added diamond 2-pass #11
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Added a couple of functions in
humann/search/translated.pyto enable a "2-pass" approach to DIAMOND:--sensitivemode on all query sequences that were unaligned from the first passThe user can enable this mode versus the standard "1-pass" diamond alignment method by including
--two-passin the diamond options (eg.,--diamond-options "--two-pass --query-cover 80 --id 50 --max-target-seqs 1").The approach was recommended by Benjamin Buchfink, the developer of DIAMOND. I've used this approach with humann2 for quite a while now, and it has helped speed up the translated search part of humann. I don't want to continue "patching" newer versions of humann3 as they are released; hence this PR.