Missing options in `--orient`

[mirand863]

Hi, I am trying to replace --usearch_global with --orient for a third-party package that depends on vsearch, but --orient does not have some parameters that exist with --usearch_global, i.e.:

--id
--maxaccepts
--strand
--query_cov
--userfields
--leftjust

Can you please add these parameters for --orient? Or is there a reason why these parameters are not available?

[torognes]

Hi, --usearch_global and --orient are quite different commands and it does not make much sense to include these options for --orient. I do not understand why you would replace these commands. Usearch does not have these options for orient either.

[torognes]

I see now that this is related to an issue in RESCRIPt (https://github.com/bokulich-lab/RESCRIPt/issues/146).

I guess you would need to change a bit more than just the command. Some of the arguments (e.g. id, maxaccepts, query_cov) can probably just be dropped. What to do with the others depend on the context and how they are used.

[mirand863]

Hi, --usearch_global and --orient are quite different commands and it does not make much sense to include these options for --orient. I do not understand why you would replace these commands. Usearch does not have these options for orient either.

Thank you very much for the fast response!

You are absolutely right. These parameters do not exist in usearch and some can also be removed without any implication. Hence, I will close this issue.