[Bioperl-l] Why does Bio::DB::GFF::Feature::gff3_string swap start and stop coordinates??

[Mark Johnson]

On 5/8/07, Chris Fields <cjfields at uiuc.edu> wrote:
> I believe all seqfeature location coordinates are designed to have
> start < stop for consistency; in cases where the strand matters (CDS,
> gene, etc.) then the strand is set to 1 or -1.  When start > stop,
> the two are reversed and the strand is flipped; at least that's the
> way locations are set up in BioPerl.
>
> chris

    Oh yeah?  I always tend to ensure that (start < stop), regardless
of strand, when working with sequence features...the other day, I
caught Glimmer2 emitting a prediction on the plus strand with start >
stop.  I was going to work up a patch for the parser, but I wonder,
should I just force everything to start < stop?  Or only predictions
on the plus strand?  Should all the parsers for all the ab initio
predictors ensure they emit features with coordinates like this?