Struct LdBG

pub struct LdBG {
    pub name: String,
    pub kmer_size: usize,
    pub kmers: HashMap<Vec<u8>, Record>,
    pub scores: HashMap<Vec<u8>, f32>,
    pub links: HashMap<Vec<u8>, HashMap<Link, u16>>,
    pub sources: HashMap<Vec<u8>, Vec<usize>>,
    pub noise: HashSet<Vec<u8>>,
    pub verbose: bool,
}

Represents a linked de Bruijn graph with a k-mer size specified at construction time.

Fields

name: String

kmer_size: usize

kmers: HashMap<Vec<u8>, Record>

scores: HashMap<Vec<u8>, f32>

links: HashMap<Vec<u8>, HashMap<Link, u16>>

sources: HashMap<Vec<u8>, Vec<usize>>

noise: HashSet<Vec<u8>>

verbose: bool

Implementations

impl LdBG

pub fn new(name: String, kmer_size: usize) -> Self

pub fn from_file(name: String, kmer_size: usize, seq_path: &PathBuf) -> Self

Create a de Bruijn graph (and optional links) from a file path.

Arguments

• name - A string representing the name of the graph.
• kmer_size - The k-mer size.
• seq_path - A path to the sequence file.

Returns

A new instance of LdBG.

Panics

This function will panic if it cannot open a file.

pub fn from_files( name: String, kmer_size: usize, seq_paths: &Vec<PathBuf>, ) -> Self

Create a de Bruijn graph (and optional links) from many file paths.

Arguments

• name - A string representing the name of the graph.
• kmer_size - The k-mer size.
• seq_paths - Paths to sequence files.

Returns

A new instance of LdBG.

Panics

This function will panic if it cannot open a file.

pub fn from_sequence(name: String, kmer_size: usize, fwd_seq: &Vec<u8>) -> Self

Create a de Bruijn graph (and optional links) from a sequence.

Arguments

• name - A string representing the name of the graph.
• kmer_size - The k-mer size.
• fwd_seq - A forward sequence.

Returns

A new instance of LdBG.

pub fn from_sequences( name: String, kmer_size: usize, fwd_seqs: &Vec<Vec<u8>>, ) -> Self

Create a de Bruijn graph (and optional links) from a list of sequences.

Arguments

• name - A string representing the name of the graph.
• kmer_size - The k-mer size.
• fwd_seqs - A vector of forward sequences.

Returns

A new instance of LdBG.

pub fn name(&self) -> &String

Get the name of the graph.

Returns

A reference to the name of the graph.

pub fn verbose(self, verbose: bool) -> Self

pub fn build_links(self, fwd_seqs: &Vec<Vec<u8>>, correct: bool) -> Self

Build the links for a de Bruijn graph from a vector of sequences.

Arguments

• k - The k-mer size.
• fwd_seqs - A vector of forward sequences.

Returns

A map of links.

pub fn remove(&mut self, kmer: &[u8]) -> Option<Record>

pub fn score_kmers(self, model_path: &PathBuf) -> Self

Score k-mers using a Gradient Boosting Decision Tree model.

Arguments

• model_path - A path to the model file.

Returns

A new instance of LdBG with updated k-mer scores.

Panics

This function will panic if it cannot load the model from the specified path.

pub fn infer_edges(&mut self)

pub fn correct_seqs(&self, seqs: &Vec<Vec<u8>>) -> Vec<Vec<u8>>

pub fn correct_seq(&self, g: &DiGraph<String, f32>, seq: &[u8]) -> Vec<u8>

pub fn correct_seq_old(&self, seq: &[u8]) -> Vec<Vec<u8>>

pub fn assemble(&self, kmer: &[u8]) -> Vec<u8>

Starting at a given k-mer, assemble a contig.

Arguments

• kmer - A slice representing the starting k-mer.

Returns

A vector containing the assembled contig.

Panics

• This function will panic if the k-mer length does not match the expected length.

pub fn assemble_all(&self) -> Vec<Vec<u8>>

Assemble all contigs from the linked de Bruijn graph.

Returns

A vector of contigs.

Panics

• This function will panic if the node weight for a unique node cannot be retrieved.
• If self.kmers.get(cn_kmer).unwrap() returns None.

pub fn assemble_at_bubbles(&self) -> Vec<Vec<u8>>

Assemble contigs at superbubbles in the graph.

This function traverses all k-mers in the graph, identifies superbubbles, and assembles contigs from unique nodes within these superbubbles.

Returns

A vector of contigs, where each contig is represented as a vector of bytes.

Panics

• This function will panic if the node weight for a unique node cannot be retrieved.
• if g.node_weight(*unique_node).unwrap().as_bytes() returns None.

pub fn clean(self, threshold: f32) -> Self

pub fn clean_color_specific_paths(self, color: usize, min_score: f32) -> Self

Clean color-specific paths from the graph based on a minimum score threshold.

This function removes paths that are specific to a given color and have a score below the specified threshold.

Arguments

• color - The color index to filter paths by.
• min_score - The minimum score threshold for paths to be retained.

Returns

A new instance of the graph with the specified paths removed.

Panics

This function will panic if the assemble_forward or assemble_backward methods fail to assemble a contig.

pub fn clean_branches(self, min_score: f32) -> Self

This function removes tips from the graph. A tip is defined as a k-mer with an in-degree or out-degree of 0.

Arguments

• max_tip_length - The maximum length of a tip to remove.
• min_score - The minimum score threshold for k-mers to be considered part of a tip.

Returns

The modified de Bruijn graph with tips removed.

Panics

• This line could panic if self.kmers.get(cn_kmer).unwrap().in_degree() returns None, meaning the in-degree of the k-mer is not available.

pub fn clean_tangles(self, color: usize, limit: usize, min_score: f32) -> Self

Clean tangles from the de Bruijn graph.

This function identifies and removes tangles from the de Bruijn graph based on a specified color, traversal limit, and minimum score threshold. A tangle is defined as a region in the graph where the in-degree and out-degree of a k-mer sum to 4 or more, indicating a complex branching structure.

Arguments

• color - The color to filter k-mers by.
• limit - The maximum number of nodes to traverse before giving up.
• min_score - The minimum score threshold for k-mers to be considered part of a tangle.

Returns

The modified de Bruijn graph with tangles removed.

Panics

• This line could panic if g.node_weight(node) returns None, meaning the node does not have an associated weight.
• This line could panic if crate::utils::canonicalize_kmer(current_kmer) encounters an unexpected input that it cannot process.
• This line could panic if crate::utils::canonicalize_kmer(kmer) encounters an unexpected input that it cannot process.

pub fn clean_hairballs(self) -> Self

pub fn clean_tips(self, limit: usize, min_score: f32) -> Self

This method will remove tips that have a score below the specified minimum score. A tip is defined as a region of the graph where there is only one path from the source to the sink.

Arguments

• limit - The maximum number of nodes to traverse before giving up.
• min_score - The minimum score for a tip to be kept.

Returns

A new LdBG with the specified tips removed.

Panics

If self.kmers.get(cn_kmer) returns None, the call to unwrap() will cause a panic.

pub fn clean_superbubbles(self, color: usize, min_score: f32) -> Self

This method will remove bubbles that have a score below the specified minimum score. A bubble is defined as a region of the graph where there are two paths from the same source to the same sink.

Arguments

• min_score - The minimum score for a bubble to be kept.

Returns

A new LdBG with the specified bubbles removed.

Panics

• When calling unwrap on the result of g.node_weight(*node). If the node does not exist in the graph, this will cause a panic.
• When calling unwrap_or on the result of self.scores.get(&cn_kmer). If the canonical k-mer is not found in the scores, it will return the default value 1.0 instead of panicking.

pub fn clean_contigs(self, min_contig_length: usize) -> Self

This method will remove contigs that are shorter than the specified minimum length and that are not connected to the rest of the graph.

Arguments

• min_contig_length - The minimum length of a contig to keep.

Returns

A new LdBG with the specified contigs removed.

Panics

This method will panic if the k-mer size is not set.

pub fn traverse_kmers_until_condition<F>( &self, start_kmer: &[u8], color: usize, limit: usize, stopping_condition: F, ) -> DiGraph<String, f32>

where F: Fn(&[u8], usize, &Self) -> bool,

pub fn traverse_kmers(&self, start_kmer: &[u8]) -> DiGraph<String, f32>

Traverse kmers starting from a given kmer and build a graph.

pub fn traverse_contigs(&self, start_kmer: &[u8]) -> DiGraph<String, f32>

The traverse_contigs function traverses kmers starting from a given kmer and builds a directed graph of contigs. It marks all kmers in the start contig as visited, then traverses forward and backward to build the graph, ensuring that each kmer is only visited once. The function returns the constructed graph.

Arguments

• start_kmer - A vector of bytes representing the start kmer.

Returns

A directed graph of contigs.

Panics

1. Unwrapping Option values:

   • If graph.node_weight(node) returns None, the call to unwrap() will panic.
   • If self.last_kmer(this_contig) or self.first_kmer(this_contig) returns None, the call to unwrap() will panic.
   • If visited.get(&canonical_kmer) returns None, the call to unwrap() will panic.

2. Indexing operations:

   • If contig.windows(self.kmer_size) is called with a kmer_size larger than the length of contig, it will panic.

pub fn traverse_all_kmers(&self) -> DiGraph<String, f32>

Traverse all kmers in the graph and return a new graph with all kmers merged. This function is useful for collapsing kmers that are separated by bubbles. The new graph will contain all kmers as nodes and edges between kmers as weights.

Returns

A new graph with all kmers merged.

Panics

Panics if the graph is not a directed graph.

pub fn traverse_all_contigs(&self) -> DiGraph<String, f32>

Traverse all contigs in the graph and return a new graph with all contigs merged. This function is useful for collapsing contigs that are separated by bubbles. The new graph will contain all contigs as nodes and edges between contigs as weights.

Returns

A new graph with all contigs merged.

Panics

Panics if the graph is not a directed graph.

Trait Implementations

impl Clone for LdBG

fn clone(&self) -> LdBG

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Debug for LdBG

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

Formats the value using the given formatter.