Struct ContigExtender 

pub struct ContigExtender { /* private fields */ }

K-mer based contig extender using paired-end reads.

Loads reads into memory for efficient repeated scanning. Supports both sequential and parallel extension strategies.

Implementations

impl ContigExtender

pub fn new(config: ExtenderConfig) -> Self

Creates a new contig extender with the given configuration.

pub fn load_reads_shared( r1_path: &Path, r2_path: &Path, ) -> Result<Arc<Vec<String>>>

Loads paired-end reads (R1 then R2) into a shared Arc<Vec<String>>, in parallel from both files. Reusable across extender instances.

pub fn load_reads(&mut self, r1_path: &Path, r2_path: &Path) -> Result<()>

Loads reads from the two FASTQs into this extender.

pub fn set_reads(&mut self, reads: Arc<Vec<String>>)

Reuses an already-loaded shared read set (see load_reads_shared).

pub fn extend_contigs( &self, contigs: &[FastaRecord], ) -> Result<Vec<ExtendedContig>>

Extends all contigs using hybrid parallel strategy.

Combines shared read scanning with parallel extension application. This is the recommended method for most use cases.

Algorithm

1. Build edge k-mer index for active contigs
2. Parallel read scanning (shared across all contigs)
3. Parallel extension application per contig
4. Repeat until no contigs can be extended

pub fn extend_all_hybrid( &self, contigs: &[FastaRecord], ) -> Result<Vec<ExtendedContig>>

Alias for extend_contigs() - hybrid parallel method.