[Bioperl-l] Re: bioperl-run Codeml.pm fix_blength

[Jason Stajich]

sure - fix away.

I think it was a bit misguided on my part to think we could really  
capture all the valid values in this init hash - possibly could  
remove the whole system of checking and just establish default  
values.  Anyways, feel free to check that it.

-jason
On Jul 12, 2005, at 11:19 AM, Albert Vilella wrote:

> Hi,
>
> I noticed that the valid values for fix_blength in Codeml.pm do not
> include option "fix_blength 1: initial",
>
> I agreed, I would add it myself in cvs:
>
> bioperl-run/Bio/Tools/Run/Phylo/PAML/Codeml.pm
>
>              'fix_blength'   => [0,-1,2],
> change to:
>              'fix_blength'   => [0,-1,1,2],
>
> Jason?
>
> Bests,
>
>     Albert.
>
>

--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/