fix up for earlier change

Ensembl · Jun 22, 2017 · d316dd0 · d316dd0
1 parent 66a60eb
commit d316dd0
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Showing 2 changed files with 9 additions and 33 deletions.
diff --git a/modules/Bio/EnsEMBL/VEP/InputBuffer.pm b/modules/Bio/EnsEMBL/VEP/InputBuffer.pm
@@ -157,16 +157,16 @@ sub get_overlapping_vfs {
   ($start, $end) = ($end, $start) if $start > $end;
 
   if(my $tree = $self->interval_tree) {
-    return $tree->fetch($start - 1, $end);
+    return [
+      grep { overlap($_->{start}, $_->{end}, $start, $end) }
+      @{$tree->fetch($start - 1, $end)}
+    ];
   }
   else {
     my $hash_tree = $self->hash_tree;
 
     return [
-      grep {  # checking both overlaps is quicker than sorting here
-        overlap($_->{start}, $_->{end}, $start, $end) ||
-        overlap($_->{end}, $_->{start}, $start, $end)
-      }
+      grep { overlap($_->{start}, $_->{end}, $start, $end) }
       values %{{
         map {$_->{_hash_tree_id} => $_}                  # use _hash_tree_id to uniquify
         map {@{$hash_tree->{$_} || []}}                  # tree might be empty

diff --git a/t/InputBuffer.t b/t/InputBuffer.t
@@ -193,13 +193,13 @@ delete $ib->{temp}->{hash_tree};
 
 is_deeply(
   $ib->get_overlapping_vfs(25592910, 25592911),
-  [$ib->buffer->[0]],
+  [],
   'get_overlapping_vfs - ins 1'
 );
 
 is_deeply(
   $ib->get_overlapping_vfs(25592912, 25592913),
-  [$ib->buffer->[0]],
+  [],
   'get_overlapping_vfs - ins 2'
 );
 
@@ -209,18 +209,6 @@ is_deeply(
   'get_overlapping_vfs - ins 3'
 );
 
-is_deeply(
-  $ib->get_overlapping_vfs(25592909, 25592910),
-  [],
-  'get_overlapping_vfs - ins 4'
-);
-
-is_deeply(
-  $ib->get_overlapping_vfs(25592913, 25592914),
-  [],
-  'get_overlapping_vfs - ins 5'
-);
-
 $ib->buffer->[0]->{start}--;
 
 SKIP: {
@@ -306,13 +294,13 @@ SKIP: {
 
   is_deeply(
     $ib->get_overlapping_vfs(25592910, 25592911),
-    [$ib->buffer->[0]],
+    [],
     'get_overlapping_vfs no tree - ins 1'
   );
 
   is_deeply(
     $ib->get_overlapping_vfs(25592912, 25592913),
-    [$ib->buffer->[0]],
+    [],
     'get_overlapping_vfs no tree - ins 2'
   );
 
@@ -322,18 +310,6 @@ SKIP: {
     'get_overlapping_vfs no tree - ins 3'
   );
 
-  is_deeply(
-    $ib->get_overlapping_vfs(25592909, 25592910),
-    [],
-    'get_overlapping_vfs no tree - ins 4'
-  );
-
-  is_deeply(
-    $ib->get_overlapping_vfs(25592913, 25592914),
-    [],
-    'get_overlapping_vfs no tree - ins 5'
-  );
-
   $ib->buffer->[0]->{start}--;
 
   $Bio::EnsEMBL::VEP::InputBuffer::CAN_USE_INTERVAL_TREE = $orig;