Commit 6ef56d00 authored by Francisco Arcila Salamanca's avatar Francisco Arcila Salamanca
Browse files

db changes for airr files with string identifiers in output

parent 48cbfdbf
...@@ -28,7 +28,7 @@ SHOW WARNINGS; ...@@ -28,7 +28,7 @@ SHOW WARNINGS;
-- Table `sample` -- Table `sample`
-- ----------------------------------------------------- -- -----------------------------------------------------
CREATE TABLE IF NOT EXISTS `sample` ( CREATE TABLE IF NOT EXISTS `sample` (
`sample_id` INT UNSIGNED NOT NULL AUTO_INCREMENT, `sample_id` VARCHAR(200) NOT NULL,
`donor_id` INT NOT NULL, `donor_id` INT NOT NULL,
`tissue` VARCHAR(45) NOT NULL, `tissue` VARCHAR(45) NOT NULL,
`sampling_date` DATETIME NULL, #importer change `sampling_date` DATETIME NULL, #importer change
...@@ -63,7 +63,7 @@ SHOW WARNINGS; ...@@ -63,7 +63,7 @@ SHOW WARNINGS;
-- Table `sequences` -- Table `sequences`
-- ----------------------------------------------------- -- -----------------------------------------------------
CREATE TABLE IF NOT EXISTS `sequences` ( CREATE TABLE IF NOT EXISTS `sequences` (
`seq_id` INT UNSIGNED NOT NULL AUTO_INCREMENT, `seq_id` VARCHAR(200) NOT NULL,
`name` VARCHAR(45) NULL, `name` VARCHAR(45) NULL,
`consensus_rank` INT NULL, `consensus_rank` INT NULL,
`locus` CHAR NULL, `locus` CHAR NULL,
...@@ -87,7 +87,7 @@ SHOW WARNINGS; ...@@ -87,7 +87,7 @@ SHOW WARNINGS;
-- ----------------------------------------------------- -- -----------------------------------------------------
CREATE TABLE IF NOT EXISTS `constant_segments` ( CREATE TABLE IF NOT EXISTS `constant_segments` (
`constant_segments_id` INT NOT NULL AUTO_INCREMENT, `constant_segments_id` INT NOT NULL AUTO_INCREMENT,
`seq_id` INT UNSIGNED NOT NULL, `seq_id` VARCHAR(200) NOT NULL,
`name` VARCHAR(20) NOT NULL, `name` VARCHAR(20) NOT NULL,
`percid` FLOAT NOT NULL, `percid` FLOAT NOT NULL,
`length` INT UNSIGNED NOT NULL, `length` INT UNSIGNED NOT NULL,
...@@ -110,7 +110,7 @@ SHOW WARNINGS; ...@@ -110,7 +110,7 @@ SHOW WARNINGS;
-- ----------------------------------------------------- -- -----------------------------------------------------
CREATE TABLE IF NOT EXISTS `VDJ_segments` ( CREATE TABLE IF NOT EXISTS `VDJ_segments` (
`VDJ_segments_id` INT NOT NULL AUTO_INCREMENT, `VDJ_segments_id` INT NOT NULL AUTO_INCREMENT,
`seq_id` INT UNSIGNED NOT NULL, `seq_id` VARCHAR(200) NOT NULL,
`type` CHAR(1) NOT NULL, `type` CHAR(1) NOT NULL,
`locus` CHAR NOT NULL, `locus` CHAR NOT NULL,
`igblast_rank` INT(1) UNSIGNED NOT NULL, `igblast_rank` INT(1) UNSIGNED NOT NULL,
...@@ -131,7 +131,7 @@ SHOW WARNINGS; ...@@ -131,7 +131,7 @@ SHOW WARNINGS;
-- ----------------------------------------------------- -- -----------------------------------------------------
CREATE TABLE IF NOT EXISTS `CDR_FWR` ( CREATE TABLE IF NOT EXISTS `CDR_FWR` (
`CDR_FWR_id` INT NOT NULL AUTO_INCREMENT, `CDR_FWR_id` INT NOT NULL AUTO_INCREMENT,
`seq_id` INT UNSIGNED NOT NULL, `seq_id` VARCHAR(200) NOT NULL,
`region` VARCHAR(20) NOT NULL, `region` VARCHAR(20) NOT NULL,
`start` INT UNSIGNED NOT NULL, `start` INT UNSIGNED NOT NULL,
`end` INT UNSIGNED NOT NULL, `end` INT UNSIGNED NOT NULL,
...@@ -151,7 +151,7 @@ SHOW WARNINGS; ...@@ -151,7 +151,7 @@ SHOW WARNINGS;
-- ----------------------------------------------------- -- -----------------------------------------------------
CREATE TABLE IF NOT EXISTS `warnings` ( CREATE TABLE IF NOT EXISTS `warnings` (
`warnings_id` INT NOT NULL AUTO_INCREMENT, `warnings_id` INT NOT NULL AUTO_INCREMENT,
`seq_id` INT UNSIGNED NOT NULL, `seq_id` VARCHAR(200) NOT NULL,
`quality_score` INT NULL, `quality_score` INT NULL,
`FWR3_igblast_output` TINYINT(1) NOT NULL, `FWR3_igblast_output` TINYINT(1) NOT NULL,
`CDR3_start_C` TINYINT(1) NOT NULL, `CDR3_start_C` TINYINT(1) NOT NULL,
...@@ -170,7 +170,7 @@ SHOW WARNINGS; ...@@ -170,7 +170,7 @@ SHOW WARNINGS;
-- ----------------------------------------------------- -- -----------------------------------------------------
CREATE TABLE IF NOT EXISTS `sequencing_run` ( CREATE TABLE IF NOT EXISTS `sequencing_run` (
`sequencing_run_id` INT UNSIGNED NOT NULL AUTO_INCREMENT, `sequencing_run_id` INT UNSIGNED NOT NULL AUTO_INCREMENT,
`date` DATETIME NOT NULL, `date` DATETIME NULL,
`name` VARCHAR(45) NULL, # changed for importer `name` VARCHAR(45) NULL, # changed for importer
`processed_by` VARCHAR(45) NOT NULL, `processed_by` VARCHAR(45) NOT NULL,
`experiment_id` VARCHAR(10) NULL, # changed for importer `experiment_id` VARCHAR(10) NULL, # changed for importer
...@@ -208,7 +208,7 @@ SHOW WARNINGS; ...@@ -208,7 +208,7 @@ SHOW WARNINGS;
-- ----------------------------------------------------- -- -----------------------------------------------------
CREATE TABLE IF NOT EXISTS `igblast_alignment` ( CREATE TABLE IF NOT EXISTS `igblast_alignment` (
`igblast_alignment_id` INT NOT NULL AUTO_INCREMENT, `igblast_alignment_id` INT NOT NULL AUTO_INCREMENT,
`seq_id` INT UNSIGNED NOT NULL, `seq_id` VARCHAR(200) NOT NULL,
`query_start` INT UNSIGNED NOT NULL, `query_start` INT UNSIGNED NOT NULL,
`germline_start` INT UNSIGNED NOT NULL, `germline_start` INT UNSIGNED NOT NULL,
`query_seq` VARCHAR(500) NOT NULL, `query_seq` VARCHAR(500) NOT NULL,
......
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