diagnostics hide <run_id>

sqlite3 <path/to/biolite.sqlite>

BEGIN TRANSACTION;
ALTER TABLE runs RENAME TO runs_old;
DROP INDEX runs_name;
DROP INDEX runs_id;
CREATE TABLE runs (
   done INTEGER DEFAULT '0',
   run_id INTEGER PRIMARY KEY AUTOINCREMENT,
   id VARCHAR(256),
   name VARCHAR(32),
   hostname VARCHAR(32),
   username VARCHAR(32),
   timestamp DATETIME,
   hidden INTEGER DEFAULT '0');
CREATE INDEX runs_done ON runs(done);
CREATE INDEX runs_hidden ON runs(hidden);
CREATE INDEX runs_id ON runs(id);
CREATE INDEX runs_name ON runs(name);
INSERT INTO runs (run_id,id,name,hostname,username,timestamp,hidden) SELECT * FROM runs_old;
UPDATE runs SET done=1 WHERE hidden=0;
DROP TABLE runs_old;
COMMIT;

sqlite3 <path/to/agalma.sqlite>

BEGIN TRANSACTION;
ALTER TABLE sequences RENAME TO sequences_old;
DROP INDEX sequences_catalog_id;
DROP INDEX sequences_locus;
DROP INDEX sequences_transcript;
DROP INDEX sequences_run_id;
CREATE TABLE sequences (
   sequence_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   run_id INTEGER,
   catalog_id VARCHAR(256),
   locus INTEGER,
   transcript INTEGER,
   confidence FLOAT,
   expression FLOAT,
   nucleotide_seq TEXT,
   nucleotide_quality TEXT,
   protein_seq TEXT,
   translation_method VARCHAR(256),
   organelle VARCHAR(256),
   blast_hit TEXT,
   nucleotide_header TEXT,
   protein_header TEXT,
   note TEXT);
CREATE INDEX sequences_catalog_id ON sequences(catalog_id);
CREATE INDEX sequences_expression ON sequences(expression);
CREATE INDEX sequences_locus ON sequences(locus);
CREATE INDEX sequences_run_id ON sequences(run_id);
CREATE INDEX sequences_transcript ON sequences(transcript);
INSERT INTO sequences SELECT sequence_id,run_id,catalog_id,locus,transcript,confidence,rpkm,nucleotide_seq,nucleotide_quality,protein_seq,translation_method,organelle,blast_hit,nucleotide_header,protein_header,note FROM sequences_old;
DROP TABLE sequences_old;
COMMIT;