[Bioperl-l] bioperl-run parameter question

Sendu Bala bix at sendu.me.uk
Mon Dec 11 13:21:42 EST 2006

Chris Fields wrote:
> I am writing up a few bioperl-run modules and have a simple question,  
> though I don't know if anyone knows the answer.  I was curious as to  
> why parameters for most (all?) bioperl-run modules lack the '-'  
> preceding them.  This came up re: StandAloneBlast last week  
> (something Torsten fixed), but I noticed just about every bioperl-run  
> module uses the dashless parameters.

I didn't follow that particular thread, but from my experience there is 
a useful distinction between bioperl options using the - as normal for 
full consistency with core (eg. -verbose), whilst the options that 
belong to the program the run module is a wrapper for do not take 
dashes. Again, this seems consistent within the run package.

I'd suggest sticking to the current pattern.


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