k-mer Index

Implementation of shapes for a k-mer Index. More...

Collaboration diagram for k-mer Index:

Classes
struct	seqan3::bin_literal
	A strong type of underlying type uint64_t that represents the shape in binary representation. More...
class	seqan3::shape
	A class that defines which positions of a pattern to hash. More...
struct	seqan3::ungapped
	A strong type of underlying type uint8_t that represents the ungapped shape size. More...

Detailed Description

Implementation of shapes for a k-mer Index.

Note

The k-mer index is not yet implemented.

A k-mer index is a data structure that stores all occurrences of k-mers in a text. A k-mer can be either an exact string of length k or it can contain one or more wildcards, which denote positions of arbitrary characters.

The index is very fast for retrieving all occurrences of a k-mer in the underlying text. Usually the query length (k) is small and the underlying text is very large. The parameter k and the position(s) of wildcards must be fixed at index creation with seqan3::ungapped or seqan3::shape.