[gt-users] range assertion failed

[Sascha Steinbiss]

On 01/13/2010 07:12 PM, Brent Pedersen wrote:
> hi, i have a long-running python script, and after about an hour, it
> err's out with:
> 
> Assertion failed: (range->start <= range->end), function
> gt_range_length, file src/core/range.c, line 186.
> This is probably a bug, please report it.
> 
> i've added python assertions everywhere to make sure it's only getting
> start < end, all of my gff input validates
> (through gt gff3validator), and i'm not creating any new features. and
> this happens much after i've created a FeatureIndexMemory
> and done add_gff3file(), so it's definitely not on the initial
> creation. and anywhere i'm doing a range query, i've added a test to
> make
> sure the start < stop? could it be an overflow error in ctypes or c--
> (actually, i'll add a check for that now...)

What exactly do you plan to do? Just so I do not try the same thing
redundantly...

> any other ideas on how i can track this down?

This should be enough to make sure it's not something on the Python
side. Can you provide a minimal example piece of code that shows the
problem? Can it be reproduced across multiple runs?

If you can give me some sample code, I will try to debug the C code, if
the problem is on the C side.

> thanks,
> -brent

No problem,
Sascha

-- 
Sascha Steinbiss
Center for Bioinformatics
University of Hamburg
Bundesstr. 43
20146 Hamburg
Germany

Email:  steinbiss at zbh.uni-hamburg.de
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