Re: cct test issue: blast: Error: Unknown argument: "query_gencode"
Hi Aaron,
thanks a lot for your patches. Unfortunately the test suite does
not pass yet. I need more time to investigate (would be great if
others would beat me).
Kind regards
Andreas.
On Mon, Oct 19, 2020 at 04:19:55PM -0400, Aaron M. Ucko wrote:
> ucko@debian.org (Aaron M. Ucko) writes:
>
> > and should be able to supply a proper patch within the next day or two.
>
> Pushed. As noted in both my commit message and the patch's description,
> though:
>
> NB: The use of -v $settings{HITLIST_SIZE} in conjunction with the
> supplied $format_type value (7 or 9) results in the warning
>
> Warning: [tblastn] The parameter -num_descriptions is ignored for output formats > 4 . Use -max_target_seqs to control output
>
> Actually substituting -max_target_seqs would require bypassing the
> legacy blastall wrapper, which isn't entirely straightforward in this
> instance due to the need to convert a variable format string to modern
> options. (Also, this script technically only knows the path to
> blastall, though that shouldn't be a concern in practice on Debian.)
>
> --
> Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
> http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?amu@monk.mit.edu
>
>
--
http://fam-tille.de
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