Struct FracMinHash 

pub struct FracMinHash { /* private fields */ }

Scaled (FracMinHash) sketch for rapid genome comparison.

Keeps all canonical k-mer hash values below u64::MAX / scale. This gives a predictable sampling fraction regardless of genome size, making containment estimation more accurate for genomes of different sizes.

Implementations

impl FracMinHash

pub fn new(k: usize, scale: u64) -> Result<Self>

Create a new empty FracMinHash sketch.

Errors

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

pub fn from_sequence(seq: &[u8], k: usize, scale: u64) -> Result<Self>

Build a FracMinHash sketch from a DNA sequence.

Errors

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

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

Estimate Jaccard similarity between this sketch and another.

Jaccard = |A intersect B| / |A union B|, computed exactly over the hashes below the shared threshold.

Errors

Returns an error if the sketches have different k or scale values.

pub fn containment(&self, other: &FracMinHash) -> 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 or scale values.

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

Estimate average nucleotide identity (ANI) from Jaccard similarity.

Errors

Returns an error if the sketches are incompatible or Jaccard is zero.

pub fn len(&self) -> usize

Number of hash values in the sketch.

pub fn is_empty(&self) -> bool

Whether the sketch is empty.

pub fn k(&self) -> usize

The k-mer size used by this sketch.

pub fn scale(&self) -> u64

The scale factor.

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

Return a reference to the sorted hash values.

Trait Implementations

impl Clone for FracMinHash

fn clone(&self) -> FracMinHash

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for FracMinHash

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

Formats the value using the given formatter.