Re: cct test issue: blast: Error: Unknown argument: "query_gencode"
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
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