[Bioperl-l] BEDTools.pm update

Chris Fields cjfields at illinois.edu
Thu Mar 31 20:43:33 EDT 2011


I would say push away, I don't think this will be a problem. 

chris

On Mar 31, 2011, at 6:24 PM, Dan Kortschak wrote:

> 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
> 
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