Make gene order in genotype color-by customizable

[joverlee521]

Context

Related to #1548

Description

Currently, the order of genes in the genotype color-by dropdown option is listed alphabetically, with the exception of "nucleotide" which is added last (which will soon be changed in response to #1548).

Users may want to highlight an antigenically important gene (e.g. the "S" gene in SARS-CoV-2) and display the gene first in the dropdown. We should allow users to customize the display order of genes in this dropdown in the dataset JSON.

[jameshadfield]

They are only alphabetical because that's how augur is exporting them -- the order they appear in the json→meta→genome_annotations dict is the order they will appear in auspice's dropdown. It would be nice to be able to customise this, but I think that functionality belongs in augur. (Not sure whether the place for this is augur translate or augur export v2).

Note: This relies on stable key ordering going from JSON to JS. This isn't always the case -- for instance, a gene name which is a (string) integer will be lifted to the top of the order. I'm not aware of any genes which are integers, so for our purposes I think we can treat it as stable and avoid a schema change.

[jameshadfield]

I'm going to close this as nextstrain/augur#1052 should resolve

[joverlee521]

Hmm, I was thinking the key ordering in genome_annotations is not reliable, so it should be a separate array field for listing the order of genes.

[tsibley]

JSON objects are technically unordered, but some languages (incl. Python and JS) preserve order when encoding/decoding their native equivalent type to/from JSON objects. So if we care about interop with other JSON encoders/decoders, we may not want to rely on ordering of object fields.

[j23414]

Linking the Advanced Gene Viewing Options question to this issue