[mira_talk] Re: RE reading fasta files

On Thursday 02 April 2009 Jan Paces wrote:
> Jorge.DUARTE@xxxxxxxxxxxx wrote:
> > I had a similar problem myself, and changing the default value for
> > option -AS:bdq solved it.
> > SANGER_SETTINGS -AS:bdq=40
> Thanks, works now.

Thanks Jorge for answering as I had been on a business trip without much 
internet access.

The above problem has popped a number of times and I'm struggling with myself 
on how to configure MIRA best so that people get what they expect ...

Problem is: normally, an assembler should have qualities given to work well. 
On the other hand, some data sets in hybrid assemblies simply don't have any 
data which can be given.

So, if a user now gives MIRA data with qualities (as should normally be the 
case), but the clipping is weak or non-existent, then all hell breaks loose if 
there is bad quality remaining in the data and one gets sub-optimal assemblies 
(in the best case) or simply a whole lot of small contigs (leading to "MIRA 
does not perform!" mails *sigh*).

In earlier times MIRA insisted to have qualities or being explicitly told via 
parameters that there would be no qualities for a given data set. Which led to 
a number of questions like "I don't have qualities, how can I still use MIRA?" 
when users didn't find the correct parameter (and the number of these has grown 
since).

So, at the moment, I settled for "if there are no qualities, the user has to 
know what he's doing and sets flags accordingly.

I'd be happy to hear suggestions for a better handling though. I personally am 
a big fan of "if it does not meet the expectations of the program, fail".

Regards,
  Bastien


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