Add coverage per CDS to output

[joverlee521]

Motivated by https://github.com/nextstrain/pathogen-repo-guide/issues/50:

It seems like a common pattern for sequencing efforts to focus on specific genes instead of the full genome. It would be helpful for ingest to annotate each record's gene coverage to explore the data.

We are currently doing this in what feels like a very "hacky" way of using the Nextclade translations outputs to calculate gene coverage (e.g. dengue).

Would it possible to directly output gene/CDS coverage from Nextclade?