Thomas Sibley

I suggested it under the thinking that `augur.filter` is the "facade" of the API, while everything else can be thought of as "behind the curtain". Exception classes are just as...

@victorlin > In my opinion, these are to be used internally, and we should just reference them from the original location so that we as developers can clearly see that...

[Canonical BED format specification](https://genome.ucsc.edu/FAQ/FAQformat.html#format1)

> are you saying an empty bed file is not legal? No, not saying that. Was just linking to the spec for reference. Sorry I didn't include more context.

Keeping this comment descriptive rather than prescriptive (at least for the moment). There's two separate things here: 1. BED files with no regions/data lines ("empty") 2. BED files with a...

[More context on the usage of these](https://github.com/nextstrain/docker-base/pull/50#discussion_r956227258), which I sifted thru before I knew about this issue :upside_down_face:

@corneliusroemer Can you try using another browser for a bit to see if this is limited to Brave or more widespread for you?

@corneliusroemer Not Edge, no, but Chrome or Chromium instead of Brave would be a decent comparison.

+1 for "spend[ing] some time with [the GFF3 specification](https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md)"

gffutils doesn't parse any directives/pragmas, but it does extract them. Parsing is a simple matter after that: ``` >>> { fields[0]: tuple(fields[1:]) for fields in (line.split() for line in db.directives)...