[BioRuby] BioRuby and log4r

[Pjotr Prins]

If anyone is interested, the bio-logger plugin is fully functional (I
am using it in the GFF3 plugin):

This is a plugin for nailing down problems with big data parsers,
common in bioinformatics, and sane handling of errors and exceptions
in different situations.

In Bioinformatics the following is a common scenario when dealing with
parsers: Large data files sometimes contain errors. As a user you want
to continue and hope for the best (logging the error). As a developer
you want to see how you can fix the problem. Waiting for a full run
and checking the logs is tedious. The logger can be helpful here, and
avoids sticking temporary solutions in code. Read on...

  https://github.com/pjotrp/bioruby-logger-plugin

I think we should use this throughout BioRuby to get consistent error
handling and logging. No more $stderr.print statements.

Pj.