Struct ExtenderConfig 

pub struct ExtenderConfig {
    pub kmer_size: usize,
    pub num_edge_kmers: usize,
    pub min_coverage: usize,
    pub branching_threshold: f64,
    pub max_n_ratio: f64,
    pub extension_step: usize,
    pub max_consecutive_failures: usize,
    pub max_extension_per_side: usize,
}

Configuration parameters for contig extension.

Strict vs Relaxed Mode

Strict mode (default) prioritises accuracy over length. Relaxed mode allows more aggressive extension for difficult cases.

Parameter	Strict	Relaxed	Description
min_coverage	3	2	Minimum read support
branching_threshold	0.1	0.2	Minor allele frequency for N
max_n_ratio	0.02	0.05	Maximum allowed N proportion

Fields

kmer_size: usize

K-mer size for extension (default: 21).

num_edge_kmers: usize

Number of edge k-mers to use from each end (default: 5).

min_coverage: usize

Minimum read coverage for consensus building (default: 2).

branching_threshold: f64

Branching threshold: if minor allele frequency >= this, mark as N (default: 0.2). Lower values = stricter, fewer Ns allowed.

max_n_ratio: f64

Maximum N ratio allowed in extension (default: 0.05). Extensions exceeding this are rejected.

extension_step: usize

Extension length per iteration in base pairs (default: 200).

max_consecutive_failures: usize

Maximum consecutive failures before stopping (default: 2).

max_extension_per_side: usize

Cap on total bp added to EACH contig end (default: 2000). Genus/species classification only uses ~max_flanking (1000 bp) of flanking, so extending a runaway (repetitive/high-coverage) contig for many more rounds is wasted work — and re-scanning all reads each round is the dominant runtime. Capping each side stops runaways early without affecting classification.

Trait Implementations

impl Clone for ExtenderConfig

fn clone(&self) -> ExtenderConfig

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Default for ExtenderConfig

fn default() -> Self

Returns the “default value” for a type.