Merge pull request #312 from aparton/feature/xrefsymbol

Feature/xrefsymbol
Ensembl · Oct 30, 2018 · 9560a06 · 9560a06
2 parents ce3d340 + 322124e
commit 9560a06
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/modules/Bio/EnsEMBL/VEP/AnnotationSource/Database/Transcript.pm b/modules/Bio/EnsEMBL/VEP/AnnotationSource/Database/Transcript.pm
@@ -201,7 +201,7 @@ sub get_features_by_regions_uncached {
   my $pfa = $self->get_adaptor('variation', 'PhenotypeFeature');
 
   my $cache_region_size = $self->{cache_region_size};
-
+  
   foreach my $region(@{$regions}) {
     my ($c, $region_start) = @$region;
 
@@ -242,7 +242,7 @@ sub get_features_by_regions_uncached {
         my $pfs = $pfa->fetch_all_by_Gene($gene);
         $gene_has_phenotype = $pfs && scalar @$pfs;
       }
-
+      
       foreach my $tr(@{$gene->get_all_Transcripts}) {
         next unless $self->filter_transcript($tr);
         next if $tr->analysis() && $tr->analysis()->logic_name() eq 'estgene';
@@ -542,7 +542,7 @@ sub prefetch_gene_ids {
     {
       my $xref_obj = $tr->{_gene}->display_xref;
       $tr->get_Gene()->stable_id($entries[0]->{primary_id});
-      $tr->{_gene_symbol}  = $xref_obj ? $xref_obj->display_id : $entries[0]->{primary_id};
+      $tr->{_gene_symbol}  = $xref_obj ? $xref_obj->display_id : $entries[0]->{display_id};
       $tr->{_gene_symbol_source} = $entries[0]->{dbname};
       $tr->{_gene_symbol_id} = $entries[0]->{primary_id};
       $tr->{_gene_hgnc_id} = $entries[0]->{primary_id} if $entries[0]->{dbname} eq 'HGNC';

diff --git a/modules/Bio/EnsEMBL/VEP/Constants.pm b/modules/Bio/EnsEMBL/VEP/Constants.pm
@@ -53,7 +53,7 @@ use warnings;
 use base qw(Exporter);
 
 our $VEP_VERSION     = 94;
-our $VEP_SUB_VERSION = 4;
+our $VEP_SUB_VERSION = 5;
 
 our @EXPORT_OK = qw(
   @FLAG_FIELDS