Cornelius Roemer

fix: translate `-` strand annotation

6

Annotations output by augur translate always contained `+` irrespective of what the input gff or gb file specified and biopython returned This bug was down to the assumption that biopython...

BUG: `augur translate` not faithful to `gff3` standard, can't annotate nucs, which are required.

6

Related to #881 Currently, `augur translate` does not implement `gff3` standard properly. Confusingly, if you use `.gff` files generated automatically by Genbank from a given `.gb` file, augur translate will...

BUG: filter outputs stats to stdout instead of stderr

1

### Current Behavior When running `augur filter`, certain stats are output to stdout rather than stderr as would be conventional: The following is an example of output that wrongly appears...

ENH: Validate clades.tsv file and provide helpful error message if it doesn't conform to requirements

3

It would be good to explicitly validate the clades.tsv file and give a helpful error message if it doesn't conform to expectations. This would help users like this one, who...

Unhandled exception in `clades`: index error in `is_node_in_clade`

1

Running augur clade I got the following unhandled exception that I didn't know immediately how to debug: ``` monkeypox-nextclade on  nextclade [$!] via 🅒 nextstrain took 2m16s ❯ augur...

Validate annotations produced from ancestral + translate

4

I've encountered a bug that took me very long to figure out. Augur export reported the following error: ``` Validating schema of 'auspice/monkeypox_global.json'... ERROR: 'nuc' is a required property. Trace:...

BUG in mask: empty (header only) .bed file causes unhandled error

7

### Current Behavior When the `.bed` file passed to `mask` contains just a header and nothing to mask, an unhandled error is thrown. ### Expected behavior Empty, header only `.bed`...

BUG: Mask should not fail if no sites are to be masked

2

### Current Behavior When mask is told to mask nothing, it throws an error and doesn't exit successfully. ### Expected behavior It is perfectly legal to mask nothing, e.g. by...

During our issue triage meeting, we couldn't agree on the desired behaviour for `augur mask` if no change is made: Should mask error, warn, or do nothing at all. As...

### Current Behavior Filter throws an unhandled error when reading a metadata file. I'm not quite sure what's wrong with the file. ### Expected behavior Error is handled and I...