Module classify 

Hit classification — port of src/analyse_alignments.R:108–143.

Inputs:

• per-reaction reference-FASTA presence (did we have sequences to search?)
• raw alignment hits for this reaction (possibly many, possibly none)
• bitscore / identity / coverage / exception-EC cutoffs

Output: a HitStatus plus the best hit (largest bitscore) when present.

Structs

ClassifyOptions

Functions

classify_hits

Legacy one-shot classifier preserved for API callers that operate on a slice of (bitscore, pident) pairs. Not used by the runner.

classify_reaction

Classify a single reaction’s hits. Returns (status, is_exception, best_hit_index) — the index points back into hits so the caller can attach the winning hit’s fields to the reaction row.

ec_is_exception

Decide whether an EC belongs in the exception table. Handles both exact-match EC codes and EC/EC-style entries (enzyme/reaction column in dat/exception.tbl).