fix out-by-1 error on BED custom files

Ensembl · Dec 19, 2014 · 0f40683 · 0f40683
1 parent 8824d10
commit 0f40683
Showing 1 changed file with 12 additions and 5 deletions.
diff --git a/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm b/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm
@@ -2742,16 +2742,23 @@ sub get_custom_annotation {
     }
 
     foreach my $custom(@{$config->{custom}}) {
+
         next unless defined($cache->{$chr}->{$custom->{name}});
+
+        my ($s, $e) = ($vf->{start}, $vf->{end});
+
+        # adjust start for BED as it is 0-based
+        $s-- if $custom->{format} eq 'bed';
 
         # exact type must match coords of variant exactly
         if($custom->{type} eq 'exact') {
-            foreach my $feature(values %{$cache->{$chr}->{$custom->{name}}->{$vf->{start}}}) {
+
+            foreach my $feature(values %{$cache->{$chr}->{$custom->{name}}->{$s}}) {
 
                 next unless
                     $feature->{chr}   eq $chr &&
-                    $feature->{start} eq $vf->{start} &&
-                    $feature->{end}   eq $vf->{end};
+                    $feature->{start} == $s &&
+                    $feature->{end}   == $e;
 
                 $annotation->{$custom->{name}} .= $feature->{name}.',';
 
@@ -2768,8 +2775,8 @@ sub get_custom_annotation {
 
                     next unless
                         $feature->{chr}   eq $chr &&
-                        $feature->{end}   >= $vf->{start} &&
-                        $feature->{start} <= $vf->{end};
+                        $feature->{end}   >= $s &&
+                        $feature->{start} <= $e;
 
                     $annotation->{$custom->{name}} .= $feature->{name}.',';
                     foreach my $field(@{$custom->{fields}}) {