[Bioperl-l] Re: problem with alignment test data & parsers

[Heikki Lehvaslaiho]

Done. The bug fix turned out to be a one-liner, but the effects of the
bug were visible in a number of test data files.  Some other bugs were
fixed in the process, too. 

All the code bugs are in branch 07, too, but no one will see the data
file bugs so I am tempted to leave them as they are until the next
major release. OK?

I touched the MSF format output to align the sequence names to left
and added empty lines between interleaved blocks for readability.
Could someone actually using MSF formats try it out with e.g. PILEUP.
I think it's ok, but it would be nice to be sure.

	-Heikki





Heikki Lehvaslaiho wrote:
> 
> Peter,
> 
> I was kind of hoping you'd jump up and say "Oh that bug! Trivial. Here
> is the fix." or something to that effect.
> 
> OK. I am fixing it...
> 
>         -Heikki
> 
> Peter Schattner wrote:
> >
> > Heikki
> >
> > I can't tell whether you are saying that you intend to investigate this
> > problem yourself (which would make me happy since my plate is quite full
> > at the moment. ) or whether you would like me to look into it - in which
> > case  do e-mail the script that's demonstrating the problem and I'll add
> > this to my "to do" list.
> >
> > Cheers
> >
> > Peter
> >
> > _______________________________________________
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> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> 
> --
> ______ _/      _/_____________________________________________________
>       _/      _/                      http://www.ebi.ac.uk/mutations/
>      _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
>     _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
>    _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
>   _/  _/  _/  Cambs. CB10 1SD, United Kingdom
>      _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
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-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________