fix for VFs that dont have a proper slice from pileup input

Ensembl · Dec 16, 2014 · 8531c21 · 8531c21
1 parent 1b2af67
commit 8531c21
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm b/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm
@@ -950,7 +950,7 @@ sub convert_to_vcf {
             # default to N in case we can't get it
             my $prev_base = 'N';
 
-            if(defined($vf->slice)) {
+            if(defined($vf->slice) && UNIVERSAL::isa($vf->slice,'can')) {
                 my $slice = $vf->slice->sub_Slice($vf->start - 1, $vf->start - 1);
                 $prev_base = $slice->seq if defined($slice);
             }