Major Changes
* utils: Add a consolidated generic `load_mask_sites` function and specific `read_mask_file` and `read_bed_file` functions for reading masking sites from files. Changes the Python API by moving mask-loading functionality out of augur mask and tree into utils [514][] and [550][]
* mask: Parse BED files as zero-indexed, half-open intervals [512][]
Bug Fixes
* traits: Export mugration models to the same output directory as traits JSON [544][]
* Explicitly open files with UTF-8 file encoding [499][], [503][], and [560][]
* refine: Only request confidence intervals from TreeTime when no clock rate is provided [548][]
* refine: Catch failed skyline optimization [556][]
Features
* align: Report insertions stripped during alignment [449][]
* Require minimum pandas version of 1.0.0 [488][]
* parse: Reduce memory use and clarify code with standard Python idioms [496][]
* mask: Allow masking of specific sites passed by the user with `--mask-sites` and masking of a fixed number of sites from the beginning or end of each sequence with `--mask-from-beginning` and `--mask-from-end` [512][]
* clades, import: Use `defaultdict` to simplify code [533][]
* tests: Add initial functional tests of the augur command line interface using Cram [542][]
* refine: Add a `--seed` argument to set the random seed for more reproducible outputs across runs [542][]
* ancestral, refine, and traits: Print the version of TreeTime being used for these commands [552][]
* filter: Add support for flexible pandas-style queries with new `--query` argument [555][]
* export: Allow display defaults for transmission lines [561][]
[449]: https://github.com/nextstrain/augur/pull/449
[488]: https://github.com/nextstrain/augur/pull/488
[496]: https://github.com/nextstrain/augur/pull/496
[499]: https://github.com/nextstrain/augur/pull/499
[503]: https://github.com/nextstrain/augur/pull/503
[512]: https://github.com/nextstrain/augur/pull/512
[514]: https://github.com/nextstrain/augur/pull/514
[533]: https://github.com/nextstrain/augur/pull/533
[542]: https://github.com/nextstrain/augur/pull/542
[544]: https://github.com/nextstrain/augur/pull/544
[548]: https://github.com/nextstrain/augur/pull/548
[550]: https://github.com/nextstrain/augur/pull/550
[552]: https://github.com/nextstrain/augur/pull/552
[555]: https://github.com/nextstrain/augur/pull/555
[556]: https://github.com/nextstrain/augur/pull/556
[560]: https://github.com/nextstrain/augur/pull/560
[561]: https://github.com/nextstrain/augur/pull/561