[Bioperl-l] Should Bio::Tools::BPlite be deprecated?

Sendu Bala bix at sendu.me.uk
Mon Oct 16 13:21:58 EDT 2006


Hilmar Lapp wrote:
> The problem is it is not maintained, and there are outstanding been bug 
> reports.
> 
> If you un-deprecate it, then we need a response to people who come 
> across problems with it when using it. Either you change the POD to say 
> exactly who and when one should use it (or rather not) and point to the 
> fact that it is unsupported for all other cases.
> 
> Or what would you suggest?

I'm not sure.

Does Bio::Index::Blast even work correctly? Does it suffer from whatever 
bugs Bio::Tools::BPlite has? Is Bio::Index::Blast maintained? Should 
that be deprecated as well?

Ideally I'd like to see Bio::Index::Blast updated to use Bio::SearchIO 
and then Bio::Tools::BPlite can be deprecated. But like I say, it didn't 
seem trivial (or even appropriate).

Ultimately I just wanted to solve the warnings in the test suite. 
Thoughts, Chris?


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