Module implementation

Different implementations of genome string representations.

Modules

alphabets

Implementations of various common genomic alphabets.

array_kmer

A simple representation of a k-mer as an array.

bit_array_kmer

A simple representation of a k-mer as an array.

bit_vec_sequence

A representation of a genome as Vec<usize> where each character is encoded as bits.

bit_vec_sequence_store

A vector sequence store where each character is encoded as two bits.

handle_sequence_store

An “anti” sequence store that stores the sequences in the handles.

vec_sequence

A simple representation of a genome as Vec<u8>.

vec_sequence_store

An ASCII vector based sequence store.

Type Aliases

DefaultGenome

The default genome type that achieves a good balance between speed and size.

DefaultSequenceStore

The default genome sequence store type that achieves a good balance between speed and size.

DefaultSequenceStoreHandle

The handle type of the default genome sequence store type.

DefaultSubGenome

The default genome subsequence type that achieves a good balance between speed and size.