Re: [Gmod-ajax] trouble with GFF3 parsing

[Mitch S. <mit...@be...>]

On 01/12/2010 02:29 AM, James Casbon wrote:
> Changing the sequence-region pragma to be a larger region fixes the problem:
> ##sequence-region CYP2C8 1 46725
>
> What is going on here?  Why do I not get all the features I declared?
>    

Thanks for providing such a nice clean test case.

This sounds like it might be related to an issue in 
Bio::DB::SeqFeature::Store::memory that was fixed last year after 
bioperl 1.6 was released.  The fix is in bioperl 1.6.1, though--what 
version are you using?

Also, JBrowse used to need the sequence-region line, but in the current 
code it's no longer required.  So one work-around if you can't upgrade 
bioperl would be to leave out the sequence-region line, I think.

Regards,
Mitch