[mira_talk] Re: mira floating point exception

On Friday 24 April 2009 Andreas Petzold wrote:
> I may have found another bug in version 2.9.43 ? I want to assemble 1700
> Sanger ESTs and mira tells after clipping me that all sequences have only 0
> good bases and then crashes with a floating point exception (division by
> zero ?).

Looks like it. I think I know where it happened and have made a fix.

> The ESTs are in a fasta file (no qualities available). I start mira with:
> mira -project=clap -fasta=clap_in.fasta -job=denovo,est,normal,sanger
> -notraceinfo
>
> If I deactivate clipping with '-noclipping' then all works fine. Also if I
> use 2.9.39 ...
>
> Have I missed something ?

Not really, but I need to really handle missing qualities differently. Too many 
mails regarding this subject show me that most users are unaware that parts of 
their data could be completely clipped away. I think I'll make a strict rule 
which stops assembly if reads are missing qualities that can be overridden by 
a parameter ... but with the stern warning that users are then taking risks.

Regards,
  Bastien


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