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sqlite_schema.sql
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sqlite_schema.sql
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-- Pragmas used when creating tables in the database only
PRAGMA synchronous = OFF;
PRAGMA journal_mode = MEMORY;
PRAGMA user_version = 1;
BEGIN TRANSACTION;
CREATE TABLE IF NOT EXISTS `clusterlnk` (
`clusterid` integer NOT NULL,
`repeatid` integer NOT NULL,
`direction` char(1) NOT NULL,
`reserved` integer NOT NULL,
`reserved2` integer NOT NULL,
PRIMARY KEY (`clusterid`,`repeatid`),
UNIQUE (`repeatid`)
);
CREATE TABLE IF NOT EXISTS `clusters` (
`cid` integer NOT NULL,
`minpat` integer NOT NULL,
`maxpat` integer NOT NULL,
`refs_flank_undist` integer DEFAULT NULL,
`refs_flank_dist` integer DEFAULT NULL,
`refs_flank_undist_l` integer DEFAULT NULL,
`refs_flank_undist_r` integer DEFAULT NULL,
`refs_flank_undist_lr` integer DEFAULT NULL,
`repeatcount` integer NOT NULL,
`refcount` integer NOT NULL,
`variability` integer NOT NULL DEFAULT '0',
`assemblyreq` integer DEFAULT NULL,
`profdensity` float DEFAULT NULL,
`flankdensity` float DEFAULT NULL,
`mcpattern` varchar(5000) DEFAULT NULL,
`aveentropy` float DEFAULT NULL,
PRIMARY KEY (`cid`)
);
CREATE TABLE IF NOT EXISTS `fasta_reads` (
`sid` integer NOT NULL,
`head` varchar(500) NOT NULL,
`dna` varchar(8000) DEFAULT NULL,
`qual` varchar(8000) DEFAULT NULL,
PRIMARY KEY (`sid`),
UNIQUE (`head`)
);
-- sequence data moved to external db
CREATE TABLE IF NOT EXISTS `fasta_ref_reps` (
`rid` integer NOT NULL,
`comment` varchar(500) DEFAULT NULL,
`flank_disting` integer DEFAULT NULL,
`entropy` float NOT NULL DEFAULT '0',
`has_support` integer DEFAULT NULL,
`span1` integer DEFAULT NULL,
`spanN` integer DEFAULT NULL,
`homez_same` integer DEFAULT NULL,
`homez_diff` integer DEFAULT NULL,
`hetez_same` integer DEFAULT NULL,
`hetez_diff` integer DEFAULT NULL,
`hetez_multi` integer DEFAULT NULL,
`support_vntr` integer DEFAULT NULL,
`support_vntr_span1` integer DEFAULT NULL,
`alleles_sup` integer DEFAULT NULL,
`allele_sup_same_as_ref` integer DEFAULT NULL,
PRIMARY KEY (`rid`),
UNIQUE (`rid`,`comment`)
);
CREATE TABLE IF NOT EXISTS `flank_connection` (
`refid` integer NOT NULL,
`clusterid` integer NOT NULL,
`fcomponentsize` integer NOT NULL,
`fcomponentid` integer NOT NULL,
`paramsetid` integer NOT NULL,
PRIMARY KEY (`refid`,`paramsetid`),
CONSTRAINT `flank_connection_ibfk_1` FOREIGN KEY (`paramsetid`) REFERENCES `flank_params` (`paramsetid`)
);
CREATE TABLE IF NOT EXISTS `flank_params` (
`paramsetid` integer NOT NULL PRIMARY KEY,
`flength` integer NOT NULL,
`ferrors` integer NOT NULL
);
CREATE TABLE IF NOT EXISTS `map` (
`refid` integer NOT NULL,
`readid` integer NOT NULL,
`reserved` integer NOT NULL,
`reserved2` integer NOT NULL,
`bbb` integer NOT NULL DEFAULT '0',
PRIMARY KEY (`refid`,`readid`)
);
CREATE TABLE IF NOT EXISTS `rank` (
`refid` integer NOT NULL,
`readid` integer NOT NULL,
`score` float DEFAULT NULL,
`ties` integer NOT NULL DEFAULT '0',
`refdir` char(1) NOT NULL,
PRIMARY KEY (`refid`,`readid`)
);
CREATE TABLE IF NOT EXISTS `rankflank` (
`refid` integer NOT NULL,
`readid` integer NOT NULL,
`score` float DEFAULT NULL,
`ties` integer NOT NULL DEFAULT '0',
PRIMARY KEY (`refid`,`readid`)
);
CREATE TABLE IF NOT EXISTS `replnk` (
`rid` integer NOT NULL,
`sid` integer NOT NULL,
`first` integer NOT NULL,
`last` integer NOT NULL,
`patsize` integer NOT NULL,
`copynum` float NOT NULL,
`pattern` text NOT NULL,
`profile` text COLLATE BINARY,
`profilerc` text COLLATE BINARY,
`profsize` integer DEFAULT NULL,
PRIMARY KEY (`rid`)
);
CREATE TABLE IF NOT EXISTS `stats` (
`id` integer NOT NULL,
`MAP_ROOT` varchar(500) DEFAULT NULL,
`PARAM_TRF` varchar(500) DEFAULT NULL,
`PARAM_PROCLU` varchar(500) DEFAULT NULL,
`FOLDER_FASTA` varchar(500) DEFAULT NULL,
`FOLDER_PROFILES` varchar(500) DEFAULT NULL,
`FOLDER_PROFILES_CLEAN` varchar(500) DEFAULT NULL,
`FOLDER_REFERENCE` varchar(500) DEFAULT NULL,
`FILE_REFERENCE_LEB` varchar(500) DEFAULT NULL,
`FILE_REFERENCE_SEQ` varchar(500) DEFAULT NULL,
`NUMBER_READS` integer DEFAULT NULL,
`NUMBER_TRS_IN_READS` integer DEFAULT NULL,
`NUMBER_TRS_IN_READS_GE7` integer DEFAULT NULL,
`NUMBER_READS_WITHTRS` integer DEFAULT NULL,
`NUMBER_READS_WITHTRS_GE7` integer DEFAULT NULL,
`NUMBER_READS_WITHTRS_GE7_AFTER_REDUND` integer DEFAULT NULL,
`NUMBER_TRS_IN_READS_AFTER_REDUND` integer DEFAULT NULL,
`NUMBER_REF_TRS` integer DEFAULT NULL,
`NUMBER_REFS_TRS_AFTER_REDUND` integer DEFAULT NULL,
`CLUST_NUMBER_OF_PROCLU_CLUSTERS` integer DEFAULT NULL,
`CLUST_NUMBER_OF_PROCLU_CLUSTERS_BEFORE_REJOIN` integer DEFAULT NULL,
`CLUST_NUMBER_OF_EXACTPAT_CLUSTERS` integer DEFAULT NULL,
`CLUST_NUMBER_OF_REF_REPS_IN_CLUSTERS` integer DEFAULT NULL,
`CLUST_NUMBER_OF_READ_REPS_IN_CLUSTERS` integer DEFAULT NULL,
`CLUST_LARGEST_NUMBER_OF_TRS_IN_PROCLU_CLUSTER` integer DEFAULT NULL,
`CLUST_LARGEST_NUMBER_OF_REFS_IN_PROCLU_CLUSTER` integer DEFAULT NULL,
`CLUST_LARGEST_PATRANGE_IN_PROCLU_CLUSTER` integer DEFAULT NULL,
`CLUST_LARGEST_NUMBER_OF_TRS_IN_EXACTPAT_CLUSTER` integer DEFAULT NULL,
`CLUST_LARGEST_NUMBER_OF_REFS_IN_EXACTPAT_CLUSTER` integer DEFAULT NULL,
`CLUST_NUMBER_OF_REFS_WITH_PREDICTED_VNTR` integer DEFAULT NULL,
`CLUST_NUMBER_OF_CLUSTERS_WITH_PREDICTED_VNTR` integer DEFAULT NULL,
`NUMBER_REFS_VNTR_SPAN_N` integer DEFAULT NULL,
`NUMBER_REFS_SINGLE_REF_CLUSTER` integer DEFAULT NULL,
`NUMBER_REFS_SINGLE_REF_CLUSTER_WITH_READS_MAPPED` integer DEFAULT NULL,
`NUMBER_REFS_SINGLE_REF_CLUSTER_WITH_NO_READS_MAPPED` integer DEFAULT NULL,
`NUMBER_MAPPED` integer DEFAULT NULL,
`NUMBER_RANK` integer DEFAULT NULL,
`NUMBER_RANKFLANK` integer DEFAULT NULL,
`INTERSECT_RANK_AND_RANKFLANK` integer DEFAULT NULL,
`INTERSECT_RANK_AND_RANKFLANK_BEFORE_PCR` integer DEFAULT NULL,
`BBB_WITH_MAP_DUPS` integer DEFAULT NULL,
`BBB` integer DEFAULT NULL,
`RANK_EDGES_OVERCUTOFF` integer DEFAULT NULL,
`RANK_REMOVED_SAMEREF` integer DEFAULT NULL,
`RANK_REMOVED_SAMESEQ` integer DEFAULT NULL,
`RANK_REMOVED_PCRDUP` integer DEFAULT NULL,
`RANKFLANK_EDGES_INSERTED` integer DEFAULT NULL,
`RANKFLANK_REMOVED_SAMEREF` integer DEFAULT NULL,
`RANKFLANK_REMOVED_SAMESEQ` integer DEFAULT NULL,
`RANKFLANK_REMOVED_PCRDUP` integer DEFAULT NULL,
`TIME_MYSQLCREATE` integer DEFAULT NULL,
`TIME_TRF` integer DEFAULT NULL,
`TIME_RENUMB` integer DEFAULT NULL,
`TIME_REDUND` integer DEFAULT NULL,
`TIME_PROCLU` integer DEFAULT NULL,
`TIME_JOINCLUST` integer DEFAULT NULL,
`TIME_DB_INSERT_REFS` integer DEFAULT NULL,
`TIME_DB_INSERT_READS` integer DEFAULT NULL,
`TIME_WRITE_FLANKS` integer DEFAULT NULL,
`TIME_MAP_FLANKS` integer DEFAULT NULL,
`TIME_MAP_REFFLANKS` integer DEFAULT NULL,
`TIME_MAP_INSERT` integer DEFAULT NULL,
`TIME_EDGES` integer DEFAULT NULL,
`TIME_INDEX_PCR` integer DEFAULT NULL,
`TIME_PCR_DUP` integer DEFAULT NULL,
`TIME_MAP_DUP` integer DEFAULT NULL,
`TIME_VNTR_PREDICT` integer DEFAULT NULL,
`TIME_ASSEMBLYREQ` integer DEFAULT NULL,
`TIME_REPORTS` integer DEFAULT NULL,
`TIME_DB_CONVERSION_AND_READ_COMPRESSION` integer DEFAULT NULL,
`DATE_MYSQLCREATE` text DEFAULT NULL,
`DATE_TRF` text DEFAULT NULL,
`DATE_RENUMB` text DEFAULT NULL,
`DATE_REDUND` text DEFAULT NULL,
`DATE_PROCLU` text DEFAULT NULL,
`DATE_JOINCLUST` text DEFAULT NULL,
`DATE_DB_INSERT_REFS` text DEFAULT NULL,
`DATE_DB_INSERT_READS` text DEFAULT NULL,
`DATE_WRITE_FLANKS` text DEFAULT NULL,
`DATE_MAP_FLANKS` text DEFAULT NULL,
`DATE_MAP_REFFLANKS` text DEFAULT NULL,
`DATE_MAP_INSERT` text DEFAULT NULL,
`DATE_EDGES` text DEFAULT NULL,
`DATE_INDEX_PCR` text DEFAULT NULL,
`DATE_PCR_DUP` text DEFAULT NULL,
`DATE_MAP_DUP` text DEFAULT NULL,
`DATE_VNTR_PREDICT` text DEFAULT NULL,
`DATE_ASSEMBLYREQ` text DEFAULT NULL,
`DATE_REPORTS` text DEFAULT NULL,
`DATE_DB_CONVERSION_AND_READ_COMPRESSION` text DEFAULT NULL,
`ERROR_STEP` integer NOT NULL DEFAULT '0',
`ERROR_DESC` varchar(500) NOT NULL DEFAULT '',
`ERROR_CODE` integer NOT NULL DEFAULT '0',
`N_MIN_SUPPORT` integer NOT NULL DEFAULT '0',
`MIN_FLANK_REQUIRED` integer NOT NULL DEFAULT '0',
`MAX_FLANK_CONSIDERED` integer NOT NULL DEFAULT '0',
PRIMARY KEY (`id`)
);
CREATE TABLE IF NOT EXISTS `vntr_support` (
`refid` integer NOT NULL,
`copies` integer NOT NULL,
`sameasref` integer NOT NULL,
`support` integer NOT NULL DEFAULT '0',
`copiesfloat` float NOT NULL,
`representative` integer DEFAULT NULL,
PRIMARY KEY (`refid`,`copies`)
);
CREATE INDEX IF NOT EXISTS "idx_map_read_index" ON "map" (`readid`);
CREATE INDEX IF NOT EXISTS "idx_replnk_sid" ON "replnk" (`sid`);
CREATE INDEX IF NOT EXISTS "idx_vntr_support_read_index" ON "vntr_support" (`representative`);
CREATE INDEX IF NOT EXISTS "idx_vntr_support_copies_support" ON "vntr_support" (`copies`,`support`);
--CREATE INDEX IF NOT EXISTS "idx_fasta_ref_reps_head" ON "fasta_ref_reps" (`head`);
CREATE INDEX IF NOT EXISTS "idx_flank_connection_paramsetid" ON "flank_connection" (`paramsetid`);
DELETE FROM stats;
INSERT INTO stats DEFAULT VALUES;
END TRANSACTION;