Struct MinHash 

pub struct MinHash { /* private fields */ }

Bottom-k MinHash sketch for rapid genome comparison.

Keeps the sketch_size smallest canonical k-mer hash values from a DNA sequence. Jaccard similarity between two sketches is estimated from the overlap of their bottom-k hash sets.

Implementations

impl MinHash

pub fn new(k: usize, sketch_size: usize) -> Result<Self>

Create a new empty MinHash sketch.

Errors

Returns an error if k == 0 or sketch_size == 0.

pub fn from_sequence(seq: &[u8], k: usize, sketch_size: usize) -> Result<Self>

Build a MinHash sketch from a DNA sequence.

Non-ACGT bases act as k-mer break points (k-mers spanning them are skipped). Input is case-insensitive.

Errors

Returns an error if k == 0 or sketch_size == 0.

pub fn add_sequence(&mut self, seq: &[u8])

Add k-mers from a DNA sequence to this sketch.

Non-ACGT bases act as k-mer break points. The sketch is maintained as a sorted bottom-k set.

pub fn jaccard(&self, other: &MinHash) -> Result<f64>

Estimate Jaccard similarity between this sketch and another.

Uses the merge-based estimator: merge both sorted hash arrays, count how many of the bottom-k values from the union appear in both sketches.

Errors

Returns an error if the sketches have different k values.

pub fn containment(&self, other: &MinHash) -> Result<f64>

Estimate containment of self in other.

Containment C(A, B) = |A intersect B| / |A|.

Errors

Returns an error if the sketches have different k values.

pub fn ani(&self, other: &MinHash) -> Result<f64>

Estimate average nucleotide identity (ANI) from Jaccard similarity.

Uses the Mash formula: ANI = 1 + (2/k) * ln(2J / (1 + J))

Errors

Returns an error if the sketches have different k values, or if the Jaccard similarity is zero (ANI undefined).

pub fn len(&self) -> usize

Number of hash values currently in the sketch.

pub fn is_empty(&self) -> bool

Whether the sketch is empty (no k-mers hashed).

pub fn k(&self) -> usize

The k-mer size used by this sketch.

pub fn sketch_size(&self) -> usize

The target sketch size (bottom-k parameter).

pub fn hashes(&self) -> &[u64]

Return a reference to the sorted hash values.

Trait Implementations

impl Clone for MinHash

fn clone(&self) -> MinHash

Returns a duplicate of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for MinHash

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.