[ensembl-dev] variation effect pipeline module bug?

Sharon Wei weix at cshl.edu
Tue Feb 7 17:16:18 GMT 2012

Hi Ensembl Variation Developers,

I think the following code in BaseVariationProcess needs an eval to 
catch the exceptions. Otherwise the pipeline will quit before gets its 
chance to load the reg_file.
This is ensembl-variation branch-ensembl-65 code base.

[weix at blade170 Pipeline]$ cvs diff BaseVariationProcess.pm
Index: BaseVariationProcess.pm
RCS file: 
retrieving revision 1.4
diff -r1.4 BaseVariationProcess.pm

<     my $dba = Bio::EnsEMBL::Registry->get_DBAdaptor($species, $group);
 >     my $dba;
 >     eval{$dba = Bio::EnsEMBL::Registry->get_DBAdaptor($species, 


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