nextstrain
Support compressed alignments
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 work in progress that builds on #652 and still requires focused work to add support for compressed output files.
Testing
Adds functional tests to the Zika compressed build in tests/builds/zika_compressed.t.
Thank you, @tsibley! A rebase would be really helpful here. Your comments highlights parts of the align module that are unclear to me, too. We may need to revisit the general approach of this module to make it easier to follow and also to better support new features like additional alignment backends.
@huddlej do you think this is something that could be picked back up, or has the codebase moved on past this and the best course of action is closing this out?
This is still an important feature, but I don't know how important compared to other priorities. I'd either leave this open as the reflection of the issue or convert to an issue before closing.