-- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-- Copyright [2016-2019] EMBL-European Bioinformatics Institute
-- 
-- Licensed under the Apache License, Version 2.0 (the "License");
-- you may not use this file except in compliance with the License.
-- You may obtain a copy of the License at
-- 
--      http://www.apache.org/licenses/LICENSE-2.0
-- 
-- Unless required by applicable law or agreed to in writing, software
-- distributed under the License is distributed on an "AS IS" BASIS,
-- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-- See the License for the specific language governing permissions and
-- limitations under the License.


# add a table to hold structural variations
CREATE TABLE structural_variation (
  structural_variation_id int(10) unsigned NOT NULL AUTO_INCREMENT,
  seq_region_id int(10) unsigned NOT NULL,
  seq_region_start int(11) NOT NULL,
  seq_region_end int(11) NOT NULL,
  seq_region_strand tinyint(4) NOT NULL,
  variation_name varchar(255) DEFAULT NULL,
  source_id int(10) unsigned NOT NULL,
  class varchar(255) DEFAULT NULL,
  bound_start int(11) DEFAULT NULL,
  bound_end int(11) DEFAULT NULL,
  PRIMARY KEY (structural_variation_id),
  KEY pos_idx (seq_region_id,seq_region_start)
);

# patch identifier
INSERT INTO meta (species_id, meta_key, meta_value) VALUES (NULL,'patch', 'patch_56_57_c.sql|add structural variation');
