Type Members

1.  case class GeneCentric(rc: RuntimeETLContext) extends SimpleSingleETL with Product with Serializable
2.  case class GenesSuggestions(rc: RuntimeETLContext) extends SimpleSingleETL with Product with Serializable
3.  case class VariantCentric(rc: RuntimeETLContext) extends SimpleSingleETL with Product with Serializable

   This ETL is used to prepare data that will be indexed into ElasticSearch.

   This ETL is used to prepare data that will be indexed into ElasticSearch. It is used to create a variant centric index. Each row contain a variant. The genes field is an array of genes, each gene contains an array of consequences. Consequences that have no gene are grouped under a fake gene with symbol "NO_GENE".

   rc

   the etl context

   Example:

   1. For simplicity, columns not relevant to the example are omitted. In variant table:

      +----------+-----+---------+---------+-----------------------+
      |chromosome|start|reference|alternate|symbols                |
      +----------+-----+---------+---------+-----------------------+
      |1         |69897|T        |C        |[GENE1, GENE2]         |
      +----------+-----+---------+---------+-----------------------+

      In consequence table:

      +----------+-----+---------+---------+--------+-------------+
      |chromosome|start|reference|alternate|symbol  |transcript_id|
      +----------+-----+---------+---------+--------+-------------+
      |1         |69897|T        |C        |GENE1   |T1           |
      |1         |69897|T        |C        |GENE1   |T2           |
      |1         |69897|T        |C        |GENE2   |T3           |
      |1         |69897|T        |C        |null    |T4           |
      +----------+-----+---------+---------+-------=+-------------+

      Will generate this row in the variant centric index:

      {
       "chromosome": "1",
       "start": 69897,
       "reference": "T",
       "alternate": "C",
       "locus": "1-69897-T-C",
       "genes": {
         "symbol": "GENE1",
         "consequences": [
           {
             "transcript_id": "T1"
             ....
           },
           {
             "transcript_id": "T2"
           },
           ....
         ],
         ....
         },
         {
         "symbol": "GENE2",
         "consequences": [
           {
             "transcript_id": "T3"
             ....
           }
           ....
         ],
         ....
         },
         {
         "symbol": "NO_GENE",
         "consequences": [
           {
             "transcript_id": "T4"
             ....
           }
           ....
         ],
         ....
         },
       }

4.  case class VariantsSuggestions(rc: RuntimeETLContext) extends SimpleSingleETL with Product with Serializable