Struct Sketcher

pub struct Sketcher { /* private fields */ }

An object containing the sketch parameters.

Contains internal state to optimize the implementation when sketching multiple similar sequences.

Implementations

impl Sketcher

pub fn default(k: usize) -> Self

Default sketcher that very fast at comparisons, but 20% slower at sketching. Use for >= 50000 seqs, and safe default when input sequences are > 500’000 characters.

When sequences are < 100’000 characters, inaccuracies may occur due to empty buckets.

pub fn default_fast_sketching(k: usize) -> Self

Default sketcher that is fast at sketching, but somewhat slower at comparisons. Use for <= 5000 seqs, or when input sequences are < 100’000 characters.

pub fn new_fwd(k: usize, s: usize, b: usize) -> Self

Construct a new forward-only Sketcher object.

pub fn new_rc(k: usize, s: usize, b: usize) -> Self

Construct a new reverse-complement-aware Sketcher object.

impl Sketcher

pub fn bottom_sketch<'s, S: Seq<'s>>(&self, seq: S) -> BottomSketch

Return the s smallest u32 k-mer hashes. Prefer Sketcher::sketch instead, which is much faster and just as accurate when input sequences are not too short.

pub fn sketch<'s, S: Seq<'s>>(&self, seq: S) -> BucketSketch

s-buckets sketch. Splits the hashes into s buckets and returns the smallest hash per bucket. Buckets are determined via the remainder mod s.