is_ref added to alt_allele

modules/t/gene.t

@@ -3,7 +3,7 @@ use warnings;
 
 BEGIN { $| = 1;
 	use Test;
-	plan tests => 92;
+	plan tests => 93;
 }
 
 use Bio::EnsEMBL::Test::MultiTestDB;
@@ -488,6 +488,8 @@ ok(@genes == 20);
 $gene = $ga->fetch_by_dbID( 18256 );
 my $alt_genes = $gene->get_all_alt_alleles();
 
+ok( $gene->is_ref == 1);
+
 ok( scalar( @$alt_genes ) == 3 );
 
 # expect the following alleles
@@ -495,6 +497,7 @@ my %gene_ids = ( 18257 => 1, 18258 => 1, 18259 => 1);
 my $ok = 1;
 for my $gene ( @$alt_genes ) {
   $ok = $ok && $gene_ids{$gene->dbID()};
+  $ok = $ok && !($gene->is_ref);
 }
 ok( $ok );
 

modules/t/test-genome-DBs/homo_sapiens/core/alt_allele.sql

 CREATE TABLE `alt_allele` (
   `alt_allele_id` int(11) NOT NULL auto_increment,
   `gene_id` int(11) NOT NULL default '0',
+  `is_ref`  BOOLEAN NOT NULL DEFAULT '0',
   UNIQUE KEY `gene_idx` (`gene_id`),
   UNIQUE KEY `allele_idx` (`alt_allele_id`,`gene_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;

modules/t/test-genome-DBs/homo_sapiens/core/alt_allele.txt

-1	18256
-1	18257
-1	18258
-1	18259
+1	18256	1
+1	18257	0
+1	18258	0
+1	18259	0