identify_sequence_16s

cosmic_files::sequencing::rrs

Function identify_sequence_16s 

Source 
pub fn identify_sequence_16s(query: &[u8]) -> Vec<SeqIdHit>
Expand description

Align query against every Mycobacteriaceae 16S rRNA reference in REF_MYCO_RRS and return all hits sorted by identity (highest first).

§Algorithm

For each reference sequence (filtered to ≥ [MIN_RRS_REF_LEN] bp to avoid inflated scores from truncated entries):

  1. Strand: both forward and reverse-complement alignments are scored via [best_alignment]; the strand with the higher identity wins.
  2. Identity: gapless (shift-only) alignment — the shorter sequence is slid along the longer and the best-matching offset is chosen. Identity = matching bases / shorter length.
  3. SNP calls: for species that have an entry in RRS_RESISTANCE_SNPS (accession contains ':'), aminoglycoside-resistance SNPs are mapped from reference coordinates to query coordinates using the alignment offset.