james hadfield

causes phylocanvas to re-load tree -> view is reset

ensure blocks are displayed correctly

2

I'm pretty sure the blocks are not being displayed correctly, and it changes while interacting with the canvases. What's the best way to identify the problem? Design a custom set...

Introduce minimum augur version check

2

I implemented this as part of updating #1000, but there are so many ways this pipeline may be run (and which I don't have experience with) that it's not appropriate...

I looked into the feasibility of adding the 16 NSPs into the exported (Auspice) dataset. This'll need nextclade v3 since RdRp includes the slip site, so perhaps a time to...

Validation against schemas is currently extremely useful at identifying when a dataset doesn't conform but often doesn't help pinpoint the part of the dataset that needs fixing. As an example,...

[ancestral] VCF REF != reference base resulting in missing variation

1

### Current Behavior This is a pretty fun bug but a bit hard to explain. Thankfully very easy to fix. When using VCF inputs to `augur ancestral` we need a...

[ancestral] reference seq may be reference or inferred tree root

2

### Current Behavior `augur ancestral` exports a "reference" sequence via `.reference.nuc`. Depending on the usage this is: 1. For VCF inputs this is simply the FASTA input `--vcf-reference` 2. For...

[vcf] Replace `write_VCF_translation` with treetime's `write_vcf`

3

`augur.io.vcf` includes `write_VCF_translation` which is used by `augur translate`. This functionality is better implemented ([and now tested](https://github.com/neherlab/treetime/pull/263)) in treetime so we should use that function instead.

Running `augur ancestral` with a gzipped output `--output-vcf fileName.vcf.gz` results in ``` Traceback (most recent call last): File "/Users/enigma/projects/nextstrain/augur/augur/__init__.py", line 66, in run return args.__command__.run(args) File "/Users/enigma/projects/nextstrain/augur/augur/ancestral.py", line 411, in...