Merge pull request #546 from aparton/bugfix/phenofix97

Fix for 97 rest tests
Ensembl · Jul 26, 2019 · 8bf4349 · 8bf4349
2 parents 306e3f4 + f8b4044
commit 8bf4349
Showing 1 changed file with 4 additions and 4 deletions.
diff --git a/modules/Bio/EnsEMBL/VEP/AnnotationSource/Database/Variation.pm b/modules/Bio/EnsEMBL/VEP/AnnotationSource/Database/Variation.pm
@@ -150,6 +150,10 @@ sub get_features_by_regions_uncached {
       ($region_start * $cache_region_size) + 1,
       ($region_start + 1) * $cache_region_size
     );
+
+    my $adaptor = $self->get_adaptor('variation', 'phenotypefeature');
+    my $source_id = $self->clinvar_source_id_cache;
+    my $attribs = $adaptor->get_clinsig_alleles_by_location($chr_is_seq_region ? $chr : $sr_cache->{$chr}, $s, $e, $source_id) if defined($adaptor) && defined($source_id);
 
     # no seq_region_id?
     next unless $sr_cache->{$chr} || $chr_is_seq_region;
@@ -178,10 +182,6 @@ sub get_features_by_regions_uncached {
     my ($var_id, %vars_by_id);
     $sth->bind_col(1, \$var_id);
     $sth->bind_col($_+2, \$v{$VAR_CACHE_COLS[$_]}) for (0..$#VAR_CACHE_COLS);
-
-    my $adaptor = $self->get_adaptor('variation', 'phenotypefeature');
-    my $source_id = $self->clinvar_source_id_cache;
-    my $attribs = $adaptor->get_clinsig_alleles_by_location($chr_is_seq_region ? $chr : $sr_cache->{$chr}, $s, $e, $source_id) if defined($adaptor) && defined($source_id);
 
     my @vars;
     while($sth->fetch) {