Struct DeBruijnGraph 

pub struct DeBruijnGraph { /* private fields */ }

A node-centric De Bruijn graph built from k-mers.

Each k-mer is an edge from its (k-1)-prefix to its (k-1)-suffix. Nodes are the (k-1)-mers; edges are the original k-mers.

Implementations

impl DeBruijnGraph

pub fn from_sequences(sequences: &[&[u8]], k: usize) -> Result<Self>

Build a De Bruijn graph from a set of input sequences.

Extracts all k-mers from each sequence and adds them as edges. Bases are uppercased; only A/C/G/T bases are accepted.

Errors

Returns an error if k < 2, any sequence is shorter than k, or a sequence contains non-ACGT characters.

pub fn from_kmers(kmers: &[&[u8]]) -> Result<Self>

Build a De Bruijn graph from pre-extracted k-mers.

All k-mers must have the same length (≥ 2).

Errors

Returns an error if the k-mer slice is empty or k-mers differ in length.

pub fn node_count(&self) -> usize

Number of distinct (k-1)-mer nodes in the graph.

pub fn edge_count(&self) -> usize

Number of k-mer edges in the graph (including duplicates).

pub fn contains_kmer(&self, kmer: &[u8]) -> bool

Check whether a specific k-mer exists as an edge in the graph.

pub fn unitigs(&self) -> Vec<Unitig>

Extract all unitigs (maximal non-branching paths).

A unitig is a path where every internal node has exactly one incoming and one outgoing edge. Coverage is the mean count of constituent k-mers.

Trait Implementations

impl Clone for DeBruijnGraph

fn clone(&self) -> DeBruijnGraph

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for DeBruijnGraph

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

Formats the value using the given formatter.