[mira_talk] Re: How does Mira determine quality scores?

On Donnerstag 30 Juli 2009 Davide Sassera wrote:
> [...]
> I would love to try a version with this algorithm, so for once I can
> help instead of just using the software.
> I cannot guarantee on how fast I will be able to give you some results
> as I'm very busy, but I'll do my best.

http://www.chevreux.org/tmp/mira_3rc1b1_dev_linux-gnu_x86_64_static.tar.bz2

I'm putting some last finishing touches on version 3 in the next two weeks, if 
I hear back from you before release that the base calling gets better I'll 
include that change :-)

> Reasoning from another point of view, couldn't Mira give quality score
> to gaps also?  it could either be a fixed number or something like the
> mean value of the two bases around the gap?
> maybe this does not make sense, what do you think?

Ummm ... MIRA already does exactly this?! At least it's intended to do so and 
from I what I can see after a quick check in the unpadded fasta of a test 
project, it does.

Where are you missing the quality value for the gap?

Regards,
  Bastien

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