added tests for assembly exceptions on patches

was not tested by PAR, as patches are stored on scaffolds, ie a different coord system

modules/t/assemblyExceptionFeature.t

@@ -43,10 +43,19 @@ is(ref($aef->adaptor), 'Bio::EnsEMBL::DBSQL::AssemblyExceptionFeatureAdaptor', "
 # fetch all
 my $chr_slice = $dba->get_SliceAdaptor->fetch_by_region('chromosome', 
                                                         '20_HAP1');
+my $ref_slice = $dba->get_SliceAdaptor->fetch_by_region('chromosome', 'X');
+my $patch_slice = $dba->get_SliceAdaptor->fetch_by_region('supercontig', 'HG480_HG481_PATCH');
+
 my @features = @{$aefa->fetch_all_by_Slice($chr_slice)};
 
 is(@features, 1, "Fetched one assembly exception feature for 20_HAP1");
 
+my @ref_features = @{$aefa->fetch_all_by_Slice($ref_slice)};
+is(@ref_features, 1, "Fetched one assembly exception features for chromosome X");
+
+my @patch_features = @{ $aefa->fetch_all_by_Slice($patch_slice) };
+is(@patch_features, 1, "Fetched one assembly exception for HG480_HG481_PATCH");
+
 foreach my $f (@features) {
   debug( "Feature: " . $f->slice->seq_region_name . " " . 
          $f->start . " " . $f->end . " " . $f->type);
@@ -55,6 +64,22 @@ foreach my $f (@features) {
         $as->start . " " . $as->end);
 }
 
+foreach my $f (@ref_features) {
+  debug( "Feature: " . $f->slice->seq_region_name . " " .
+         $f->start . " " . $f->end . " " . $f->type);
+  my $as = $f->alternate_slice();
+  debug(" Alternate slice: " . $as->seq_region_name . " " .
+        $as->start . " " . $as->end);
+}
+
+foreach my $f (@patch_features) {
+  debug( "Feature: " . $f->slice->seq_region_name . " " .
+         $f->start . " " . $f->end . " " . $f->type);
+  my $as = $f->alternate_slice();
+  debug(" Alternate slice: " . $as->seq_region_name . " " .
+        $as->start . " " . $as->end);
+}
+
 my ($f) = @features;
 is($f->display_id, $f->alternate_slice->seq_region_name, "Feature display id matches feature's alternate slice name");