[ensembl-dev] Bug in VEP

[Nathan Johnson]

Hi Duarte

That is caused by a bad logical test which I have corrected in the patch below(updated on the head). However, this is indicative of another problem as the reason it is dying is due to the Slice argument being passed to the method in question, being undefined.

...over to Will

Thanks

Nath


Index: BaseFeatureAdaptor.pm
===================================================================
RCS file: /nfs/ensembl/cvsroot/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/DBSQL/BaseFeatureAdaptor.pm,v
retrieving revision 1.65
diff -u -r1.65 BaseFeatureAdaptor.pm
--- BaseFeatureAdaptor.pm       16 Jul 2012 12:10:40 -0000      1.65
+++ BaseFeatureAdaptor.pm       14 Sep 2012 11:52:48 -0000
@@ -5,7 +5,7 @@
 
 =head1 LICENSE
 
-  Copyright (c) 1999-2011 The European Bioinformatics Institute and
+  Copyright (c) 1999-2012 The European Bioinformatics Institute and
   Genome Research Limited.  All rights reserved.
 
   This software is distributed under a modified Apache license.
@@ -132,8 +132,8 @@
 
   my @result;
 
-  if(!ref($slice) || !$slice->isa("Bio::EnsEMBL::Slice")) {
-    throw("Bio::EnsEMBL::Slice argument expected.");
+  if(! (ref($slice) && $slice->isa('Bio::EnsEMBL::Slice')) {
+    throw('Bio::EnsEMBL::Slice argument expected.');
   }
 
   $constraint ||= '';





On 14 Sep 2012, at 12:44, Duarte Molha wrote:

> Dear developers,
>  
> I am sorry to bother you again (especially Will J ) but in testing the VEP26, I got a crash using the command:
>  
> perl variant_effect_predictor.pl -i input_variants.vcf.gz -o output.ann --config vep.ini
>  
> Here is the error output:
>  
> 2012-09-14 12:29:30 - Reading regulatory data from cache and/or database
> [==================================>                                                                                                                                 ]   [ 22% ]
> Can't call method "isa" on unblessed reference at /NGS_Tools/bin/VEP_26_testing/Bio/EnsEMBL/Funcgen/DBSQL/BaseFeatureAdaptor.pm line 135, <GEN0> line 28406.
>  
> In attachment is the config file I use.
>  
> Best regards,
>  
> Duarte Molha
>  
> <vep.ini>_______________________________________________
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Nathan Johnson
Senior Scientific Programmer
Ensembl Regulation
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD

http://www.ensembl.info/
http://twitter.com/#!/ensembl






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