Module diamond 

Diamond aligner (protein-protein).

Command template mirrors src/gapseq_find.sh:592–600:

diamond makedb --in TARGET -d orgdb
diamond blastp -d orgdb.dmnd -q QUERY --threads N --out alignments.tsv
               --outfmt 6 qseqid pident evalue bitscore qcovhsp stitle sstart send
               --query-cover 75

By default we pass --more-sensitive, matching gapseq’s default aliArgs for diamond.

Structs

DiamondAligner