[ensembl-dev] Uncached variants + Offline mode

[Sebastian Ginzel]

Hi,

I am using VEP 80 and use the --offline and --cache option, which 
usually works fine, but now fails on one input file with the message:

Can't call method "db" on an undefined value at 
/path_to_lib/ensembl_80/lib/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm 
line 6360, <GEN0> line 190004

After digging into the code I found that this line is called when a 
variant is not available in the cache and VEP tries to retrieve the 
information from the database via through the get_variations_from_region 
function.

The line where the script fails is:
     if(defined($config->{vfa}->db)) {

Other functions such as 'have_pubmed' have an additional condition which 
prevents the error:
     if(defined($config->{vfa}) && defined($config->{vfa}->db)) {

I fixed the error for my VEP script by adding the 
"defined($config->{vfa})" condition. But now I am wondering if the error 
is intentional and if not which should be the default return value, if 
the script is running in offline mode.


Best wishes,
Sebastian Ginzel