Added new option to method fetch_all which is include_lrg. By defualt lrg...

Added new option to method fetch_all which is include_lrg. By defualt lrg slices willl NOT be returned if this is not set (default is off) also since at present all lrg regions are non reference this flag must be set too to get the lrg regions.

modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm

@@ -699,6 +699,10 @@ sub get_seq_region_id {
                then your slice will not start at position 1, so coordinates
                retrieved from this slice might not be what you expected.
 
+  Arg[5]     : bool $include_lrg (optional)  (default 0)
+               If set lrg regions will be returned aswell.
+
+
   Example    : @chromos = @{$slice_adaptor->fetch_all('chromosome','NCBI33')};
                @contigs = @{$slice_adaptor->fetch_all('contig')};
 
@@ -734,7 +738,7 @@ sub fetch_all {
   my $cs_name = shift;
   my $cs_version = shift || '';
 
-  my ($include_non_reference, $include_duplicates) = @_;
+  my ($include_non_reference, $include_duplicates, $include_lrg) = @_;
 
   #
   # verify existance of requested coord system and get its id
@@ -775,6 +779,33 @@ sub fetch_all {
     $sth2->finish();
   }
 
+  #
+  # if we do not want lrg's then add them to the bad list;
+  #
+  if (!$include_lrg) {
+    my $sth2 =
+      $self->prepare(   'SELECT sr.seq_region_id '
+                      . 'FROM seq_region sr, seq_region_attrib sra, '
+                      . 'attrib_type at, coord_system cs '
+                      . 'WHERE at.code = "LRG" '
+                      . 'AND sra.seq_region_id = sr.seq_region_id '
+                      . 'AND at.attrib_type_id = sra.attrib_type_id '
+                      . 'AND sr.coord_system_id = cs.coord_system_id '
+                      . 'AND cs.species_id = ?' );
+
+    $sth2->bind_param( 1, $self->species_id(), SQL_INTEGER );
+    $sth2->execute();
+
+    my ($seq_region_id);
+    $sth2->bind_columns( \$seq_region_id );
+
+    while ( $sth2->fetch() ) {
+      $bad_vals{$seq_region_id} = 1;
+    }
+
+    $sth2->finish();
+  }
+
   #
   # Retrieve the seq_regions from the database
   #