if all you want to test is if a transcript has a mapping, don't add any additional conditions

modules/Bio/EnsEMBL/IdMapping/ExonScoreBuilder.pm

@@ -784,7 +784,7 @@ sub non_mapped_transcript_rescore {
          'Need a Bio::EnsEMBL::IdMapping::MappingList of transcripts.');
   }
 
-  # create of lookup hash of mapped source transcripts to target
+  # create a lookup hash of mapped source transcripts to target
   # transcripts
   my %transcript_lookup =
     map { $_->source => $_->target }
@@ -808,7 +808,7 @@ sub non_mapped_transcript_rescore {
       foreach my $target_tr (@target_transcripts) {
         my $mapped_target = $transcript_lookup{ $source_tr->id };
 
-        if ( $mapped_target and ( $mapped_target == $target_tr->id ) ) {
+        if ( $mapped_target ) {
           $found_mapped = 1;
           last TR;
         }
@@ -828,4 +828,5 @@ sub non_mapped_transcript_rescore {
                         1 );
 } ## end sub non_mapped_transcript_rescore
 
+
 1;