John Huddleston
John Huddleston
### Description of proposed changes Adds support for compressed inputs (reference files and alignment sequences) in augur align by refactoring existing code to use Augur's `io` module. This is a...
## Current Behavior For seasonal flu builds, we need to annotate alternate clade labels including one called `proposed_subclade`. We want to show these proposed subclades by default in some analyses,...
## Current Behavior The `io.open_file` function uses xopen as its backend to transparently support compressed inputs and outputs. By default, [xopen uses multiple threads in a separate process to write...