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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... | |

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.