Fix for custom VCF overlapping insertions

modules/Bio/EnsEMBL/VEP/AnnotationSource/File.pm

@@ -216,7 +216,12 @@ sub _record_overlaps_VF {
   my $type = $self->type();
 
   if($type eq 'overlap') {
-    return overlap($parser->get_start, $parser->get_end, $vf->{start}, $vf->{end});
+
+    # account for insertions in Ensembl world where s = e+1
+    my ($vs, $ve) = ($vf->{start}, $vf->{end});
+    ($vs, $ve) = ($ve, $vs) if $vs > $ve;
+
+    return overlap($parser->get_start, $parser->get_end, $vs, $ve);
   }
   elsif($type eq 'exact') {
     return $parser->get_start == $vf->{start} && $parser->get_end == $vf->{end};

modules/Bio/EnsEMBL/VEP/Constants.pm

@@ -20,7 +20,7 @@ use warnings;
 use base qw(Exporter);
 
 our $VEP_VERSION     = 87;
-our $VEP_SUB_VERSION = 17;
+our $VEP_SUB_VERSION = 18;
 
 our @EXPORT_OK = qw(
   @FLAG_FIELDS

t/AnnotationSource_File_VCF.t

@@ -80,8 +80,42 @@ SKIP: {
     'annotate_InputBuffer - overlap'
   );
 
+  # overlap with insertions
+  $ib = Bio::EnsEMBL::VEP::InputBuffer->new({
+    config => $cfg,
+    parser => Bio::EnsEMBL::VEP::Parser::VEP_input->new({
+      config => $cfg,
+      file => $test_cfg->create_input_file([qw(21 25585746 25585745 -/C)]),
+      valid_chromosomes => [21]
+    })
+  });
+  $ib->next;
+  $as->annotate_InputBuffer($ib);
+
+  is_deeply(
+    $ib->buffer->[0]->{_custom_annotations},
+    {
+      'test.vcf.gz' => [
+        {
+          'name' => 'ins2'
+        }
+      ]
+    },
+    'annotate_InputBuffer - overlap - insertion'
+  );
+
+
   # report_coords
-  delete($ib->buffer->[0]->{_custom_annotations});
+  $ib = Bio::EnsEMBL::VEP::InputBuffer->new({
+    config => $cfg,
+    parser => Bio::EnsEMBL::VEP::Parser::VEP_input->new({
+      config => $cfg,
+      file => $test_cfg->create_input_file([qw(21 25585733 25585733 C/T + rs142513484)]),
+      valid_chromosomes => [21]
+    })
+  });
+  $ib->next;
+
   $as->report_coords(1);
   $as->annotate_InputBuffer($ib);
   is_deeply(
@@ -96,6 +130,7 @@ SKIP: {
   $as->report_coords(0);
 
 
+
   # VCF info fields
   delete($ib->buffer->[0]->{_custom_annotations});
   $as->fields(['FOO', 'GOO']);