sequence returnes by seq call returns the number of bases specified by the...

sequence returnes by seq call returns the number of bases specified by the length of the StrainSlice

modules/Bio/EnsEMBL/StrainSlice.pm

@@ -256,7 +256,7 @@ sub seq {
     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 ${$reference_sequence}; #returns the reference sequence, applying the variationFeatures
+    return substr(${$reference_sequence},0,$self->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