View source for ABGSA

== Rationale of the ABGSA ==

== Description of the layout ==

== Metadata database ==

  +-----------------------+
  | Tables_in_ABGSAschema |
  +-----------------------+
  | ABGSAschema_main      |
  | filesize              |
  | fqfile_attributes     |
  | gc_cont               |
  +-----------------------+

  +-------------------------+--------------+------+-----+---------+-------+
  | Field                   | Type         | Null | Key | Default | Extra |
  +-------------------------+--------------+------+-----+---------+-------+
  | archive_name            | varchar(9)   | YES  |     | NULL    |       |
  | lane_names_orig         | varchar(120) | NO   | PRI |         |       |
  | readno                  | varchar(6)   | YES  |     | NULL    |       |
  | ABG_individual_id       | varchar(40)  | YES  |     | NULL    |       |
  | PORHAPNUMBER            | varchar(40)  | YES  |     | NULL    |       |
  | HapMap60Kcheck          | varchar(45)  | YES  |     | NULL    |       |
  | perc_ident              | float        | YES  |     | NULL    |       |
  | indiv_pop_generic_name  | varchar(60)  | YES  |     | NULL    |       |
  | library_type            | varchar(40)  | YES  |     | NULL    |       |
  | md5sum_gzip             | varchar(35)  | YES  |     | NULL    |       |
  | md5sum_txt              | varchar(35)  | YES  |     | NULL    |       |
  | seq_format              | varchar(8)   | YES  |     | NULL    |       |
  | qscore_format           | varchar(16)  | YES  |     | NULL    |       |
  | generated_by            | varchar(30)  | YES  |     | NULL    |       |
  | Machine_type            | varchar(30)  | YES  |     | NULL    |       |
  | date_generated          | varchar(12)  | YES  |     | NULL    |       |
  | Lane_in_run             | varchar(4)   | YES  |     | NULL    |       |
  | lib_previously_known_as | varchar(30)  | YES  |     | NULL    |       |
  | remark                  | varchar(100) | YES  |     | NULL    |       |
  +-------------------------+--------------+------+-----+---------+-------+

<source lang='mysql'>
CREATE TABLE `ABGSAschema_main` (
  `archive_name` varchar(9) DEFAULT NULL,
  `lane_names_orig` varchar(120) NOT NULL DEFAULT '',
  `readno` varchar(6) DEFAULT NULL,
  `ABG_individual_id` varchar(40) DEFAULT NULL,
  `PORHAPNUMBER` varchar(40) DEFAULT NULL,
  `HapMap60Kcheck` varchar(45) DEFAULT NULL,
  `perc_ident` float DEFAULT NULL,
  `indiv_pop_generic_name` varchar(60) DEFAULT NULL,
  `library_type` varchar(40) DEFAULT NULL,
  `md5sum_gzip` varchar(35) DEFAULT NULL,
  `md5sum_txt` varchar(35) DEFAULT NULL,
  `seq_format` varchar(8) DEFAULT NULL,
  `qscore_format` varchar(16) DEFAULT NULL,
  `generated_by` varchar(30) DEFAULT NULL,
  `Machine_type` varchar(30) DEFAULT NULL,
  `date_generated` varchar(12) DEFAULT NULL,
  `Lane_in_run` varchar(4) DEFAULT NULL,
  `lib_previously_known_as` varchar(30) DEFAULT NULL,
  `remark` varchar(100) DEFAULT NULL,
  PRIMARY KEY (`lane_names_orig`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1 |
</source>

  +------------------+--------------+------+-----+-------------------+----------------+
  | Field            | Type         | Null | Key | Default           | Extra          |
  +------------------+--------------+------+-----+-------------------+----------------+
  | id               | int(11)      | NO   | PRI | NULL              | auto_increment |
  | lane_names_orig  | varchar(120) | YES  |     | NULL              |                |
  | md5check         | varchar(120) | YES  |     | NULL              |                |
  | filesize         | bigint(15)   | YES  |     | NULL              |                |
  | numlines_in_gzip | bigint(15)   | YES  |     | NULL              |                |
  | qval_offset      | varchar(10)  | YES  |     | NULL              |                |
  | maxlength_seq    | int(6)       | YES  |     | NULL              |                |
  | totnumbases      | bigint(15)   | YES  |     | NULL              |                |
  | totnumreads      | int(12)      | YES  |     | NULL              |                |
  | firstreadname    | varchar(120) | YES  |     | NULL              |                |
  | lastreadname     | varchar(120) | YES  |     | NULL              |                |
  | ts_create        | timestamp    | NO   |     | CURRENT_TIMESTAMP |                |
  +------------------+--------------+------+-----+-------------------+----------------+

<source lang='mysql'>
CREATE TABLE `fqfile_attributes` (
  `id` int(11) NOT NULL AUTO_INCREMENT,
  `lane_names_orig` varchar(120) DEFAULT NULL,
  `md5check` varchar(120) DEFAULT NULL,
  `filesize` bigint(15) DEFAULT NULL,
  `numlines_in_gzip` bigint(15) DEFAULT NULL,
  `qval_offset` varchar(10) DEFAULT NULL,
  `maxlength_seq` int(6) DEFAULT NULL,
  `totnumbases` bigint(15) DEFAULT NULL,
  `totnumreads` int(12) DEFAULT NULL,
  `firstreadname` varchar(120) DEFAULT NULL,
  `lastreadname` varchar(120) DEFAULT NULL,
  `ts_create` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP,
  PRIMARY KEY (`id`)
) ENGINE=InnoDB AUTO_INCREMENT=1561 DEFAULT CHARSET=latin1 
</source>

  +-----------------+--------------+------+-----+-------------------+----------------+
  | Field           | Type         | Null | Key | Default           | Extra          |
  +-----------------+--------------+------+-----+-------------------+----------------+
  | id              | int(11)      | NO   | PRI | NULL              | auto_increment |
  | lane_names_orig | varchar(120) | YES  |     | NULL              |                |
  | gc_cont         | float        | YES  |     | NULL              |                |
  | ts_create       | timestamp    | NO   |     | CURRENT_TIMESTAMP |                |
  +-----------------+--------------+------+-----+-------------------+----------------+


<source lang='mysql'>
 CREATE TABLE `gc_cont` (
  `id` int(11) NOT NULL AUTO_INCREMENT,
  `lane_names_orig` varchar(120) DEFAULT NULL,
  `gc_cont` float DEFAULT NULL,
  `ts_create` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP,
  PRIMARY KEY (`id`)
) ENGINE=InnoDB AUTO_INCREMENT=1561 DEFAULT CHARSET=latin1
</source>

  +-----------------+--------------+------+-----+---------+-------+
  | Field           | Type         | Null | Key | Default | Extra |
  +-----------------+--------------+------+-----+---------+-------+
  | lane_names_orig | varchar(120) | YES  |     | NULL    |       |
  | filesize        | bigint(15)   | YES  |     | NULL    |       |
  | md5check        | varchar(35)  | YES  |     | NULL    |       |
  +-----------------+--------------+------+-----+---------+-------+
<source lang='mysql'>
CREATE TABLE `filesize` (
  `lane_names_orig` varchar(120) DEFAULT NULL,
  `filesize` bigint(15) DEFAULT NULL,
  `md5check` varchar(35) DEFAULT NULL
) ENGINE=MyISAM DEFAULT CHARSET=latin1
</source>

== Checking data integrity ==

== Backing up ==

== See also ==

== External links ==