text: -- 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 HGMD_MUTATION consequence to variation_feature
  ALTER TABLE `variation_feature` CHANGE `consequence_type` `consequence_type` set('ESSENTIAL_SPLICE_SITE','STOP_GAINED','STOP_LOST','COMPLEX_INDEL','FRAMESHIFT_CODING','NON_SYNONYMOUS_CODING','SPLICE_SITE','PARTIAL_CODON','SYNONYMOUS_CODING','REGULATORY_REGION','WITHIN_MATURE_miRNA','5PRIME_UTR','3PRIME_UTR','INTRONIC','NMD_TRANSCRIPT','UPSTREAM','DOWNSTREAM','WITHIN_NON_CODING_GENE','NO_CONSEQUENCE','INTERGENIC','HGMD_MUTATION') NOT NULL DEFAULT 'INTERGENIC';
  
  # add HGMD_MUTATION consequence to transcript_variation
  ALTER TABLE `transcript_variation` CHANGE `consequence_type` `consequence_type` set('ESSENTIAL_SPLICE_SITE','STOP_GAINED','STOP_LOST','COMPLEX_INDEL','FRAMESHIFT_CODING','NON_SYNONYMOUS_CODING','SPLICE_SITE','PARTIAL_CODON','SYNONYMOUS_CODING','REGULATORY_REGION','WITHIN_MATURE_miRNA','5PRIME_UTR','3PRIME_UTR','INTRONIC','NMD_TRANSCRIPT','UPSTREAM','DOWNSTREAM','WITHIN_NON_CODING_GENE','NO_CONSEQUENCE','INTERGENIC','HGMD_MUTATION') NOT NULL DEFAULT 'INTERGENIC';
  
  # patch identifier
  INSERT INTO meta (species_id, meta_key, meta_value) VALUES (NULL,'patch', 'patch_57_58_e.sql|new consequence type HGMD_MUTATION');
  