[EMBOSS] Jemboss problems with fuzzpro and fuzznuc

Tim Carver tjc at sanger.ac.uk
Tue Sep 26 09:26:28 UTC 2006

Hi Neil

Thanks for your message. This is a known bug. As far as I understand the new
pattern qualifier has associated qualifiers -pmismatch (also pformat and
pname) which Jemboss does not know about (yet) as it just treats the pattern
as a string.


On 13/9/06 11:19, "Neil Brookes" <neil.brookes at cancer.org.uk> wrote:

> Hi,
> I think I have unearthed an issue with fuzzpro/fuzznuz and EMBOSS 4.0.0
> The old version in 3.0.0 had a '-mismatch' option. This has changed in
> version 4.0.0 to '-pmismatch'.
> The 'mismatch' integer element seems to have been removed from the
> fuzzpro/nuc ACD files.
> I'm not sure how/when Jemboss parses the ACD flies, but it doesn't seem
> to be allowing for the  new '-pmismatch' option, and users are unable to
> specify a value.
> any ideas ?
> cheers
> Neil

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