no SQLlite schema for variation

modules/t/test-genome-DBs/homo_sapiens/variation/SQLite/table.sql

--- 
--- Created by SQL::Translator::Producer::SQLite
--- Created on Fri May  6 15:44:47 2016
--- 
-
-BEGIN TRANSACTION;
-
---
--- Table: allele
---
-CREATE TABLE allele (
-  allele_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  variation_id integer NOT NULL,
-  subsnp_id integer,
-  allele_code_id integer NOT NULL,
-  population_id integer,
-  frequency float,
-  count integer,
-  frequency_submitter_handle integer
-);
-
---
--- Table: allele_code
---
-CREATE TABLE allele_code (
-  allele_code_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  allele varchar(255)
-);
-
-CREATE UNIQUE INDEX allele_idx ON allele_code (allele);
-
---
--- Table: associate_study
---
-CREATE TABLE associate_study (
-  study1_id integer NOT NULL,
-  study2_id integer NOT NULL,
-  PRIMARY KEY (study1_id, study2_id)
-);
-
---
--- Table: attrib
---
-CREATE TABLE attrib (
-  attrib_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  attrib_type_id smallint NOT NULL DEFAULT 0,
-  value text NOT NULL
-);
-
-CREATE UNIQUE INDEX type_val_idx ON attrib (attrib_type_id, value);
-
---
--- Table: attrib_set
---
-CREATE TABLE attrib_set (
-  attrib_set_id integer NOT NULL DEFAULT 0,
-  attrib_id integer NOT NULL DEFAULT 0
-);
-
-CREATE UNIQUE INDEX set_idx ON attrib_set (attrib_set_id, attrib_id);
-
---
--- Table: attrib_type
---
-CREATE TABLE attrib_type (
-  attrib_type_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL DEFAULT 0,
-  code varchar(20) NOT NULL DEFAULT '',
-  name varchar(255) NOT NULL DEFAULT '',
-  description text
-);
-
-CREATE UNIQUE INDEX code_idx ON attrib_type (code);
-
---
--- Table: compressed_genotype_region
---
-CREATE TABLE compressed_genotype_region (
-  sample_id integer NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  seq_region_strand tinyint NOT NULL,
-  genotypes blob
-);
-
---
--- Table: compressed_genotype_var
---
-CREATE TABLE compressed_genotype_var (
-  variation_id integer NOT NULL,
-  subsnp_id integer,
-  genotypes blob
-);
-
---
--- Table: coord_system
---
-CREATE TABLE coord_system (
-  coord_system_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  species_id integer NOT NULL DEFAULT 1,
-  name varchar(40) NOT NULL,
-  version varchar(255),
-  rank integer NOT NULL,
-  attrib varchar
-);
-
-CREATE UNIQUE INDEX name_idx ON coord_system (name, version, species_id);
-
-CREATE UNIQUE INDEX rank_idx ON coord_system (rank, species_id);
-
---
--- Table: display_group
---
-CREATE TABLE display_group (
-  display_group_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  display_priority integer NOT NULL,
-  display_name varchar(255) NOT NULL
-);
-
-CREATE UNIQUE INDEX display_name ON display_group (display_name);
-
-CREATE UNIQUE INDEX display_priority ON display_group (display_priority);
-
---
--- Table: failed_allele
---
-CREATE TABLE failed_allele (
-  failed_allele_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  allele_id integer NOT NULL,
-  failed_description_id integer NOT NULL
-);
-
-CREATE UNIQUE INDEX allele_idx02 ON failed_allele (allele_id, failed_description_id);
-
---
--- Table: failed_description
---
-CREATE TABLE failed_description (
-  failed_description_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  description text NOT NULL
-);
-
---
--- Table: failed_structural_variation
---
-CREATE TABLE failed_structural_variation (
-  failed_structural_variation_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  structural_variation_id integer NOT NULL,
-  failed_description_id integer NOT NULL
-);
-
-CREATE UNIQUE INDEX structural_variation_idx ON failed_structural_variation (structural_variation_id, failed_description_id);
-
---
--- Table: failed_variation
---
-CREATE TABLE failed_variation (
-  failed_variation_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  variation_id integer NOT NULL,
-  failed_description_id integer NOT NULL
-);
-
-CREATE UNIQUE INDEX variation_idx ON failed_variation (variation_id, failed_description_id);
-
---
--- Table: genotype_code
---
-CREATE TABLE genotype_code (
-  genotype_code_id integer NOT NULL,
-  allele_code_id integer NOT NULL,
-  haplotype_id tinyint NOT NULL,
-  phased tinyint
-);
-
---
--- Table: individual
---
-CREATE TABLE individual (
-  individual_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  name varchar(255),
-  description text,
-  gender enum NOT NULL DEFAULT 'Unknown',
-  father_individual_id integer,
-  mother_individual_id integer,
-  individual_type_id integer NOT NULL DEFAULT 0
-);
-
---
--- Table: individual_synonym
---
-CREATE TABLE individual_synonym (
-  synonym_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  individual_id integer NOT NULL,
-  source_id integer NOT NULL,
-  name varchar(255)
-);
-
---
--- Table: individual_type
---
-CREATE TABLE individual_type (
-  individual_type_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  name varchar(255) NOT NULL,
-  description text
-);
-
---
--- Table: meta
---
-CREATE TABLE meta (
-  meta_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  species_id integer DEFAULT 1,
-  meta_key varchar(40) NOT NULL,
-  meta_value varchar(255) NOT NULL
-);
-
-CREATE UNIQUE INDEX species_key_value_idx ON meta (species_id, meta_key, meta_value);
-
---
--- Table: meta_coord
---
-CREATE TABLE meta_coord (
-  table_name varchar(40) NOT NULL,
-  coord_system_id integer NOT NULL,
-  max_length integer
-);
-
-CREATE UNIQUE INDEX table_name ON meta_coord (table_name, coord_system_id);
-
---
--- Table: motif_feature_variation
---
-CREATE TABLE motif_feature_variation (
-  motif_feature_variation_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  variation_feature_id integer NOT NULL,
-  feature_stable_id varchar(128),
-  motif_feature_id integer NOT NULL,
-  allele_string text,
-  somatic tinyint NOT NULL DEFAULT 0,
-  consequence_types varchar,
-  motif_name text,
-  motif_start integer,
-  motif_end integer,
-  motif_score_delta float,
-  in_informative_position tinyint NOT NULL DEFAULT 0
-);
-
---
--- Table: phenotype
---
-CREATE TABLE phenotype (
-  phenotype_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  stable_id varchar(255),
-  name varchar(50),
-  description varchar(255)
-);
-
-CREATE UNIQUE INDEX desc_idx ON phenotype (description);
-
---
--- Table: phenotype_feature
---
-CREATE TABLE phenotype_feature (
-  phenotype_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  phenotype_id integer,
-  source_id integer,
-  study_id integer,
-  type enum,
-  object_id varchar(255),
-  is_significant tinyint DEFAULT 1,
-  seq_region_id integer,
-  seq_region_start integer,
-  seq_region_end integer,
-  seq_region_strand tinyint
-);
-
---
--- Table: phenotype_feature_attrib
---
-CREATE TABLE phenotype_feature_attrib (
-  phenotype_feature_id integer NOT NULL,
-  attrib_type_id integer,
-  value varchar(255)
-);
-
---
--- Table: population
---
-CREATE TABLE population (
-  population_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  name varchar(255),
-  size integer,
-  description text,
-  collection tinyint DEFAULT 0,
-  freqs_from_gts tinyint,
-  display enum DEFAULT 'UNDISPLAYABLE',
-  display_group_id tinyint
-);
-
---
--- Table: population_genotype
---
-CREATE TABLE population_genotype (
-  population_genotype_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  variation_id integer NOT NULL,
-  subsnp_id integer,
-  genotype_code_id integer,
-  frequency float,
-  population_id integer,
-  count integer
-);
-
---
--- Table: population_structure
---
-CREATE TABLE population_structure (
-  super_population_id integer NOT NULL,
-  sub_population_id integer NOT NULL
-);
-
-CREATE UNIQUE INDEX super_population_idx ON population_structure (super_population_id, sub_population_id);
-
---
--- Table: population_synonym
---
-CREATE TABLE population_synonym (
-  synonym_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  population_id integer NOT NULL,
-  source_id integer NOT NULL,
-  name varchar(255)
-);
-
---
--- Table: protein_function_predictions
---
-CREATE TABLE protein_function_predictions (
-  translation_md5_id integer NOT NULL,
-  analysis_attrib_id integer NOT NULL,
-  prediction_matrix mediumblob,
-  PRIMARY KEY (translation_md5_id, analysis_attrib_id)
-);
-
---
--- Table: protein_function_predictions_attrib
---
-CREATE TABLE protein_function_predictions_attrib (
-  translation_md5_id integer NOT NULL,
-  analysis_attrib_id integer NOT NULL,
-  attrib_type_id integer NOT NULL,
-  position_values blob,
-  PRIMARY KEY (translation_md5_id, analysis_attrib_id, attrib_type_id)
-);
-
---
--- Table: publication
---
-CREATE TABLE publication (
-  publication_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  title varchar(255),
-  authors varchar(255),
-  pmid integer,
-  pmcid varchar(255),
-  year integer,
-  doi varchar(50),
-  ucsc_id varchar(50)
-);
-
---
--- Table: read_coverage
---
-CREATE TABLE read_coverage (
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  level tinyint NOT NULL,
-  sample_id integer NOT NULL
-);
-
---
--- Table: regulatory_feature_variation
---
-CREATE TABLE regulatory_feature_variation (
-  regulatory_feature_variation_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  variation_feature_id integer NOT NULL,
-  feature_stable_id varchar(128),
-  feature_type text,
-  allele_string text,
-  somatic tinyint NOT NULL DEFAULT 0,
-  consequence_types varchar
-);
-
---
--- Table: sample
---
-CREATE TABLE sample (
-  sample_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  individual_id integer NOT NULL,
-  name varchar(255),
-  description text,
-  study_id integer,
-  display enum DEFAULT 'UNDISPLAYABLE',
-  has_coverage tinyint NOT NULL DEFAULT 0,
-  variation_set_id varchar
-);
-
---
--- Table: sample_genotype_multiple_bp
---
-CREATE TABLE sample_genotype_multiple_bp (
-  variation_id integer NOT NULL,
-  subsnp_id integer,
-  allele_1 varchar(255),
-  allele_2 varchar(255),
-  sample_id integer
-);
-
---
--- Table: sample_population
---
-CREATE TABLE sample_population (
-  sample_id integer NOT NULL,
-  population_id integer NOT NULL
-);
-
---
--- Table: sample_synonym
---
-CREATE TABLE sample_synonym (
-  synonym_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  sample_id integer NOT NULL,
-  source_id integer NOT NULL,
-  name varchar(255)
-);
-
---
--- Table: seq_region
---
-CREATE TABLE seq_region (
-  seq_region_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  name varchar(40) NOT NULL,
-  coord_system_id integer NOT NULL
-);
-
-CREATE UNIQUE INDEX name_cs_idx ON seq_region (name, coord_system_id);
-
---
--- Table: source
---
-CREATE TABLE source (
-  source_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  name varchar(24) NOT NULL,
-  version integer,
-  description varchar(255),
-  url varchar(255),
-  type enum,
-  somatic_status enum DEFAULT 'germline',
-  data_types varchar
-);
-
---
--- Table: strain_gtype_poly
---
-CREATE TABLE strain_gtype_poly (
-  variation_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  sample_name varchar(100)
-);
-
---
--- Table: structural_variation
---
-CREATE TABLE structural_variation (
-  structural_variation_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  variation_name varchar(255),
-  alias varchar(255),
-  source_id integer NOT NULL,
-  study_id integer,
-  class_attrib_id integer NOT NULL DEFAULT 0,
-  clinical_significance varchar,
-  validation_status enum,
-  is_evidence tinyint DEFAULT 0,
-  somatic tinyint NOT NULL DEFAULT 0,
-  copy_number tinyint
-);
-
-CREATE UNIQUE INDEX variation_name ON structural_variation (variation_name);
-
---
--- Table: structural_variation_association
---
-CREATE TABLE structural_variation_association (
-  structural_variation_id integer NOT NULL,
-  supporting_structural_variation_id integer NOT NULL,
-  PRIMARY KEY (structural_variation_id, supporting_structural_variation_id)
-);
-
---
--- Table: structural_variation_feature
---
-CREATE TABLE structural_variation_feature (
-  structural_variation_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  outer_start integer,
-  seq_region_start integer NOT NULL,
-  inner_start integer,
-  inner_end integer,
-  seq_region_end integer NOT NULL,
-  outer_end integer,
-  seq_region_strand tinyint NOT NULL,
-  structural_variation_id integer NOT NULL,
-  variation_name varchar(255),
-  source_id integer NOT NULL,
-  study_id integer,
-  class_attrib_id integer NOT NULL DEFAULT 0,
-  allele_string longtext,
-  is_evidence tinyint NOT NULL DEFAULT 0,
-  somatic tinyint NOT NULL DEFAULT 0,
-  breakpoint_order tinyint,
-  length integer,
-  variation_set_id varchar NOT NULL DEFAULT ''
-);
-
---
--- Table: structural_variation_sample
---
-CREATE TABLE structural_variation_sample (
-  structural_variation_sample_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  structural_variation_id integer NOT NULL,
-  sample_id integer,
-  strain_id integer
-);
-
---
--- Table: study
---
-CREATE TABLE study (
-  study_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  source_id integer NOT NULL,
-  name varchar(255),
-  description text,
-  url varchar(255),
-  external_reference varchar(255),
-  study_type varchar(255)
-);
-
---
--- Table: submitter_handle
---
-CREATE TABLE submitter_handle (
-  handle_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  handle varchar(25)
-);
-
-CREATE UNIQUE INDEX handle ON submitter_handle (handle);
-
---
--- Table: subsnp_handle
---
-CREATE TABLE subsnp_handle (
-  subsnp_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  handle varchar(20)
-);
-
---
--- Table: subsnp_map
---
-CREATE TABLE subsnp_map (
-  variation_id integer NOT NULL,
-  subsnp_id integer NOT NULL,
-  PRIMARY KEY (variation_id, subsnp_id)
-);
-
---
--- Table: tmp_individual_genotype_single_bp
---
-CREATE TABLE tmp_individual_genotype_single_bp (
-  variation_id integer NOT NULL,
-  subsnp_id integer,
-  allele_1 char(1),
-  allele_2 char(1),
-  individual_id integer
-);
-
---
--- Table: transcript_variation
---
-CREATE TABLE transcript_variation (
-  transcript_variation_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  variation_feature_id integer NOT NULL,
-  feature_stable_id varchar(128),
-  allele_string text,
-  somatic tinyint NOT NULL DEFAULT 0,
-  consequence_types varchar,
-  cds_start integer,
-  cds_end integer,
-  cdna_start integer,
-  cdna_end integer,
-  translation_start integer,
-  translation_end integer,
-  distance_to_transcript integer,
-  codon_allele_string text,
-  pep_allele_string text,
-  hgvs_genomic text,
-  hgvs_transcript text,
-  hgvs_protein text,
-  polyphen_prediction enum,
-  polyphen_score float,
-  sift_prediction enum,
-  sift_score float,
-  display integer DEFAULT 1
-);
-
---
--- Table: translation_md5
---
-CREATE TABLE translation_md5 (
-  translation_md5_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  translation_md5 char(32) NOT NULL
-);
-
-CREATE UNIQUE INDEX md5_idx ON translation_md5 (translation_md5);
-
---
--- Table: variation
---
-CREATE TABLE variation (
-  variation_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  source_id integer NOT NULL,
-  name varchar(255),
-  ancestral_allele varchar(255),
-  flipped tinyint,
-  class_attrib_id integer DEFAULT 0,
-  somatic tinyint NOT NULL DEFAULT 0,
-  minor_allele varchar(50),
-  minor_allele_freq float,
-  minor_allele_count integer,
-  clinical_significance varchar,
-  evidence_attribs varchar,
-  display integer DEFAULT 1
-);
-
-CREATE UNIQUE INDEX name ON variation (name);
-
---
--- Table: variation_attrib
---
-CREATE TABLE variation_attrib (
-  variation_id integer NOT NULL,
-  attrib_id integer,
-  value varchar(255)
-);
-
---
--- Table: variation_citation
---
-CREATE TABLE variation_citation (
-  variation_id integer NOT NULL,
-  publication_id integer NOT NULL,
-  PRIMARY KEY (variation_id, publication_id)
-);
-
---
--- Table: variation_feature
---
-CREATE TABLE variation_feature (
-  variation_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  seq_region_strand tinyint NOT NULL,
-  variation_id integer NOT NULL,
-  allele_string varchar(50000),
-  variation_name varchar(255),
-  map_weight integer NOT NULL,
-  flags varchar,
-  source_id integer NOT NULL,
-  consequence_types varchar NOT NULL DEFAULT 'intergenic_variant',
-  variation_set_id varchar NOT NULL DEFAULT '',
-  class_attrib_id integer DEFAULT 0,
-  somatic tinyint NOT NULL DEFAULT 0,
-  minor_allele varchar(50),
-  minor_allele_freq float,
-  minor_allele_count integer,
-  alignment_quality double precision,
-  clinical_significance varchar,
-  evidence_attribs varchar,
-  display integer DEFAULT 1
-);
-
---
--- Table: variation_feature_bak
---
-CREATE TABLE variation_feature_bak (
-  variation_feature_id integer NOT NULL DEFAULT 0,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  seq_region_strand tinyint NOT NULL,
-  variation_id integer NOT NULL,
-  allele_string varchar(50000),
-  variation_name varchar(255),
-  map_weight integer NOT NULL,
-  flags varchar,
-  source_id integer NOT NULL,
-  validation_status varchar,
-  consequence_types varchar NOT NULL DEFAULT 'intergenic_variant',
-  variation_set_id varchar NOT NULL DEFAULT '',
-  class_attrib_id integer DEFAULT 0,
-  somatic tinyint NOT NULL DEFAULT 0,
-  minor_allele varchar(50),
-  minor_allele_freq float,
-  minor_allele_count integer,
-  alignment_quality double precision,
-  evidence varchar
-);
-
---
--- Table: variation_genename
---
-CREATE TABLE variation_genename (
-  variation_id integer NOT NULL,
-  gene_name varchar(255) NOT NULL,
-  PRIMARY KEY (variation_id, gene_name)
-);
-
---
--- Table: variation_hgvs
---
-CREATE TABLE variation_hgvs (
-  variation_id integer NOT NULL,
-  hgvs_name varchar(255) NOT NULL,
-  PRIMARY KEY (variation_id, hgvs_name)
-);
-
---
--- Table: variation_set
---
-CREATE TABLE variation_set (
-  variation_set_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  name varchar(255),
-  description text,
-  short_name_attrib_id integer
-);
-
---
--- Table: variation_set_structural_variation
---
-CREATE TABLE variation_set_structural_variation (
-  structural_variation_id integer NOT NULL,
-  variation_set_id integer NOT NULL,
-  PRIMARY KEY (structural_variation_id, variation_set_id)
-);
-
---
--- Table: variation_set_structure
---
-CREATE TABLE variation_set_structure (
-  variation_set_super integer NOT NULL,
-  variation_set_sub integer NOT NULL,
-  PRIMARY KEY (variation_set_super, variation_set_sub)
-);
-
---
--- Table: variation_set_variation
---
-CREATE TABLE variation_set_variation (
-  variation_id integer NOT NULL,
-  variation_set_id integer NOT NULL,
-  PRIMARY KEY (variation_id, variation_set_id)
-);
-
---
--- Table: variation_synonym
---
-CREATE TABLE variation_synonym (
-  variation_synonym_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  variation_id integer NOT NULL,
-  subsnp_id integer,
-  source_id integer NOT NULL,
-  name varchar(255)
-);
-
-CREATE UNIQUE INDEX name02 ON variation_synonym (name, source_id);
-
-COMMIT;

modules/t/test-genome-DBs/mus_musculus/variation/SQLite/table.sql

--- 
--- Created by SQL::Translator::Producer::SQLite
--- Created on Fri May  6 15:45:33 2016
--- 
-
-BEGIN TRANSACTION;
-
---
--- Table: allele
---
-CREATE TABLE allele (
-  allele_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  variation_id integer NOT NULL,
-  subsnp_id integer,
-  allele_code_id integer NOT NULL,
-  population_id integer,
-  frequency float,
-  count integer,
-  frequency_submitter_handle integer
-);
-
---
--- Table: allele_code
---
-CREATE TABLE allele_code (
-  allele_code_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  allele varchar(100)
-);
-
-CREATE UNIQUE INDEX allele_idx ON allele_code (allele);
-
---
--- Table: associate_study
---
-CREATE TABLE associate_study (
-  study1_id integer NOT NULL,
-  study2_id integer NOT NULL,
-  PRIMARY KEY (study1_id, study2_id)
-);
-
---
--- Table: attrib
---
-CREATE TABLE attrib (
-  attrib_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  attrib_type_id smallint NOT NULL DEFAULT 0,
-  value text NOT NULL
-);
-
-CREATE UNIQUE INDEX type_val_idx ON attrib (attrib_type_id, value);
-
---
--- Table: attrib_set
---
-CREATE TABLE attrib_set (
-  attrib_set_id integer NOT NULL DEFAULT 0,
-  attrib_id integer NOT NULL DEFAULT 0
-);
-
-CREATE UNIQUE INDEX set_idx ON attrib_set (attrib_set_id, attrib_id);
-
---
--- Table: attrib_type
---
-CREATE TABLE attrib_type (
-  attrib_type_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL DEFAULT 0,
-  code varchar(20) NOT NULL DEFAULT '',
-  name varchar(255) NOT NULL DEFAULT '',
-  description text
-);
-
-CREATE UNIQUE INDEX code_idx ON attrib_type (code);
-
---
--- Table: compressed_genotype_region
---
-CREATE TABLE compressed_genotype_region (
-  sample_id integer NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  seq_region_strand tinyint NOT NULL,
-  genotypes blob
-);
-
---
--- Table: compressed_genotype_var
---
-CREATE TABLE compressed_genotype_var (
-  variation_id integer NOT NULL,
-  subsnp_id integer,
-  genotypes blob
-);
-
---
--- Table: coord_system
---
-CREATE TABLE coord_system (
-  coord_system_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  species_id integer NOT NULL DEFAULT 1,
-  name varchar(40) NOT NULL,
-  version varchar(255),
-  rank integer NOT NULL,
-  attrib varchar
-);
-
-CREATE UNIQUE INDEX name_idx ON coord_system (name, version, species_id);
-
-CREATE UNIQUE INDEX rank_idx ON coord_system (rank, species_id);
-
---
--- Table: display_group
---
-CREATE TABLE display_group (
-  display_group_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  display_priority integer NOT NULL,
-  display_name varchar(255) NOT NULL
-);
-
-CREATE UNIQUE INDEX display_name ON display_group (display_name);
-
-CREATE UNIQUE INDEX display_priority ON display_group (display_priority);
-
---
--- Table: failed_allele
---
-CREATE TABLE failed_allele (
-  failed_allele_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  allele_id integer NOT NULL,
-  failed_description_id integer NOT NULL
-);
-
-CREATE UNIQUE INDEX allele_idx02 ON failed_allele (allele_id, failed_description_id);
-
---
--- Table: failed_description
---
-CREATE TABLE failed_description (
-  failed_description_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  description text NOT NULL
-);
-
---
--- Table: failed_structural_variation
---
-CREATE TABLE failed_structural_variation (
-  failed_structural_variation_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  structural_variation_id integer NOT NULL,
-  failed_description_id integer NOT NULL
-);
-
-CREATE UNIQUE INDEX structural_variation_idx ON failed_structural_variation (structural_variation_id, failed_description_id);
-
---
--- Table: failed_variation
---
-CREATE TABLE failed_variation (
-  failed_variation_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  variation_id integer NOT NULL,
-  failed_description_id integer NOT NULL
-);
-
-CREATE UNIQUE INDEX variation_idx ON failed_variation (variation_id, failed_description_id);
-
---
--- Table: genotype_code
---
-CREATE TABLE genotype_code (
-  genotype_code_id integer NOT NULL,
-  allele_code_id integer NOT NULL,
-  haplotype_id tinyint NOT NULL,
-  phased tinyint
-);
-
---
--- Table: individual
---
-CREATE TABLE individual (
-  individual_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  name varchar(255),
-  description text,
-  gender enum NOT NULL DEFAULT 'Unknown',
-  father_individual_id integer,
-  mother_individual_id integer,
-  individual_type_id integer NOT NULL DEFAULT 0
-);
-
---
--- Table: individual_synonym
---
-CREATE TABLE individual_synonym (
-  synonym_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  individual_id integer NOT NULL,
-  source_id integer NOT NULL,
-  name varchar(255)
-);
-
---
--- Table: individual_type
---
-CREATE TABLE individual_type (
-  individual_type_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  name varchar(255) NOT NULL,
-  description text
-);
-
---
--- Table: meta
---
-CREATE TABLE meta (
-  meta_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  species_id integer DEFAULT 1,
-  meta_key varchar(40) NOT NULL,
-  meta_value varchar(255) NOT NULL
-);
-
-CREATE UNIQUE INDEX species_key_value_idx ON meta (species_id, meta_key, meta_value);
-
---
--- Table: meta_coord
---
-CREATE TABLE meta_coord (
-  table_name varchar(40) NOT NULL,
-  coord_system_id integer NOT NULL,
-  max_length integer
-);
-
-CREATE UNIQUE INDEX table_name ON meta_coord (table_name, coord_system_id);
-
---
--- Table: motif_feature_variation
---
-CREATE TABLE motif_feature_variation (
-  motif_feature_variation_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  variation_feature_id integer NOT NULL,
-  feature_stable_id varchar(128),
-  motif_feature_id integer NOT NULL,
-  allele_string text,
-  somatic tinyint NOT NULL DEFAULT 0,
-  consequence_types varchar,
-  motif_name varchar(60),
-  motif_start integer,
-  motif_end integer,
-  motif_score_delta float,
-  in_informative_position tinyint NOT NULL DEFAULT 0
-);
-
---
--- Table: phenotype
---
-CREATE TABLE phenotype (
-  phenotype_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  stable_id varchar(255),
-  name varchar(50),
-  description varchar(255)
-);
-
-CREATE UNIQUE INDEX desc_idx ON phenotype (description);
-
---
--- Table: phenotype_feature
---
-CREATE TABLE phenotype_feature (
-  phenotype_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  phenotype_id integer,
-  source_id integer,
-  study_id integer,
-  type enum,
-  object_id varchar(255),
-  is_significant tinyint DEFAULT 1,
-  seq_region_id integer,
-  seq_region_start integer,
-  seq_region_end integer,
-  seq_region_strand tinyint
-);
-
---
--- Table: phenotype_feature_attrib
---
-CREATE TABLE phenotype_feature_attrib (
-  phenotype_feature_id integer NOT NULL,
-  attrib_type_id integer,
-  value varchar(255)
-);
-
---
--- Table: population
---
-CREATE TABLE population (
-  population_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  name varchar(255),
-  size integer,
-  description text,
-  collection tinyint DEFAULT 0,
-  freqs_from_gts tinyint,
-  display enum DEFAULT 'UNDISPLAYABLE',
-  display_group_id tinyint
-);
-
---
--- Table: population_genotype
---
-CREATE TABLE population_genotype (
-  population_genotype_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  variation_id integer NOT NULL,
-  subsnp_id integer,
-  genotype_code_id integer,
-  frequency float,
-  population_id integer,
-  count integer
-);
-
---
--- Table: population_structure
---
-CREATE TABLE population_structure (
-  super_population_id integer NOT NULL,
-  sub_population_id integer NOT NULL
-);
-
-CREATE UNIQUE INDEX super_population_idx ON population_structure (super_population_id, sub_population_id);
-
---
--- Table: population_synonym
---
-CREATE TABLE population_synonym (
-  synonym_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  population_id integer NOT NULL,
-  source_id integer NOT NULL,
-  name varchar(255)
-);
-
---
--- Table: protein_function_predictions
---
-CREATE TABLE protein_function_predictions (
-  translation_md5_id integer NOT NULL,
-  analysis_attrib_id integer NOT NULL,
-  prediction_matrix mediumblob,
-  PRIMARY KEY (translation_md5_id, analysis_attrib_id)
-);
-
---
--- Table: protein_function_predictions_attrib
---
-CREATE TABLE protein_function_predictions_attrib (
-  translation_md5_id integer NOT NULL,
-  analysis_attrib_id integer NOT NULL,
-  attrib_type_id integer NOT NULL,
-  position_values blob,
-  PRIMARY KEY (translation_md5_id, analysis_attrib_id, attrib_type_id)
-);
-
---
--- Table: publication
---
-CREATE TABLE publication (
-  publication_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  title varchar(255),
-  authors varchar(255),
-  pmid integer,
-  pmcid varchar(255),
-  year integer,
-  doi varchar(50),
-  ucsc_id varchar(50)
-);
-
---
--- Table: read_coverage
---
-CREATE TABLE read_coverage (
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  level tinyint NOT NULL,
-  sample_id integer NOT NULL
-);
-
---
--- Table: regulatory_feature_variation
---
-CREATE TABLE regulatory_feature_variation (
-  regulatory_feature_variation_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  variation_feature_id integer NOT NULL,
-  feature_stable_id varchar(128),
-  feature_type text,
-  allele_string text,
-  somatic tinyint NOT NULL DEFAULT 0,
-  consequence_types varchar
-);
-
---
--- Table: sample
---
-CREATE TABLE sample (
-  sample_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  individual_id integer NOT NULL,
-  name varchar(255),
-  description text,
-  study_id integer,
-  display enum DEFAULT 'UNDISPLAYABLE',
-  has_coverage tinyint NOT NULL DEFAULT 0,
-  variation_set_id varchar
-);
-
---
--- Table: sample_genotype_multiple_bp
---
-CREATE TABLE sample_genotype_multiple_bp (
-  variation_id integer NOT NULL,
-  subsnp_id integer,
-  allele_1 varchar(100),
-  allele_2 varchar(100),
-  sample_id integer
-);
-
---
--- Table: sample_population
---
-CREATE TABLE sample_population (
-  sample_id integer NOT NULL,
-  population_id integer NOT NULL
-);
-
---
--- Table: sample_synonym
---
-CREATE TABLE sample_synonym (
-  synonym_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  sample_id integer NOT NULL,
-  source_id integer NOT NULL,
-  name varchar(255)
-);
-
---
--- Table: seq_region
---
-CREATE TABLE seq_region (
-  seq_region_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  name varchar(40) NOT NULL,
-  coord_system_id integer NOT NULL
-);
-
-CREATE UNIQUE INDEX name_cs_idx ON seq_region (name, coord_system_id);
-
---
--- Table: source
---
-CREATE TABLE source (
-  source_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  name varchar(24) NOT NULL,
-  version integer,
-  description varchar(255),
-  url varchar(255),
-  type enum,
-  somatic_status enum DEFAULT 'germline',
-  data_types varchar
-);
-
---
--- Table: structural_variation
---
-CREATE TABLE structural_variation (
-  structural_variation_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  variation_name varchar(255),
-  alias varchar(255),
-  source_id integer NOT NULL,
-  study_id integer,
-  class_attrib_id integer NOT NULL DEFAULT 0,
-  clinical_significance varchar,
-  validation_status enum,
-  is_evidence tinyint DEFAULT 0,
-  somatic tinyint NOT NULL DEFAULT 0,
-  copy_number tinyint
-);
-
-CREATE UNIQUE INDEX variation_name ON structural_variation (variation_name);
-
---
--- Table: structural_variation_association
---
-CREATE TABLE structural_variation_association (
-  structural_variation_id integer NOT NULL,
-  supporting_structural_variation_id integer NOT NULL,
-  PRIMARY KEY (structural_variation_id, supporting_structural_variation_id)
-);
-
---
--- Table: structural_variation_feature
---
-CREATE TABLE structural_variation_feature (
-  structural_variation_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  outer_start integer,
-  seq_region_start integer NOT NULL,
-  inner_start integer,
-  inner_end integer,
-  seq_region_end integer NOT NULL,
-  outer_end integer,
-  seq_region_strand tinyint NOT NULL,
-  structural_variation_id integer NOT NULL,
-  variation_name varchar(255),
-  source_id integer NOT NULL,
-  study_id integer,
-  class_attrib_id integer NOT NULL DEFAULT 0,
-  allele_string longtext,
-  is_evidence tinyint NOT NULL DEFAULT 0,
-  variation_set_id varchar NOT NULL DEFAULT '',
-  somatic tinyint NOT NULL DEFAULT 0,
-  breakpoint_order tinyint,
-  length integer
-);
-
---
--- Table: structural_variation_sample
---
-CREATE TABLE structural_variation_sample (
-  structural_variation_sample_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  structural_variation_id integer NOT NULL,
-  sample_id integer
-);
-
---
--- Table: study
---
-CREATE TABLE study (
-  study_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  source_id integer NOT NULL,
-  name varchar(255),
-  description text,
-  url varchar(255),
-  external_reference varchar(255),
-  study_type varchar(255)
-);
-
---
--- Table: submitter_handle
---
-CREATE TABLE submitter_handle (
-  handle_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  handle varchar(25)
-);
-
-CREATE UNIQUE INDEX handle ON submitter_handle (handle);
-
---
--- Table: subsnp_handle
---
-CREATE TABLE subsnp_handle (
-  subsnp_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  handle varchar(20)
-);
-
---
--- Table: subsnp_map
---
-CREATE TABLE subsnp_map (
-  variation_id integer NOT NULL,
-  subsnp_id integer
-);
-
---
--- Table: tmp_sample_genotype_single_bp
---
-CREATE TABLE tmp_sample_genotype_single_bp (
-  variation_id integer NOT NULL,
-  subsnp_id integer,
-  allele_1 char(1),
-  allele_2 char(1),
-  sample_id integer NOT NULL
-);
-
---
--- Table: transcript_variation
---
-CREATE TABLE transcript_variation (
-  transcript_variation_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  variation_feature_id integer NOT NULL,
-  feature_stable_id varchar(128),
-  allele_string text,
-  somatic tinyint NOT NULL DEFAULT 0,
-  consequence_types varchar,
-  cds_start integer,
-  cds_end integer,
-  cdna_start integer,
-  cdna_end integer,
-  translation_start integer,
-  translation_end integer,
-  distance_to_transcript integer,
-  codon_allele_string text,
-  pep_allele_string text,
-  hgvs_genomic text,
-  hgvs_transcript text,
-  hgvs_protein text,
-  polyphen_prediction enum,
-  sift_prediction enum,
-  polyphen_score float,
-  sift_score float,
-  display integer DEFAULT 1
-);
-
---
--- Table: translation_md5
---
-CREATE TABLE translation_md5 (
-  translation_md5_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  translation_md5 char(32) NOT NULL
-);
-
-CREATE UNIQUE INDEX md5_idx ON translation_md5 (translation_md5);
-
---
--- Table: variation
---
-CREATE TABLE variation (
-  variation_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  source_id integer NOT NULL,
-  name varchar(255),
-  ancestral_allele varchar(255),
-  flipped tinyint,
-  class_attrib_id integer DEFAULT 0,
-  somatic tinyint NOT NULL DEFAULT 0,
-  minor_allele varchar(50),
-  minor_allele_freq float,
-  minor_allele_count integer,
-  clinical_significance varchar,
-  evidence_attribs varchar,
-  display integer DEFAULT 1
-);
-
-CREATE UNIQUE INDEX name ON variation (name);
-
---
--- Table: variation_attrib
---
-CREATE TABLE variation_attrib (
-  variation_id integer NOT NULL,
-  attrib_id integer,
-  value varchar(255)
-);
-
---
--- Table: variation_citation
---
-CREATE TABLE variation_citation (
-  variation_id integer NOT NULL,
-  publication_id integer NOT NULL,
-  PRIMARY KEY (variation_id, publication_id)
-);
-
---
--- Table: variation_feature
---
-CREATE TABLE variation_feature (
-  variation_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  seq_region_strand tinyint NOT NULL,
-  variation_id integer NOT NULL,
-  allele_string varchar(100),
-  variation_name varchar(255),
-  map_weight integer NOT NULL,
-  flags varchar,
-  source_id integer NOT NULL,
-  consequence_types varchar NOT NULL DEFAULT 'intergenic_variant',
-  variation_set_id varchar NOT NULL DEFAULT '',
-  class_attrib_id integer DEFAULT 0,
-  somatic tinyint NOT NULL DEFAULT 0,
-  minor_allele varchar(50),
-  minor_allele_freq float,
-  minor_allele_count integer,
-  alignment_quality double precision,
-  evidence_attribs varchar,
-  clinical_significance varchar,
-  display integer DEFAULT 1
-);
-
---
--- Table: variation_genename
---
-CREATE TABLE variation_genename (
-  variation_id integer NOT NULL,
-  gene_name varchar(255) NOT NULL,
-  PRIMARY KEY (variation_id, gene_name)
-);
-
---
--- Table: variation_hgvs
---
-CREATE TABLE variation_hgvs (
-  variation_id integer NOT NULL,
-  hgvs_name varchar(255) NOT NULL,
-  PRIMARY KEY (variation_id, hgvs_name)
-);
-
---
--- Table: variation_set
---
-CREATE TABLE variation_set (
-  variation_set_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  name varchar(255),
-  description text,
-  short_name_attrib_id integer
-);
-
---
--- Table: variation_set_structural_variation
---
-CREATE TABLE variation_set_structural_variation (
-  structural_variation_id integer NOT NULL,
-  variation_set_id integer NOT NULL,
-  PRIMARY KEY (structural_variation_id, variation_set_id)
-);
-
---
--- Table: variation_set_structure
---
-CREATE TABLE variation_set_structure (
-  variation_set_super integer NOT NULL,
-  variation_set_sub integer NOT NULL,
-  PRIMARY KEY (variation_set_super, variation_set_sub)
-);
-
---
--- Table: variation_set_variation
---
-CREATE TABLE variation_set_variation (
-  variation_id integer NOT NULL,
-  variation_set_id integer NOT NULL,
-  PRIMARY KEY (variation_id, variation_set_id)
-);
-
---
--- Table: variation_synonym
---
-CREATE TABLE variation_synonym (
-  variation_synonym_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  variation_id integer NOT NULL,
-  subsnp_id integer,
-  source_id integer NOT NULL,
-  name varchar(255)
-);
-
-CREATE UNIQUE INDEX name02 ON variation_synonym (name, source_id);
-
-COMMIT;