[Bioperl-l] Help with Bio::SeqIO

Jay Hannah jay at jays.net
Mon Nov 5 11:54:13 EST 2007

On Nov 5, 2007, at 11:03 AM, Hilmar Lapp wrote:
> I agree that there should be a meaningful default that results in
> "doing the right thing" in most cases if the user doesn't intervene.
> I'm not sure I understand all the details, but it sounds sorting or
> not sorting should depend on the split location type unless the user
> overrides it by argument. That's what you're suggesting, right?

If someone knows why spliced_seq() should ever sort then I'm  
suggesting we add a test demonstrating a useful example of that.

If no one has a useful example of when you would want spliced_seq()  
to sort then I'm suggesting we remove the sorting altogether and  
nosort goes away.

I can provide/add many examples where sorting is bad. I do not know  
of a case where sorting is good.


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