From 3230acf108989a940688a70ac13d63b87da6f15b Mon Sep 17 00:00:00 2001
From: Syed Nakib Hossain <snhossain@ebi.ac.uk>
Date: Thu, 26 Sep 2024 12:33:34 +0100
Subject: [PATCH 1/2] Fix hgvsg for insertion

---
 modules/Bio/EnsEMBL/Variation/VariationFeature.pm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/Bio/EnsEMBL/Variation/VariationFeature.pm b/modules/Bio/EnsEMBL/Variation/VariationFeature.pm
index 4a7b84bdf..fea2dc754 100755
--- a/modules/Bio/EnsEMBL/Variation/VariationFeature.pm
+++ b/modules/Bio/EnsEMBL/Variation/VariationFeature.pm
@@ -1967,7 +1967,7 @@ sub hgvs_genomic {
     if ($is_multi_allelic) {
       # fix for multi-allelic variants
       my $old_chr_start = $chr_start;
-      ($ref_allele, $allele, $chr_start, $chr_end) = @{trim_sequences($original_ref_allele, $allele, $chr_start)};
+      ($ref_allele, $allele, $chr_start, $chr_end) = @{trim_sequences($original_ref_allele, $allele, $chr_start, $chr_end)};
       $allele ||= '-';
       $offset = $chr_start - $old_chr_start;
       $ref_start = $original_ref_start + $offset;

From e5165b7b35309f8ada3bbee6de87fcb760776d69 Mon Sep 17 00:00:00 2001
From: Syed Nakib Hossain <snhossain@ebi.ac.uk>
Date: Fri, 27 Sep 2024 11:52:02 +0100
Subject: [PATCH 2/2] Fix for reverse trim

---
 modules/Bio/EnsEMBL/Variation/VariationFeature.pm | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/modules/Bio/EnsEMBL/Variation/VariationFeature.pm b/modules/Bio/EnsEMBL/Variation/VariationFeature.pm
index fea2dc754..965583793 100755
--- a/modules/Bio/EnsEMBL/Variation/VariationFeature.pm
+++ b/modules/Bio/EnsEMBL/Variation/VariationFeature.pm
@@ -1929,7 +1929,7 @@ sub hgvs_genomic {
   my @all_alleles = split(/\//,$tr_vf->allele_string());
   my $ref_allele = shift @all_alleles;  ## remove reference allele - not useful for HGVS
   my $original_ref_allele = $ref_allele;
-  my $original_ref_start  = $ref_start;
+  my ($original_ref_start, $original_ref_end)  = ($ref_start, $ref_end);
 
   my $is_multi_allelic = scalar @all_alleles > 1;
   foreach my $original_allele ( @all_alleles ) {
@@ -1966,11 +1966,12 @@ sub hgvs_genomic {
 
     if ($is_multi_allelic) {
       # fix for multi-allelic variants
-      my $old_chr_start = $chr_start;
+      my ($old_chr_start, $old_chr_end) = ($chr_start, $chr_end);
       ($ref_allele, $allele, $chr_start, $chr_end) = @{trim_sequences($original_ref_allele, $allele, $chr_start, $chr_end)};
       $allele ||= '-';
-      $offset = $chr_start - $old_chr_start;
-      $ref_start = $original_ref_start + $offset;
+
+      $ref_start = $original_ref_start + ($chr_start - $old_chr_start);
+      $ref_end = $original_ref_end + ($chr_end - $old_chr_end);
       $ref_allele ||= '-';
     }
     my $var_class  =  $self->var_allele_class($ref_allele . '/' . $allele);