Added expanded_length method and changed seq method to use it

modules/Bio/EnsEMBL/StrainSlice.pm

@@ -261,6 +261,7 @@ sub seq {
   if($self->adaptor()) {
     my $seqAdaptor = $self->adaptor()->db()->get_SequenceAdaptor();
     my $reference_sequence = $seqAdaptor->fetch_by_Slice_start_end_strand($self,1,undef,1); #get the reference sequence for that slice
+	
     #apply all differences to the reference sequence
     #first, in case there are any indels, create the new sequence (containing the '-' bases)
    # sort edits in reverse order to remove complication of
@@ -270,6 +271,7 @@ sub seq {
     foreach my $vf (@indels_ordered){
 	$vf->apply_edit($reference_sequence); #change, in the reference sequence, the vf
     }
+	
     #need to find coverage information if diffe
     # sort edits in reverse order to remove complication of
     # adjusting downstream edits
@@ -278,18 +280,32 @@ sub seq {
     foreach my $vf (@variation_features_ordered){
 	$vf->apply_edit($reference_sequence); #change, in the reference sequence, the vf
     }
+	
     #need to find coverage information if different from reference
     my $indAdaptor = $self->adaptor->db->get_db_adaptor('variation')->get_IndividualAdaptor;
     my $ref_strain = $indAdaptor->get_reference_strain_name;
     $self->_add_coverage_information($reference_sequence) if ($with_coverage == 1 && $self->strain_name ne $ref_strain);
     return substr(${$reference_sequence},0,1) if ($self->length == 1); 
-    return substr(${$reference_sequence},0,$self->length); #returns the reference sequence, applying the variationFeatures. Remove additional bases added due to indels
+    return substr(${$reference_sequence},0,$self->expanded_length); #returns the reference sequence, applying the variationFeatures. Remove additional bases added due to indels
   }
 
   # no attached sequence, and no db, so just return Ns
   return 'N' x $self->length();
 }
 
+sub expanded_length() {
+	my $self = shift;
+	
+	my $length = $self->SUPER::length();
+	
+	foreach my $af(@{$self->{'alleleFeatures'}}) {
+		$length += $af->length_diff() if $af->length_diff > 0;
+	}
+	
+	return $length;
+}
+
+
 
 sub _add_coverage_information{
     my $self = shift;