Punish stable IDs that change biotype harder.

modules/Bio/EnsEMBL/IdMapping/GeneScoreBuilder.pm

@@ -391,34 +391,37 @@ sub simple_gene_rescore {
 # entries are modified in place
 #
 sub biotype_gene_rescore {
-  my $self = shift;
+  my $self   = shift;
   my $matrix = shift;
 
-  unless ($matrix and
-          $matrix->isa('Bio::EnsEMBL::IdMapping::ScoredMappingMatrix')) {
+  unless ($matrix
+      and $matrix->isa('Bio::EnsEMBL::IdMapping::ScoredMappingMatrix') )
+  {
     throw('Need a Bio::EnsEMBL::IdMapping::ScoredMappingMatrix.');
   }
 
   my $i = 0;
 
-  foreach my $entry (@{ $matrix->get_all_Entries }) {
+  foreach my $entry ( @{ $matrix->get_all_Entries } ) {
 
-    my $source_gene = $self->cache->get_by_key('genes_by_id', 'source',
-      $entry->source);
+    my $source_gene =
+      $self->cache->get_by_key( 'genes_by_id', 'source',
+                                $entry->source );
 
-    my $target_gene = $self->cache->get_by_key('genes_by_id', 'target',
-      $entry->target);
+    my $target_gene =
+      $self->cache->get_by_key( 'genes_by_id', 'target',
+                                $entry->target );
 
     if ( $source_gene->biotype() ne $target_gene->biotype() ) {
       #$self->logger->debug("biotype ".$entry->to_string."\n");
       $matrix->set_score( $entry->source(), $entry->target(),
-                          ( $entry->score()*0.5 ) );
+                          ( $entry->score()*0.25 ) );
       $i++;
     }
   }
-  
-  $self->logger->debug("Scored genes with biotype mismatch: $i\n", 1);
-}
+
+  $self->logger->debug( "Scored genes with biotype mismatch: $i\n", 1 );
+} ## end sub biotype_gene_rescore
 
 
 1;