Generalize backend handling of genome types

[Fattigman]

Background

One of the goals of this application was to be able to adapt to different genome types other than sars, which is linear single stranded RNA.

Can be closed when

• [ ] Distance matrix can be calculated with following genomes
  • [ ] Fragmented genomes
  • [ ] Circular genomes
• [ ] Generalize typing annotation of viruses

Implementation details

Distance Matrix

Population scripts needs to be expanded to handle different genomes. Different assumptions are made when calculating genetic distance. As to what assumptions need to be made needs to be discussed and documented here. The python application shouldn't need any major change.

Generalize type annotations

Populations scripts need to be expanded to handle other outputs from typing packages. Database structure will get a revision of how it stores typing of viruses. A proposal is to create a type structure like following.

[
  {
    "sample_id" : "test_name",
    "type": [
      {
        "pangolin" : "B.1.1.7"
      },
      {
        "nextclade" : "23B"
      },
    ]
  }
]

[talnor]

Structure looks good! So one column/field per type in the all the frontend views to make the frontend generalized as well.