anchor.diff:  |        10 |            1 | C      |     0.978 |       661 |
   +-----------+--------------+--------+-----------+-----------+
   10 rows in set (0.04 sec)
  +||#
  +
  +(def-view-class allele ()
  +  ((allele-id :db-type :key :type integer)
  +   (variation-id :db-type :key :type integer)
  +   (variation :db-type :join :db-info (:join-class variation
  +				       :foreign-key variation-id
  +				       :home-key variation-id
  +				       :retrieval :delayed))
  +   (allele :db-type :base :type (string 255))
  +   (frequency :db-type :base :type float)
  +   (sample-id :db-type :base :type integer)
  +   (sample :db-type :join :db-info (:join-class sample
  +				    :foreign-key sample-id
  +				    :home-key sample-id)))
  +   (:base-table "allele")
  +   (:documentation "The allele links the abstract notion of a variation with a particular study (see class 'sample') that identified that allele. However, the sample may also refer to 'individuals'."))
  +  
  +#|| 		sample
  ++-------------+------------------+------+-----+---------+----------------+
  +| sample_id   | int(10) unsigned |      | PRI | NULL    | auto_increment |
  +| name        | varchar(255)     |      | MUL |         |                |
  +| size        | int(11)          | YES  |     | NULL    |                |
  +| description | text             | YES  |     | NULL    |                |
  ++-------------+------------------+------+-----+---------+----------------+
  +||#
  +
  +(def-view-class sample ()
  +  ((sample-id :db-type :key :type integer)
  +   (name :db-type :key :type (string 255))
  +   (size :db-type :base :type integer)
  +   (description :db-type :base :type string))
  +  (:base-table "sample")
  +  (:documentation "The sample represents the study (or sometimes the single individuum) with a collection of individuals that was studied for SNPs."))
  +
  +
  +#||			 individual;
  +| +-----------------------------+---------------------------------+------+-----+---------+-------+
  +| | sample_id                   | int(10) unsigned                |      | PRI | 0       |       |
  +| | gender                      | enum('Male','Female','Unknown') |      |     | Unknown |       |
  +| | father_individual_sample_id | int(10) unsigned                | YES  |     | NULL    |       |
  +| | mother_individual_sample_id | int(10) unsigned                | YES  |     | NULL    |       |
  +| | individual_type_id          | int(10) unsigned                |      |     | 0       |       |
  +| +-----------------------------+---------------------------------+------+-----+---------+-------+
  +||#
  +
  +(def-view-class individual ()
  +   ((sample-id :db-type :key :type integer)
  +    (gender :db-type :base :type (string 10))
  +    (father_individual_sample_id :db-type :base :type integer)
  +    (mother_individual_sample_id :db-type :base :type integer)
  +    (individual_type_id :db-type :base :type integer))
  +   (:base-table "individual")
  +   (:documentation "This class identifies relationships between samples."))
  +
  +#||
  +individual_type
  ++--------------------+------------------+------+-----+---------+----------------+
  +| individual_type_id | int(10) unsigned |      | PRI | NULL    | auto_increment |
  +| name               | varchar(255)     |      |     |         |                |
  +| description        | text             | YES  |     | NULL    |                |
  ++--------------------+------------------+------+-----+---------+----------------+
  +||#
  +
  +(def-view-class individual-type ()
  +  ((individual-type-id :db-type :key :type integer)
  +   (name :db-type :base :type (string 255))
  +   (description :db-type :base :type string))
  +  (:base-table "individual_type")
  +  (:documentation "Presentation of further information on indivuals genotyped (fully_inbred, partly_inbred, outbread, mutant)."))
  +
  +#||					 transcript_variation;
  ++-------------------------+-------------------------------+------+-----+---------+----------------+
  +| transcript_variation_id | int(10) unsigned              |      | PRI | NULL    | auto_increment |
  +| transcript_id           | int(10) unsigned              |      | MUL | 0       |                |
  +| variation_feature_id    | int(10) unsigned              |      | MUL | 0       |                |
  +| cdna_start              | int(11)                       | YES  |     | NULL    |                |
  +| cdna_end                | int(11)                       | YES  |     | NULL    |                |
  +| translation_start       | int(11)                       | YES  |     | NULL    |                |
  +| translation_end         | int(11)                       | YES  |     | NULL    |                |
  +| peptide_allele_string   | varchar(255)                  | YES  |     | NULL    |                |
  +| consequence_type        | set('ESSENTIAL_SPLICE_SITE','STOP_GAINED','STOP_LOST','COMPLEX_INDEL','FRAMESHIFT_CODING','NON_SYNONYMOUS_CODING','SPLICE_SITE','SYNONYMOUS_CODING','REGULATORY_REGION','5PRIME_UTR','3PRIME_UTR','INTRONIC','UPSTREAM','DOWNSTREAM') |      | MUL |  
  +||#
  +
  +(def-view-class transcript-variation ()
  +  ((transcript-variation-id :db-type :key :type integer)
  +   (transcript-id :db-type :key :type integer)
  +   (variation-feature-id :db-type :key :type integer)
  +   (cdna-start :db-type :base :type integer)
  +   (cdna-end :db-type :base :type integer)
  +   (translation-start :db-type :base :type integer)
  +   (translation-end :db-type :base :type integer)
  +   (peptide-allele-string :db-type :base :type integer)
  +   (consequence-type :db-type :base :type (string 50)))
  +  (:base-table "transcript_variation")
  +  (:documentation "A link from a transcript to a SNP."))
  +
  +#|| 			variation_feature
  +| variation_feature_id | int(10) unsigned       |      | PRI | NULL       | auto_increment |
  +| seq_region_id        | int(10) unsigned       |      | MUL | 0          |                |
  +| seq_region_start     | int(11)                |      |     | 0          |                |
  +| seq_region_end       | int(11)                |      |     | 0          |                |
  +| seq_region_strand    | tinyint(4)             |      |     | 0          |                |
  +| variation_id         | int(10) unsigned       |      | MUL | 0          |                |
  +| allele_string        | text                   | YES  |     | NULL       |                |
  +| variation_name       | varchar(255)           | YES  |     | NULL       |                |
  +| map_weight           | int(11)                |      |     | 0          |                |
  +| flags                | set('genotyped')       | YES  |     | NULL       |                |
  +| source_id            | int(10) unsigned       |      |     | 0          |                |
  +| validation_status    | set('cluster','freq','submitter','doublehit','hapmap')    | YES  |     | NULL       |                |
  +| consequence_type     | set('ESSENTIAL_SPLICE_SITE','STOP_GAINED','STOP_LOST','COMPLEX_INDEL','FRAMESHIFT_CODING','NON_SYNONYMOUS_CODING','SPLICE_SITE','SYNONYMOUS_CODING','REGULATORY_REGION','5PRIME_UTR','3PRIME_UTR','INTRONIC','UPSTREAM','DOWNSTREAM','INTERGENIC') |      |     | INTERGENIC |                |
  +| +----------------------+----------------------+------+-----+------------+----------------+
  +||#
  +(def-view-class variation-feature ()
  + ((variation_feature_id :db-type :key  :type integer)
  +  (seq_region_id        :db-type :key  :type integer)
  +  (seq_region_start     :db-type :base :type integer)
  +  (seq_region_end       :db-type :base :type integer)
  +  (seq_region_strand    :db-type :base :type integer)
  +  (variation_id         :db-type :key  :type integer)
  +  (allele_string        :db-type :base :type string)
  +  (variation_name       :db-type :base :type (string 255))
  +  (map_weight           :db-type :base :type integer)
  +  (flags                :db-type :base :type (string 15))
  +  (source_id            :db-type :base :type integer)
  +  (validation_status    :db-type :base :type (string 15))
  +  (consequence_type     :db-type :base :type (string 30)))
  + (:base-table "variation_feature")
  + (:documentation "Link from transcript_variation to the abstract representation of a validation."))
  +
  +
  +#||
   
   select * from allele_group_allele join variation using (variation_id)
   		join variation_group_variation using(variation_id)
  
positive.code: |             12219634 |        225652 |             6306 |           6306 |                 1 |      4384489 | C/T           | rs7047363      |          2 | NULL  |         1 | NULL              | UPSTREAM              |
  +----------------------+---------------+------------------+----------------+-------------------+--------------+---------------+----------------+------------+-------+-----------+-------------------+-----------------------+
  
  ||#
  
  ;; To access a strech of DNA 
  
  
negative.code: ;; This packages aims at characterising the link from genes to SNPs
  
  (in-package :clcb-ensembl)
  
  #||
   
  select * from source limit 10;
  +-----------+----------------------------------+---------+
  | source_id | name                             | version |
  +-----------+----------------------------------+---------+
  |         1 | dbSNP                            |     127 |
  |         3 | HGVbase                          |      15 |
  |         5 | TSC                              |       1 |
  |        11 | ENSEMBL:Watson                   |    NULL |
  |        10 | ENSEMBL:Venter                   |    NULL |
  |         9 | Affy GenomeWideSNP_6.0           |    NULL |
  |         8 | ENSEMBL:celera                   |    NULL |
  |         7 | Affy GeneChip 100K Mapping Array |    NULL |
  |         6 | Affy GeneChip 500K Mapping Array |    NULL |
  +-----------+----------------------------------+---------+
  
  ||#
  
  (def-view-class source ()
    ((source-id :db-type :key :type integer)
     (name :db-type base :type (string 255))
     (version :db-type base :type integer))
    (:base-table "source")
    (:documentation "This class answers how a particular variation was defined. A link from here to the variations with that same source ID is not feasible without extra constraints on the variations because of the large number that will be assigned to a single source."))
  
  #|| 				variation
  +-------------------+-----------------------------------------------------------------+------+-----+---------+----------------+
  | variation_id      | int(10) unsigned                                                |      | PRI | NULL    | auto_increment |
  | source_id         | int(10) unsigned                                                |      |     | 0       |                |
  