[Bioperl-l] Bio::Tools::Run::Genewise and HMMs

[Keith James]

Hi,

The HMM functionality of this module is quite well hidden. I have made
it more explicit that it will accept a combination of profile HMM +
genomic sequence file / Bio::SeqI in addition to the documented
params. It now throws an exception if the hmmer switch is on and the
first argument is a Bio::SeqI.

I also clarified the docs a bit e.g. where it describes all the
supported genewise params as starting with a '-', only to have the
constructor silently discard anything of that form.

If there are no objections I'll check in the changes. They are fairly
minor (tests pass).

Keith

-- 

- Keith James <kdj at sanger.ac.uk> bioinformatics programming support -
- Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, UK -