BanzaiDB tables schema
======================

The following tables are defined in BanzaiDB

Mapping
-------


reference_genome_features
strains_under_investigation
reference_genomes


determined_variants
~~~~~~~~~~~~~~~~~~~

+------------------+----------------+----------------------------------------+
| Key              | Value (type)   | Comments                               |
+==================+================+========================================+
| id               | string         | Primary (StrainID_RefID_Position)      |
+------------------+----------------+----------------------------------------+
| StrainID          | string        |                                        |
+------------------+----------------+----------------------------------------+
| Positiion        | int            |                                        |
+------------------+----------------+----------------------------------------+
| LocusTag         | string         | Of reference                           |
+------------------+----------------+----------------------------------------+
| Class            | string         | substitution, insertion, deletion      |
+------------------+----------------+----------------------------------------+
| SubClass         | string or None | synonymous, non-synonymous             |
+------------------+----------------+----------------------------------------+
| RefBase          | char           | A T C or G (N) ?                       |
+------------------+----------------+----------------------------------------+
| ChangeBase       | char           | A T C G or (N) ?                       |
+------------------+----------------+----------------------------------------+
| CDSBaseNum       | int            |                                        |
+------------------+----------------+----------------------------------------+
| CDSAANum         | int            |                                        |
+------------------+----------------+----------------------------------------+
| CDSRegion        | string or None | x..y                                   |
+------------------+----------------+----------------------------------------+
| RefAA            | char or None   |                                        |
+------------------+----------------+----------------------------------------+
| ChangeAA         | char of None   |                                        |
+------------------+----------------+----------------------------------------+
| Product          | string         |                                        |
+------------------+----------------+----------------------------------------+
| CorrelatedChange | boolean        | If up/down-stream change effects       |
+------------------+----------------+----------------------------------------+
| Evidence         | string         |                                        |
+------------------+----------------+----------------------------------------+


strains_under_investigation
~~~~~~~~~~~~~~~~~~~~~~~~~~~

+------------------+----------------+----------------------------------------+
| Key              | Value (type)   | Comments                               |
+==================+================+========================================+
| StrainID         | string         |                                        |
+------------------+----------------+----------------------------------------+
| VarCount         | int            | total number of parsed (CDS) variants  |
+------------------+----------------+----------------------------------------+


REF
---


REF_FEATURES
------------

+------------------+----------------+----------------------------------------+
| Key              | Value (type)   | Comments                               |
+==================+================+========================================+
| LocusTag         | string         |                                        |
+------------------+----------------+----------------------------------------+
| Sequence         | int            |                                        |
+------------------+----------------+----------------------------------------+
| Translation      | string         |                                        |
+------------------+----------------+----------------------------------------+
| Start            | int            |                                        |
+------------------+----------------+----------------------------------------+
| End              | int            |                                        |
+------------------+----------------+----------------------------------------+
| Strand           | int            | 1/-1                                   |
+------------------+----------------+----------------------------------------+
| Product          | string         | Should be equal to VARIANT['CDS']      |
+------------------+----------------+----------------------------------------+

