added is)ref to alt_allele table to say which is the reference allele

sql/patch_63_64_c.sql

+# patch_63_64_c.sql
+#
+# Title:
+#   is_ref to alt_allele 
+#
+# Description:
+#    Add is_ref to alt_allele to specify which is the reference al
+
+
+# Add the new column.
+ALTER TABLE alt_allele
+  ADD COLUMN is_ref BOOLEAN NOT NULL DEFAULT 0
+    AFTER gene_id;
+
+# Insert patch identifier.
+INSERT INTO meta (species_id, meta_key, meta_value)
+  VALUES (NULL, 'patch',
+    'patch_63_64_c.sql|is_ref_added_to_alt_allele');

sql/table.sql

@@ -810,6 +810,7 @@ CREATE TABLE unconventional_transcript_association (
 CREATE TABLE alt_allele (
   alt_allele_id         INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
   gene_id               INT(10) UNSIGNED NOT NULL,
+  is_ref                BOOLEAN NOT NULL DEFAULT 0,
 
   UNIQUE KEY gene_idx (gene_id),
   UNIQUE KEY allele_idx (alt_allele_id, gene_id)