[Bioperl-l] Bug? Features with similar ranges, different IDs are considered overlapping

Dave Messina David.Messina at sbc.su.se
Tue Aug 17 05:06:05 EDT 2010

> Good point; it's probably the context the methods are used that matters.  So, maybe just a document clarification?

That's always good, but it really doesn't solve the issue you're describing.

I mean, who would expect to get overlaps for features on different chromosomes?

To me, that's a clear violation of reasonable user expectations. You shouldn't have to read the docs about something like that.

So what's the solution for these duelling use cases? I haven't thought about it much, but a first approximation might be to add a -genomic boolean flag that, when true, would do the right thing and check the ID when doing overlaps or other positional comparisons.

(Maybe -genomic is too obscure. Maybe it should be -same_id_for_overlaps or something like that.)

And maybe having to know to set a flag is effectively the same thing as having to read the docs to understand SeqFeature's overlap behavior.

What do the rest of you out there think?


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