Alt allele schema patch.

sql/patch_72_73_b.sql

+# patch_70_71_b.sql
+#
+# Title: Introduce alt allele types
+#
+# Description: Copy out existing alt allele data, create new tables and
+#              integrate old data into the new tables
+
+# Relocate existing data out of the way
+CREATE TABLE aa_bak LIKE alt_allele
+INSERT INTO aa_bak SELECT * FROM alt_allele;
+
+DROP TABLE alt_allele;
+
+# Make new table structure
+CREATE TABLE alt_allele (alt_allele_id INT UNSIGNED AUTO_INCREMENT, 
+                         alt_allele_group_id INT UNSIGNED NOT NULL, 
+                         gene_id INT UNSIGNED NOT NULL,
+                         PRIMARY KEY (alt_allele_id),
+                         KEY (gene_id,group_id)
+                         );
+
+CREATE TABLE alt_allele_attrib (alt_allele_id INT UNSIGNED,
+                                attrib ENUM('IS_REPRESENTATIVE',
+                                            'IS_MOST_COMMON_ALLELE',
+                                            'IN_CORRECTED_ASSEMBLY',
+                                            'HAS_CODING_POTENTIAL',
+                                            'IN_ARTIFICIALLY_DUPLICATED_ASSEMBLY',
+                                            'IN_SYNTENIC_REGION',
+                                            'HAS_SAME_UNDERLYING_DNA_SEQUENCE',
+                                            'IN_BROKEN_ASSEMBLY_REGION',
+                                            'IS_VALID_ALTERNATE',
+                                            'SAME_AS_REPRESENTATIVE',
+                                            'SAME_AS_ANOTHER_ALLELE',
+                                            'MANUALLY_ASSIGNED',
+                                            'AUTOMATICALLY_ASSIGNED'),
+                                KEY aa_idx (alt_allele_id,attrib)
+);
+
+CREATE TABLE alt_allele_group (alt_allele_group_id INT UNSIGNED AUTO_INCREMENT,
+                               PRIMARY KEY (alt_allele_group_id)
+                               );
+
+# Port data into new structure
+INSERT INTO alt_allele_group (alt_allele_group_id) SELECT DISTINCT alt_allele_id FROM aa_bak;
+INSERT INTO alt_allele (alt_allele_group_id,gene_id) SELECT alt_allele_id,gene_id FROM aa_bak;
+
+INSERT INTO alt_allele_attrib (alt_allele_id,attrib) SELECT a.alt_allele_id,'IS_REPRESENTATIVE' FROM alt_allele a, aa_bak b 
+    WHERE b.is_ref = 1 AND a.gene_id = b.gene_id AND a.group_id = b.alt_allele_id;
+
+# Clean up remains
+DROP TABLE aa_back;
+
+
+# Patch identifier
+INSERT INTO meta (species_id, meta_key, meta_value)
+  VALUES (NULL, 'patch', 'patch_70_71_b.sql|alt_allele_type');