[Bioperl-l] A lot of POD fixes in bioperl-live and bioperl run

[Heikki Lehvaslaiho]

I have recently done a lot fixes in the inline Plain Old Documenation
(POD) texts in bioperl-live and bioperl-run. Last ones (hopefully) were 
committed a few minutes ago. This has resulted quite large updates from SVN.

I wanted to apologize the inconvenience and to explain reasons for these small 
and pedantic fixes.

In contrast to perl, POD is sensitive to white space. This makes it relatively 
difficult to find and fix all minor errors in POD. I've now gone through the 
trouble of fixing all POD mistakes causing even the smallest warning in the 
podchecker.

The main reason for doing this was to reduce the the number of warnings
reported by the pod.pl bioperl maintenence tool. Too many minor warnings make 
it difficult to recognise more serious errors affecting the integrity and 
readability of POD documentation.

One example case is when a paragraph that was supposed to be 'in
verbatim', is in fact touching the previous paragraph and the pod
engine formats it and destroys the intended ascii graph or table.
The only way POD engine is able to report this is to warn about unescaped 
special characters.

    -Heikki
-- 
______ _/      _/_____________________________________________________
      _/      _/
     _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
    _/_/_/_/_/  Senior Scientist    skype: heikki_lehvaslaiho
   _/  _/  _/  SANBI, South African National Bioinformatics Institute
  _/  _/  _/  University of Western Cape, South Africa
     _/      Phone: +27 21 959 2096   FAX: +27 21 959 2512
___ _/_/_/_/_/________________________________________________________