Function align_to_ref 

pub fn align_to_ref(query: &[u8], reference: &[u8]) -> GappedAlignment

Align query (Sanger read) against reference (gene sequence) using semiglobal Smith-Waterman (free reference end-gaps, full query placed within reference).

Returns a GappedAlignment with gapped strings for display and SNP calling. Identity is computed as matches / reference_span × 100, which naturally penalises deletions in the query.