From 7569fabc4ea6cc3cc283cd4201a942722e4d6418 Mon Sep 17 00:00:00 2001
From: Laurent Gil <lgil@ebi.ac.uk>
Date: Thu, 12 Jul 2018 13:13:32 +0100
Subject: [PATCH 1/2] Fix an issue with the flag '--shift_hgvs'

---
 modules/Bio/EnsEMBL/VEP/BaseRunner.pm | 17 ++++++++-
 modules/Bio/EnsEMBL/VEP/Constants.pm  |  2 +-
 t/OutputFactory.t                     | 55 +++++++++++++++++++++++++++
 3 files changed, 71 insertions(+), 3 deletions(-)

diff --git a/modules/Bio/EnsEMBL/VEP/BaseRunner.pm b/modules/Bio/EnsEMBL/VEP/BaseRunner.pm
index 568afb2d5..dd29a0fea 100644
--- a/modules/Bio/EnsEMBL/VEP/BaseRunner.pm
+++ b/modules/Bio/EnsEMBL/VEP/BaseRunner.pm
@@ -423,6 +423,16 @@ sub _set_package_variables {
   $self->{_verbose_bak} = Bio::EnsEMBL::Utils::Exception::verbose();
   Bio::EnsEMBL::Utils::Exception::verbose(1999);
 
+  # HGVS shifting
+  # Variable used when DB connection
+  $self->{_shift_hgvs_db_bak} = $Bio::EnsEMBL::Variation::DBSQL::DBAdaptor::DEFAULT_SHIFT_HGVS_VARIANTS_3PRIME;
+  # Variable used when offline
+  $self->{_shift_hgvs_bak} = $Bio::EnsEMBL::Variation::DBSQL::TranscriptVariationAdaptor::DEFAULT_SHIFT_HGVS_VARIANTS_3PRIME;
+  if (defined($self->param('shift_hgvs')) && $self->param('shift_hgvs') =~ /(0|1)/ ) {
+    $Bio::EnsEMBL::Variation::DBSQL::DBAdaptor::DEFAULT_SHIFT_HGVS_VARIANTS_3PRIME = $self->param('shift_hgvs');
+    $Bio::EnsEMBL::Variation::DBSQL::TranscriptVariationAdaptor::DEFAULT_SHIFT_HGVS_VARIANTS_3PRIME = $self->param('shift_hgvs');
+  }
+
   # up/downstream distance
   if(my $distances = $self->param('distance')) {
     my ($u, $d) = @$distances;
@@ -439,7 +449,7 @@ sub _set_package_variables {
 
 =head2 _reset_package_variables
 
-  Example    : $runner->_set_package_variables();
+  Example    : $runner->_reset_package_variables();
   Description: Re-sets package variables altered by _set_package_variables
   Returntype : none
   Exceptions : none
@@ -457,8 +467,11 @@ sub _reset_package_variables {
 
   Bio::EnsEMBL::Utils::Exception::verbose($self->{_verbose_bak});
 
+  $Bio::EnsEMBL::Variation::DBSQL::TranscriptVariationAdaptor::DEFAULT_SHIFT_HGVS_VARIANTS_3PRIME = $self->{_shift_hgvs_bak} if defined($self->{_shift_hgvs_bak});
+  $Bio::EnsEMBL::Variation::DBSQL::DBAdaptor::DEFAULT_SHIFT_HGVS_VARIANTS_3PRIME = $self->{_shift_hgvs_db_bak} if defined($self->{_shift_hgvs_db_bak});
+
   $Bio::EnsEMBL::Variation::Utils::VariationEffect::UPSTREAM_DISTANCE = $self->{_upstream_bak} if defined($self->{_upstream_bak});
   $Bio::EnsEMBL::Variation::Utils::VariationEffect::DOWNSTREAM_DISTANCE = $self->{_downstream_bak} if defined($self->{_downstream_bak});
 }
 
-1;
\ No newline at end of file
+1;
diff --git a/modules/Bio/EnsEMBL/VEP/Constants.pm b/modules/Bio/EnsEMBL/VEP/Constants.pm
index ede006770..cb1b7848f 100644
--- a/modules/Bio/EnsEMBL/VEP/Constants.pm
+++ b/modules/Bio/EnsEMBL/VEP/Constants.pm
@@ -53,7 +53,7 @@ use warnings;
 use base qw(Exporter);
 
 our $VEP_VERSION     = 92;
-our $VEP_SUB_VERSION = 5;
+our $VEP_SUB_VERSION = 6;
 
 our @EXPORT_OK = qw(
   @FLAG_FIELDS
diff --git a/t/OutputFactory.t b/t/OutputFactory.t
index ada3c5c85..9efa50bc6 100644
--- a/t/OutputFactory.t
+++ b/t/OutputFactory.t
@@ -1903,12 +1903,63 @@ ok($tmp =~ /went wrong/, 'run_plugins - new fails message');
 open(STDERR, ">&SAVE") or die "Can't restore STDERR\n";
 
 
+## HGVS shifting
+################
+
+$of->{hgvs}  = 1;
+$of->{hgvsg} = 1;
+my $input_file_example = $test_cfg->create_input_file([qw(21 25592985 hgvsins A ATAAA . . .)]);
+
+# Shifting ON
+$ib = get_annotated_buffer({
+  input_file => $input_file_example,
+  shift_hgvs => 1
+},1);
+
+my $vfoa = $of->get_all_VariationFeatureOverlapAlleles($ib->buffer->[0])->[0];
+is_deeply(
+  $of->VariationFeatureOverlapAllele_to_output_hash($vfoa, {}, $ib->buffer->[0]),
+  {
+    "IMPACT" => "MODIFIER",
+    "Consequence" => [
+      "intron_variant"
+    ],
+    "HGVSg" => "21:g.25592986_25592989dup",
+    "Allele" => "TAAA"
+  },
+  'HGVS 3prime shifting - ON'
+);
+
+# Shifting OFF
+$ib = get_annotated_buffer({
+  input_file => $input_file_example,
+  shift_hgvs => 0
+},1);
+
+$vfoa = $of->get_all_VariationFeatureOverlapAlleles($ib->buffer->[0])->[0];
+is_deeply(
+  $of->VariationFeatureOverlapAllele_to_output_hash($vfoa, {}, $ib->buffer->[0]),
+  {
+    "IMPACT" => "MODIFIER",
+    "Consequence" => [
+      "intron_variant"
+    ],
+    "HGVSg" => "21:g.25592982_25592985dup",
+    "Allele" => "TAAA"
+  },
+  'HGVS 3prime shifting - OFF'
+);
+
+$of->{hgvs}  = 0;
+$of->{hgvsg} = 0;
+
 
 # done
 done_testing();
 
 sub get_annotated_buffer {
   my $tmp_cfg = shift;
+  my $set_package_variables = shift;
 
   my $runner = Bio::EnsEMBL::VEP::Runner->new({
     %$cfg_hash,
@@ -1917,6 +1968,10 @@ sub get_annotated_buffer {
   });
 
   $runner->init;
+  # Force setting the package variables as the 'run' method is not used here
+  if ($set_package_variables) {
+    $runner->_set_package_variables();
+  }
 
   my $ib = $runner->get_InputBuffer;
   $ib->next();

From cb76e2c421b00b4d65b789740f9a0e39cc2bf284 Mon Sep 17 00:00:00 2001
From: Laurent Gil <lgil@ebi.ac.uk>
Date: Tue, 17 Jul 2018 15:51:46 +0100
Subject: [PATCH 2/2] Fix test

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

diff --git a/t/OutputFactory.t b/t/OutputFactory.t
index 9efa50bc6..76590e50c 100644
--- a/t/OutputFactory.t
+++ b/t/OutputFactory.t
@@ -1916,7 +1916,7 @@ $ib = get_annotated_buffer({
   shift_hgvs => 1
 },1);
 
-my $vfoa = $of->get_all_VariationFeatureOverlapAlleles($ib->buffer->[0])->[0];
+$vfoa = $of->get_all_VariationFeatureOverlapAlleles($ib->buffer->[0])->[0];
 is_deeply(
   $of->VariationFeatureOverlapAllele_to_output_hash($vfoa, {}, $ib->buffer->[0]),
   {