REF fix for PATCH_NOVEL and PATH_FIX

modules/Bio/EnsEMBL/Feature.pm

@@ -1225,14 +1225,14 @@ sub get_all_alt_locations {
     } elsif( $axf->type() eq "PATCH_FIX"){
       push @haps, $axf;
     } elsif( $axf->type() eq "PATCH_FIX REF"){
-      push @haps, $axf;
-    } elsif( $axf->type() eq "HAP REF" ) { 
+      push @haps, $axf  if $return_all > 0 ;
+    } elsif( $axf->type() eq "HAP REF" ) {
       push @haps, $axf if $return_all > 0 ;
       # do nothing when you are on REF
     } elsif( $axf->type() eq "PATCH_NOVEL"){
       push @haps, $axf;
     }elsif( $axf->type() eq "PATCH_NOVEL REF"){
-      push @haps, $axf;
+      push @haps, $axf  if $return_all > 0 ;
     } else {
       warning("Unknown exception feature type ". $axf->type()."- ignoring.");
     }