Merge pull request #813 from at7/bugfix100/minimal_intergenic

Bugfix100/minimal intergenic
Ensembl · Jul 29, 2020 · 10932fa · 10932fa
2 parents 4be118e + 3e813d3
commit 10932fa
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Showing 3 changed files with 14 additions and 4 deletions.
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     = 100;
-our $VEP_SUB_VERSION = 3;
+our $VEP_SUB_VERSION = 4;
 
 our @EXPORT_OK = qw(
   @FLAG_FIELDS

diff --git a/modules/Bio/EnsEMBL/VEP/OutputFactory.pm b/modules/Bio/EnsEMBL/VEP/OutputFactory.pm
@@ -2125,12 +2125,15 @@ sub rejoin_variants_in_InputBuffer {
       # there is only one, and no reference feature to key on
       # means we have to copy over alleles manually
       if(my $iv = $vf->{intergenic_variation}) {
-
+        my $bfvo = $original->{intergenic_variation};
         $iv->base_variation_feature($original);
 
         if(my $oiv = $original->{intergenic_variation}) {
-            push @{$oiv->{alt_alleles}}, @{$iv->{alt_alleles}};
-            $oiv->{_alleles_by_seq}->{$_->variation_feature_seq} = $_ for @{$oiv->{alt_alleles}};
+          foreach my $alt (@{$iv->{alt_alleles}}) {
+            $alt->base_variation_feature_overlap($bfvo);
+            push @{$oiv->{alt_alleles}}, $alt;
+          }
+          $oiv->{_alleles_by_seq}->{$_->variation_feature_seq} = $_ for @{$oiv->{alt_alleles}};
         }
 
         # this probably won't happen, but can't hurt to cover all bases

diff --git a/t/OutputFactory.t b/t/OutputFactory.t
@@ -1800,6 +1800,13 @@ $of->rejoin_variants_in_InputBuffer($ib);
 
 is(scalar @{$ib->buffer}, 2, 'minimal - intergenic - rejoined count');
 
+foreach my $vf (@{$ib->buffer}) {
+  my $vfoas = $of->get_all_VariationFeatureOverlapAlleles($vf);
+  foreach my $vfoa (@{$vfoas}) {
+    is(ref($vfoa->base_variation_feature_overlap), 'Bio::EnsEMBL::Variation::IntergenicVariation', 'base_variation_feature_overlap is set after rejoin');
+  }
+}
+
 is_deeply(
   [map {$_->display_consequence} @{$ib->buffer}],
   ['intergenic_variant', 'intergenic_variant'],