Merge remote-tracking branch 'upstream/postreleasefix/112' into bug/f…

…ix-version-data

docker/Dockerfile

@@ -210,6 +210,18 @@ RUN curl -O "$PLUGIN_DEPS/requirements.txt" && \
     python2 -m pip install --no-cache-dir -r requirements.txt && \
     rm requirements.txt
 
+# Install GeneSplicer binary
+USER vep
+WORKDIR $VEP_DIR_PLUGINS
+RUN curl -O ftp://ftp.ccb.jhu.edu/pub/software/genesplicer/GeneSplicer.tar.gz && \
+    tar -xzf GeneSplicer.tar.gz && \
+    rm GeneSplicer.tar.gz && \
+    cd GeneSplicer/sources && \
+    make && \
+    mv genesplicer .. && \
+    rm -rf GeneSplicer/*/
+ENV PATH $VEP_DIR_PLUGINS/GeneSplicer:$PATH
+
 # Set working directory as symlink to $OPT/.vep (containing VEP cache and data)
 USER root
 RUN ln -s $OPT/.vep /data

modules/Bio/EnsEMBL/VEP/BaseVEP.pm

@@ -69,6 +69,9 @@ use Bio::EnsEMBL::VEP::Stats;
 use File::Spec;
 use FileHandle;
 
+use base qw(Exporter);
+
+our @EXPORT_OK = qw(_fetch_chr_synonyms);
 
 =head2 new
 
@@ -300,7 +303,7 @@ sub registry {
         my @db_names = map { $_->dbc->dbname } @{ $reg->get_all_DBAdaptors };
         my $hostname = ($user eq 'anonymous' ? '' : $user . '@') . "$host:$port";
         $self->warning_msg("No database names in $hostname contain version $db_version")
-          unless grep { /$db_version/ } @db_names;
+          if defined $db_version and not grep { /$db_version/ } @db_names;
       }
 
       eval { $reg->set_reconnect_when_lost() };

t/OutputFactory.t

@@ -1964,7 +1964,7 @@ is_deeply(
   'HGVS 3prime shifting - ON'
 );
 
-# Shifting OFF
+# Shifting OFF - the default look up is 5' direction
 $ib = get_annotated_buffer({
   input_file => $input_file_example,
   shift_hgvs => 0
@@ -1978,7 +1978,7 @@ is_deeply(
     "Consequence" => [
       "intron_variant"
     ],
-    "HGVSg" => "21:g.25592982_25592985dup",
+    "HGVSg" => "21:g.25592986_25592989dup",
     "Allele" => "TAAA"
   },
   'HGVS 3prime shifting - OFF'