[Bioperl-l] BEDTools.pm update

[Dan Kortschak]

Hi All,

I have completed a revision of the BEDTools module that makes use of the
v2.10.1 BEDTools additions, including the ability to read GFF and VCF
file formats.

Because of the interactions between CommandExts/Config and the way
BEDTools executables can receive input files, I have had to change the
parameter names for a number of the filespecs from -bed* to -bvg* (for
BED/GFF/VCF). The alternative, though possible was much more involved
for little gain in my view.

This change will break BEDTools.pm-using scripts that use the -bed[12]?
filespecs (except for those wrapping genomeCoverageBed which cannot read
bgv and so which see no change).

I just wanted to get an idea if this is going to be a significant
problem for people before I push the changes to bioperl-run.

cheers
Dan