Enable internal ID disabiguation for exons too.

modules/Bio/EnsEMBL/IdMapping/InternalIdMapper.pm

@@ -98,9 +98,9 @@ sub map_genes {
     # determine which plugin methods to run
     my @default_plugins = (qw(
       Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblGeneGeneric::init_basic
-      Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblGeneGeneric::synteny
       Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblGeneGeneric::best_transcript
       Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblGeneGeneric::biotype
+      Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblGeneGeneric::synteny
       Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblGeneGeneric::internal_id
     ));
 
@@ -198,10 +198,10 @@ sub map_transcripts {
     my @default_plugins = (qw(
       Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblTranscriptGeneric::init_basic
       Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblTranscriptGeneric::non_exact_translation
-      Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblTranscriptGeneric::mapped_gene
       Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblTranscriptGeneric::biotype
-      Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblTranscriptGeneric::internal_id
+      Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblTranscriptGeneric::mapped_gene
       Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblTranscriptGeneric::single_gene
+      Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblTranscriptGeneric::internal_id
     ));
 
     my @plugins = $self->conf->param('plugin_internal_id_mappers_transcript');
@@ -299,6 +299,7 @@ sub map_exons {
     my @default_plugins = (qw(
       Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblExonGeneric::init_basic
       Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblExonGeneric::mapped_transcript
+      Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblExonGeneric::internal_id
     ));
 
     my @plugins = $self->conf->param('plugin_internal_id_mappers_exon');

modules/Bio/EnsEMBL/IdMapping/InternalIdMapper/EnsemblExonGeneric.pm

@@ -88,5 +88,34 @@ sub mapped_transcript {
 }
   
 
+#
+# selectively rescore by penalising scores between exons with
+# different internalIDs
+#
+sub internal_id {
+  my $self        = shift;
+  my $num         = shift;
+  my $esb         = shift;
+  my $mappings    = shift;
+  my $exon_scores = shift;
+
+  $self->logger->info( "Retry with internalID disambiguation...\n",
+                       0, 'stamped' );
+
+  if ( !$exon_scores->loaded() ) {
+    $esb->internal_id_rescore($exon_scores);
+    $exon_scores->write_to_file();
+  }
+
+  $mappings = $self->basic_mapping( $exon_scores, "exon_mappings$num" );
+  $num++;
+  my $new_scores =
+    $esb->create_shrinked_matrix( $exon_scores, $mappings,
+                                  "exon_matrix$num" );
+
+  return ( $new_scores, $mappings );
+}
+
+
 1;