Merge pull request #1618 from nuno-agostinho/fix/REST-SV-warnings

Fix SV warnings for short variants in `region` format
Ensembl · Mar 4, 2024 · e10125c · e10125c
2 parents 6f0ecfc + 1e5cc05
commit e10125c
Showing 1 changed file with 14 additions and 12 deletions.
diff --git a/modules/Bio/EnsEMBL/VEP/Parser/Region.pm b/modules/Bio/EnsEMBL/VEP/Parser/Region.pm
@@ -184,33 +184,35 @@ sub create_VariationFeatures {
 
   my $vf;
 
-  # sv?
-  my $so_term = $self->get_SO_term($allele);
-  if(defined($so_term)) {
-    $vf = Bio::EnsEMBL::Variation::StructuralVariationFeature->new_fast({
+  # normal vf
+  if ($allele =~ /^[ACGTN-]+$/) {
+    my $ref = ('N' x (($end - $start) + 1)) || '-';
+
+    $vf = Bio::EnsEMBL::Variation::VariationFeature->new_fast({
       start          => $start,
       end            => $end,
+      allele_string  => $ref.'/'.$allele,
       strand         => $strand,
-      adaptor        => $self->get_adaptor('variation', 'StructuralVariationFeature'),
+      map_weight     => 1,
+      adaptor        => $self->get_adaptor('variation', 'VariationFeature'),
       variation_name => $region,
       chr            => $chr,
-      class_SO_term  => $so_term,
     });
   }
 
-  # normal vf
+  # sv
   else {
-    my $ref = ('N' x (($end - $start) + 1)) || '-';
+    my $so_term = $self->get_SO_term($allele);
+    return [] unless defined $so_term;
 
-    $vf = Bio::EnsEMBL::Variation::VariationFeature->new_fast({
+    $vf = Bio::EnsEMBL::Variation::StructuralVariationFeature->new_fast({
       start          => $start,
       end            => $end,
-      allele_string  => $ref.'/'.$allele,
       strand         => $strand,
-      map_weight     => 1,
-      adaptor        => $self->get_adaptor('variation', 'VariationFeature'),
+      adaptor        => $self->get_adaptor('variation', 'StructuralVariationFeature'),
       variation_name => $region,
       chr            => $chr,
+      class_SO_term  => $so_term,
     });
   }