Struct GenusClassifier 

pub struct GenusClassifier { /* private fields */ }

Minimap2-based genus classifier using flanking sequence alignment.

Classifies source genus by aligning extracted flanking sequences against reference flanking sequences in the database.

Implementations

impl GenusClassifier

pub fn new<P: AsRef<Path>>( db_path: P, minimap2_path: &str, min_identity: f64, min_align_len: usize, max_flanking: usize, plasmid_contigs_path: Option<&Path>, species_identity: f64, species_map_path: Option<&Path>, plasmid_hi: f64, plasmid_lo: f64, ) -> Result<Self>

Creates a new genus classifier.

Arguments

• db_path - Path to flanking database (.fdb)
• minimap2_path - Path to minimap2 executable
• min_identity - Minimum alignment identity (0-1)
• min_align_len - Minimum alignment length in bp
• max_flanking - Maximum flanking length to extract

pub fn classify_batch( &mut self, positions: &[ArgPosition], threads: usize, ) -> Result<Vec<GenusResult>>

Classifies genus for multiple ARG positions.

Processes each position sequentially to avoid temporary file conflicts.

pub fn classify_single( &mut self, pos: &ArgPosition, threads: usize, ) -> Result<GenusResult>

Classifies genus for a single ARG position.

Algorithm

1. Extract flanking sequences from contig
2. Write query and reference FASTA files
3. Run minimap2 alignment
4. Parse PAF and score genus candidates
5. Return top genus with confidence metrics