized_h=MinimizedHashType::CANON) | |
| void | roll_minimizer (unsigned amount, std::vector< uint32_t > &vec) override |
| adds up to amount of positions of minimizers into vec. Here a k-mer is considered a minimizer if its hash is congruent to congruence in the mod space. | |
| void | roll_minimizer (unsigned amount, std::vector< std::pair< uint32_t, uint32_t > > &vec) override |
| adds up to amount of positions and hashes of minimizers into vec. Here a k-mer is considered a minimizer if its hash is congruent to congruence in the mod space. | |
| uint32_t | get_mod () |
| uint32_t | get_congruence () |
 Public Member Functions inherited from digest::Digester< P > | |
| Digester (const char *seq, size_t len, unsigned k, size_t start=0, MinimizedHashType minimized_h=MinimizedHashType::CANON) | |
| Digester (const std::string &seq, unsigned k, size_t start=0, MinimizedHashType minimized_h=MinimizedHashType::CANON) | |
| bool | get_is_valid_hash () |
| unsigned | get_k () |
| size_t | get_len () |
| bool | roll_one () |
| moves the internal pointer to the next valid k-mer. Time Complexity: O(1) | |
| size_t | get_pos () |
| uint64_t | get_chash () |
| uint64_t | get_fhash () |
| uint64_t | get_rhash () |
| virtual void | new_seq (const char *seq, size_t len, size_t start) |
| replaces the current sequence with the new one. It's like starting over with a completely new seqeunce | |
| virtual void | new_seq (const std::string &seq, size_t pos) |
| replaces the current sequence with the new one. It's like starting over with a completely new sequence | |
| void | append_seq (const char *seq, size_t len) |
| simulates the appending of a new sequence to the end of the old sequence. The old sequence will no longer be stored, but the rolling hashes will be able to preceed as if the sequences were appended. Can only be called when you've reached the end of the current sequence i.e. if you're current sequence is ACTGAC, and you have reached the end of this sequence, and you call append_seq with the sequence CCGGCCGG, then the minimizers you will get after calling append_seq plus the minimizers you got from going through ACTGAC, will be equivalent to the minimizers you would have gotten from rolling across ACTGACCCGGCCGG | |
| void | append_seq (const std::string &seq) |
| simulates the appending of a new sequence to the end of the old sequence. The old sequence will no longer be stored, but the rolling hashes will be able to preceed as if the sequences were appended. Can only be called when you've reached the end of the current sequence i.e. if you're current sequence is ACTGAC, and you have reached the end of this sequence, and you call append_seq with the sequence CCGGCCGG, then the minimizers you will get after calling append_seq plus the minimizers you got from going through ACTGAC, will be equivalent to the minimizers you would have gotten from rolling across ACTGACCCGGCCGG | |
| MinimizedHashType | get_minimized_h () |
| const char * | get_sequence () |
Detailed Description
template<BadCharPolicy P>
class digest::ModMin< P >
class digest::ModMin< P >
Child class of Digester that defines a minimizer as a kmer whose hash is equal to some target value after being modded. Parameters without a description are the same as the parameters in the Digester parent class. They are simply passed up to the parent constructor.
- Template Parameters
-
P
Constructor & Destructor Documentation
◆ ModMin() [1/2]
template<BadCharPolicy P>
|
inline |
- Parameters
-
seq len k mod mod space to be used to calculate universal minimizers congruence value we want minimizer hashes to be congruent to in the mod space start minimized_h
- Exceptions
-
BadModException Thrown when congruence is greater or equal to mod
◆ ModMin() [2/2]
template<BadCharPolicy P>
|
inline |
- Parameters
-
seq k mod mod space to be used to calculate universal minimizers congruence value we want minimizer hashes to be congruent to in the mod space start minimized_h
- Exceptions
-
BadModException Thrown when congruence is greater or equal to mod
Member Function Documentation
◆ get_congruence()
template<BadCharPolicy P>
|
inline |
- Returns
- uint32_t, the value the minimized hash must be congruent to
◆ get_mod()
template<BadCharPolicy P>
|
inline |
- Returns
- uint32_t, the mod space being used
◆ roll_minimizer() [1/2]
template<BadCharPolicy P>
|
inlineoverridevirtual |
adds up to amount of positions and hashes of minimizers into vec. Here a k-mer is considered a minimizer if its hash is congruent to congruence in the mod space.
- Parameters
-
amount vec
Implements digest::Digester< P >.
◆ roll_minimizer() [2/2]
template<BadCharPolicy P>
|
inlineoverridevirtual |
adds up to amount of positions of minimizers into vec. Here a k-mer is considered a minimizer if its hash is congruent to congruence in the mod space.
- Parameters
-
amount vec
Implements digest::Digester< P >.
The documentation for this class was generated from the following file:
- include/digest/mod_minimizer.hpp
