[gt-users] bug report on release 1.3.1?

[Sascha Steinbiss]

La Rota, Mauricio wrote:
> Hi Sacha,

Hey Mauricio,

> I updated to binary release 1.3.1 and a script that was working
> previously has now the following message on stderr (stdout still the
> same as with previous release):
> 
> " Assertion failed: (gnc && gn && gn->c_class == gnc), function
> gt_genome_node_cast, file
> /home/gremme/gth_remote_builddir/genometools-unstable/src/extended/genome_node.c,
> line 136. This is probably a bug, please report it."
> 
> I am using the 64-bit linux release.

This may -- or not -- be a side effect of the forced
GenomeNode->FeatureNode cast. Unfortunately I cannot say more without
the offending script and test GFF data. Can you provide that, please?

Does the script finish or does it stop in the middle?

> The python script is accessing a gff3 file via a GFF3InStream,
> loading introns with AddIntronsStream, then making a
> FeatureIndexMemory and loading into a FeatureStream.
> 
> Then it requests all seqids and the features in them
> (FeatureIndex.get_features_for_seqid(seqid))
> 
> Finally, for each feature returned, traverse the FeatureNode with
> FeatureNodeIteratorDirect().
> 
> If you need the whole script I can append it.

Please do. I also cross-post to the mailing list for further attention ;)

> -Mauricio

Sascha

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

Email:  steinbiss at zbh.uni-hamburg.de
URL:    http://www.zbh.uni-hamburg.de/steinbiss
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