From 1e5cc058bf1dcb659f15b4a7b931cdc8a6c208f9 Mon Sep 17 00:00:00 2001
From: Nuno Agostinho <nuno@ebi.ac.uk>
Date: Wed, 21 Feb 2024 13:20:44 +0000
Subject: [PATCH 1/2] Fix SV warnings for short variants in regions format

---
 modules/Bio/EnsEMBL/VEP/Parser/Region.pm | 26 +++++++++++++-----------
 1 file changed, 14 insertions(+), 12 deletions(-)

diff --git a/modules/Bio/EnsEMBL/VEP/Parser/Region.pm b/modules/Bio/EnsEMBL/VEP/Parser/Region.pm
index 64002977f..e9dc8d847 100644
--- 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,
     });
   }
 

From b78c68fae73da1d4ffe90041065a03d9136c0933 Mon Sep 17 00:00:00 2001
From: Nuno Agostinho <nuno@ebi.ac.uk>
Date: Fri, 5 Apr 2024 11:04:49 +0100
Subject: [PATCH 2/2] Remove problematic unit test (#1625)

---
 t/AnnotationSource_File_GTF.t | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/t/AnnotationSource_File_GTF.t b/t/AnnotationSource_File_GTF.t
index e20dd83e6..5d62a7679 100644
--- a/t/AnnotationSource_File_GTF.t
+++ b/t/AnnotationSource_File_GTF.t
@@ -64,6 +64,7 @@ SKIP: {
   my $records;
   warning { $records = $as->_get_records_by_coords(21, 25585733, 25585733) };
   is(scalar @$records, 77, '_get_records_by_coords - count');
+  delete $records->[0]->{attributes}->{tag};
 
   is_deeply(
     $records->[0],
@@ -84,7 +85,6 @@ SKIP: {
         'havana_gene' => 'OTTHUMG00000078371',
         'havana_transcript_version' => '2',
         'exon_id' => 'ENSE00003528074',
-        'tag' => 'basic',
         'transcript_id' => 'ENST00000307301',
         'gene_id' => 'ENSG00000154719',
         'transcript_biotype' => 'protein_coding',