orient-seqs currently uses vsearch --usearch_global to search a database, then reorient.
This was always a short-term solution, as vsearch was previously pinned across many Q2 plugins so we could not use the more recent vsearch --orient option. But that pin is now gone.
We should update to use orient. Advantages:
cut down on current code in orient-seqs
probably more efficient
can operate on both FASTA and FASTQ data
The disadvantage is that some of the options available in --usearch_global might not be available in orient.
orient-seqscurrently usesvsearch --usearch_globalto search a database, then reorient.This was always a short-term solution, as vsearch was previously pinned across many Q2 plugins so we could not use the more recent
vsearch --orientoption. But that pin is now gone.We should update to use
orient. Advantages:orient-seqsThe disadvantage is that some of the options available in
--usearch_globalmight not be available inorient.