james hadfield

I looked into this briefly today, as I had always assumed these were ordered according to their position in the genome. `augur translate` reads in annotations and preserves [1] the...

Yes, good points. I can imagine modifying canonical GenBank files may not be appropriate, especially as my guess is a lot of people are using the reference from our ncov...

Note to self: revisit `areNucleotideMutationsPresent` function in auspice (added by auspice PR linked above) if we move to OrderedDict here.

> I would prefer all of the auspice config to be in a place that is editable outside of the pipeline so that it can be easily switched and the...

> Alternatively, some of the outgroup rooting logic could be pushed into augur tree, which is a lot slimmer than refine. Then refine could be just run with --keep-root when...

Leaving the following code snippets here which we're using to perform this function prior to building it into augur: ``` augur refine ... --root {params.root} ... ``` ``` rule prune_outgroup:...

Another bump, and a comment 😉 I'd suggest this be done inside `augur refine` so that `augur tree` can more easily be swapped out with other tree builders. In `augur...

> In the case of refine this would mean the outgroup would be a part of the tree for all calculations and then only removed at the end - do...

There is documentation of the dataset JSON settings [in auspice's docs](https://docs.nextstrain.org/projects/auspice/en/stable/advanced-functionality/view-settings.html#dataset-json-configurable-defaults), and the key names are the same (I think?) for the auspice-config JSON, but it would be good to...

👍 Create docs version of auspice config schema #819