[Bioperl-l] One hell of a bug hunt!

[Elia Stupka]

Hello folks, 

we went through one hell of a bug hunt and spotted a bug in bioperl and a
thing to change in ensembl:

The bug in bioperl is that the method overlap_extent in Bio::RangeI was
calling the old style union and intersection methods, so it wouldn't work
(i.e. expecting two values rather than an object back)

Now when we tried to test those methods on Bio::EnsEMBL::SeqFeatures we
couldn't because the new method there was old old style. So we changed
that to new style, i.e. my ($self) = $caller->SUPER::new(@args);

However, the inheritance tree in Bio::EnsEMBL::SeqFeature was the wrong
way arounf, first SeqFeatureI, then Bio::RootI, so doing the SUPER calling
new wasn't working...

...now it's all solved...

I have committed the bug fix to bioperl, are ensembl people ok for me
committing new style Ensembl SeqFeatures with the new new method?

Elia

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