Expand description
Pre-computed alignment-TSV aligner.
The user provides a TSV produced by an earlier diamond / blastp / mmseqs2
run (or a concatenation thereof — e.g. from the M4.5 batch-cluster mode).
The align method ignores the query_fasta and target_fasta
arguments and simply returns every parsed hit. Downstream layers
(find/transport) are responsible for grouping hits by qseqid and
applying bitscore / identity / coverage cutoffs.
Motivation: batch annotation of many genomes can amortize a single alignment run over a clustered reference set instead of re-running blast/diamond per genome — exactly the use case gapsmith is being built for.