digest Namespace Reference

digest code. More...

Namespaces
namespace	ds
namespace	thread_out
	Possible implementation for multi-threading the digestion of a single sequence. The key thing to note is basically by carefully telling where each digester should start digesting you can make it so each kmer is only considered once. For more details on a function, click on more and it will take you to the description that is located in modules.

Classes
class	BadConstructionException
	Exception thrown when initializing a Digister with k (kmer size) < 4 and start (starting index) < len (length of sequence). More...
class	BadModException
	Exception thrown when initializing a mod minimizer object where the target value after modding is greater than the mod value. More...
class	BadWindowSizeException
	Exception thrown when initializing a Window Minimizer or Syncmer with a large window size of 0. More...
class	Digester
	an abstract class for Digester objects. More...
class	ModMin
	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...
class	NotRolledTillEndException
	Exception thrown when append_seq() is called before all kmers/large windows in the current sequence have been iterated over. More...
class	Syncmer
	This class inherits from WindowMinimizer (implementation reasons), but the represent very different things. A Syncmer is defined as a large window where the minimal hash among all kmers in the large window belong to either the leftmost or rightmost kmer. 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...
class	WindowMin
	Child class of Digester that defines a minimizer as a kmer whose hash is minimal among those in the large window. 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...

Enumerations
enum class	MinimizedHashType { CANON , FORWARD , REVERSE }
	Enum values for the type of hash to minimize. More...
enum class	BadCharPolicy { WRITEOVER , SKIPOVER }
	Specifies behavior with non-ACTG characters. More...

Detailed Description

digest code.

Enumeration Type Documentation

BadCharPolicy

enum class digest::BadCharPolicy

strong

Specifies behavior with non-ACTG characters.

Enumerator
WRITEOVER	The WRITEOVER policy specifies that any non-ACTG character is simply replaced with an A.
SKIPOVER	The SKIPOVER policy skips over any kmers with a non-ACTG character. For example, if you have k = 4 and your sequence is ACTGNNACTGAC, then the only kmers that would be considered would be the ACTG starting at index 0, the ACTG starting at index 6, CTGA at index 7, and TGAC at index 8. Then if you had a large window of 4 (kmers), then the smallest would be picked from one of those 4.

MinimizedHashType

enum class digest::MinimizedHashType

strong

Enum values for the type of hash to minimize.

Enumerator
CANON	minimize the canonical hash
FORWARD	minimize the forward hash
REVERSE	minimize the reverse hash