text: -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
  -- Copyright [2016-2018] 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.
  
  # Patch to convert release 35 Ensembl schema to release 36
  
  UPDATE meta set meta_value="36" where meta_key="schema_version";
  
  # New table (so no data conversion required) for storing regulatory search regions
  
  CREATE TABLE regulatory_search_region (
  
    regulatory_search_region_id  INT NOT NULL auto_increment,
    name                         VARCHAR(255) NOT NULL,
    seq_region_id                INT NOT NULL,                 # FK refs seq_region
    seq_region_start             INT NOT NULL,
    seq_region_end               INT NOT NULL,
    seq_region_strand            TINYINT NOT NULL,
    ensembl_object_type          ENUM( 'Transcript', 'Translation', 'Gene') NOT NULL,
    ensembl_object_id            INT,           # FK to gene/transcript/translation
    analysis_id                  INT NOT NULL,  # FK to analysis
  
    PRIMARY KEY (regulatory_search_region_id),
    KEY rsr_idx (regulatory_search_region_id),
    KEY ensembl_object_idx (ensembl_object_type, ensembl_object_id)
  
  ) COLLATE=latin1_swedish_ci TYPE=MyISAM;
  
  ALTER TABLE density_type ADD COLUMN region_features INT NOT NULL AFTER block_size;
  ALTER TABLE density_type DROP INDEX analysis_id;
  ALTER TABLE density_type ADD UNIQUE analysis_id( analysis_id, block_size, region_features);
  
  ALTER TABLE regulatory_feature ADD INDEX seq_region_idx(seq_region_id, analysis_id, seq_region_start);
  ALTER TABLE regulatory_feature ADD INDEX seq_region_idx_2(seq_region_id, seq_region_start);
  
  ALTER TABLE regulatory_search_region ADD INDEX seq_region_idx(seq_region_id, seq_region_start);
  ALTER TABLE regulatory_search_region ADD INDEX seq_region_idx_2(seq_region_id, seq_region_start);
  
  ALTER TABLE go_xref modify linkage_type  enum('IC','IDA','IEA','IEP','IGI','IMP','IPI','ISS','NAS','ND','TAS','NR','RCA') NULL;
  