From fe6aab1b6fb2e4b78f81f0bb0853bd951275ecce Mon Sep 17 00:00:00 2001
From: Nuno Agostinho <nuno@ebi.ac.uk>
Date: Thu, 30 Nov 2023 13:21:44 +0000
Subject: [PATCH 1/2] Fix incorrect variant end in web VEP

---
 modules/Bio/EnsEMBL/Variation/VariationFeature.pm | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/modules/Bio/EnsEMBL/Variation/VariationFeature.pm b/modules/Bio/EnsEMBL/Variation/VariationFeature.pm
index 6fcf268b1..73e4d1195 100755
--- a/modules/Bio/EnsEMBL/Variation/VariationFeature.pm
+++ b/modules/Bio/EnsEMBL/Variation/VariationFeature.pm
@@ -2340,6 +2340,8 @@ sub to_VCF_record {
     $non_acgt = 1 if $allele && $allele !~ /^[ACGTN\.]+$/;
   }
 
+  my $INFO = $self->end ? 'END='.$self->end : '.';
+
   # in/del/unbalanced
   if($non_acgt || scalar keys %allele_lengths > 1) {
 
@@ -2382,7 +2384,7 @@ sub to_VCF_record {
       $self->variation_name || '.',
       shift @alleles,
       (join ",", @alleles) || '.',
-      '.', '.', '.'
+      '.', '.', $INFO
     ];
 
   }
@@ -2395,7 +2397,7 @@ sub to_VCF_record {
       $self->variation_name || '.',
       shift @alleles,
       (join ",", @alleles) || '.',
-      '.', '.', '.'
+      '.', '.', $INFO
     ];
   }
 }

From da68ff64d04b455f7a7eaa14a5fbcdd98995d09c Mon Sep 17 00:00:00 2001
From: Nuno Agostinho <nuno@ebi.ac.uk>
Date: Fri, 1 Dec 2023 15:24:55 +0000
Subject: [PATCH 2/2] Fix unit tests

---
 modules/t/variationFeature.t | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/modules/t/variationFeature.t b/modules/t/variationFeature.t
index 137c4d16f..b75e91310 100755
--- a/modules/t/variationFeature.t
+++ b/modules/t/variationFeature.t
@@ -161,14 +161,14 @@ my $sr_start = $vf->seq_region_start;
 
 is_deeply(
   $vf->to_VCF_record(),
-  [$chr, $sr_start, $vname, 'A', 'T', '.', '.', '.'],
+  [$chr, $sr_start, $vname, 'A', 'T', '.', '.', "END=$end"],
   'to_VCF_record'
 );
 
 $vf->strand(-1);
 is_deeply(
   $vf->to_VCF_record(),
-  [$chr, $sr_start, $vname, 'T', 'A', '.', '.', '.'],
+  [$chr, $sr_start, $vname, 'T', 'A', '.', '.', "END=$end"],
   'to_VCF_record - rev strand'
 );
 $vf->strand($strand);
@@ -176,35 +176,35 @@ $vf->strand($strand);
 $vf->allele_string('A/G/T');
 is_deeply(
   $vf->to_VCF_record(),
-  [$chr, $sr_start, $vname, 'A', 'G,T', '.', '.', '.'],
+  [$chr, $sr_start, $vname, 'A', 'G,T', '.', '.', "END=$end"],
   'to_VCF_record - multiple alts'
 );
 
 $vf->allele_string('AG/CT');
 is_deeply(
   $vf->to_VCF_record(),
-  [$chr, $sr_start, $vname, 'AG', 'CT', '.', '.', '.'],
+  [$chr, $sr_start, $vname, 'AG', 'CT', '.', '.', "END=$end"],
   'to_VCF_record - balanced non-SNP'
 );
 
 $vf->allele_string('A/-');
 is_deeply(
   $vf->to_VCF_record(),
-  [$chr, $sr_start - 1, $vname, 'NA', 'N', '.', '.', '.'],
+  [$chr, $sr_start - 1, $vname, 'NA', 'N', '.', '.', "END=$end"],
   'to_VCF_record - deletion'
 );
 
 $vf->allele_string('-/A');
 is_deeply(
   $vf->to_VCF_record(),
-  [$chr, $sr_start - 1, $vname, 'N', 'NA', '.', '.', '.'],
+  [$chr, $sr_start - 1, $vname, 'N', 'NA', '.', '.', "END=$end"],
   'to_VCF_record - insertion'
 );
 
 $vf->allele_string('A/-/G');
 is_deeply(
   $vf->to_VCF_record(),
-  [$chr, $sr_start - 1, $vname, 'NA', 'N,NG', '.', '.', '.'],
+  [$chr, $sr_start - 1, $vname, 'NA', 'N,NG', '.', '.', "END=$end"],
   'to_VCF_record - mixed'
 );
 
@@ -213,21 +213,21 @@ $vf->allele_string('HGMD_MUTATION');
 $vf->{class_SO_term} = 'SNV';
 is_deeply(
   $vf->to_VCF_record(),
-  [$chr, $sr_start, $vname, 'N', 'N', '.', '.', '.'],
+  [$chr, $sr_start, $vname, 'N', 'N', '.', '.', "END=$end"],
   'to_VCF_record - unknown alleles SNV'
 );
 
 $vf->{class_SO_term} = 'insertion';
 is_deeply(
   $vf->to_VCF_record(),
-  [$chr, $sr_start - 1, $vname, 'N', '<INS>', '.', '.', '.'],
+  [$chr, $sr_start - 1, $vname, 'N', '<INS>', '.', '.', "END=$end"],
   'to_VCF_record - unknown alleles insertion'
 );
 
 $vf->{class_SO_term} = 'deletion';
 is_deeply(
   $vf->to_VCF_record(),
-  [$chr, $sr_start - 1, $vname, 'NN', 'N', '.', '.', '.'],
+  [$chr, $sr_start - 1, $vname, 'NN', 'N', '.', '.', "END=$end"],
   'to_VCF_record - unknown alleles deletion'
 );
 
@@ -242,14 +242,14 @@ my $fully_justified_allele_str = 'ACGTGGACG/ACG/ACGTGGACGTGGACG';
 $vf->allele_string($fully_justified_allele_str);
 is_deeply(
   $vf->to_VCF_record(),
-  [$chr, $sr_start, $vname, 'ACGTGGA', 'A,ACGTGGACGTGGA', '.', '.', '.'],
+  [$chr, $sr_start, $vname, 'ACGTGGA', 'A,ACGTGGACGTGGA', '.', '.', "END=$end"],
   'to_VCF_record - fully justified allele string clipped'
 );
 
 
 is_deeply(
   $vf->to_VCF_record(1),
-  [$chr, $sr_start, $vname, 'ACGTGGACG', 'ACG,ACGTGGACGTGGACG', '.', '.', '.'],
+  [$chr, $sr_start, $vname, 'ACGTGGACG', 'ACG,ACGTGGACGTGGACG', '.', '.', "END=$end"],
   'to_VCF_record - fully justified allele string  not clipped'
 );