Nextstrain-augur

Bug Fixes

* filter: Clarify how the `--priority` input affects subsampling in the command line help documentation [695][]
* tests: Clean up outputs created by tests [703][], ignore log files [701][], and remove unnecessary Conda environment file [702][]

Features

* io: Add new `io` module with `open_file`, `read_sequences`, and `write_sequences` functions that support compressed inputs and outputs [652][]
* parse, index, filter, mask: Add support for compressed inputs/outputs [652][]
* export v2: Add optional `data_provenance` field to auspice JSON output for better provenance reporting in Auspice [705][]

[652]: https://github.com/nextstrain/augur/pull/652
[695]: https://github.com/nextstrain/augur/pull/695
[701]: https://github.com/nextstrain/augur/pull/701
[702]: https://github.com/nextstrain/augur/pull/702
[703]: https://github.com/nextstrain/augur/pull/703
[705]: https://github.com/nextstrain/augur/pull/705

Bug Fixes

* ancestral: Mask positions that are ambiguous in all tip sequences before inferring ancestral sequence states, to avoid assigning arbitrary ancestral values based on rounding errors [682][]
* titers: Add missing `kwargs` attribute to `TiterCollection` class [690][]

Documentation

* Update API documentation to include newer Python modules and the `index` subcommand [687][]
* Remove Zika and TB tutorials in favor of copies in docs.nextstrain.org [689][]

Features

* filter: Enable filtering by metadata only such that sequence inputs/outputs are optional and metadata/strain list outputs are now possible [679][]
* filter: Enable extraction of sequences from multiple lists of strains with a new `--exclude-all` flag and support for multiple inputs to the `--include` argument [679][]

[679]: https://github.com/nextstrain/augur/pull/679
[682]: https://github.com/nextstrain/augur/pull/682
[687]: https://github.com/nextstrain/augur/pull/687
[689]: https://github.com/nextstrain/augur/pull/689
[690]: https://github.com/nextstrain/augur/pull/690

Bug Fixes

* index: Remove call to deprecated BioPython SeqIO.close method [684][]

[684]: https://github.com/nextstrain/augur/pull/684

Bug Fixes

* filter: Retry probabilistic subsampling when it doesn't select any samples [676][]
* titers: Skip infinite log titer values caused by zero-valued raw titers [677][]
* setup: Include license file with distribution artifacts instead of Python installation root [678][]

[676]: https://github.com/nextstrain/augur/pull/676
[677]: https://github.com/nextstrain/augur/pull/677
[678]: https://github.com/nextstrain/augur/pull/678

Bug Fixes

* align/utils: Improve external command errors [638][]
* filter: Fix parsing of priorities files to allow spaces in sequence IDs [668][]
* utils: Ensure columns `strain` and `name` in metadata get parsed as strings [669][]

Features

* index/filter: Add new `index` subcommand and optional `--sequence-index` argument for `filter` command to enable filtering without inspecting sequences [651][]
* titers: Bump supported cvxopt version to latest 1.* release [671][]

[638]: https://github.com/nextstrain/augur/pull/638
[651]: https://github.com/nextstrain/augur/pull/651
[668]: https://github.com/nextstrain/augur/pull/668
[669]: https://github.com/nextstrain/augur/pull/669
[671]: https://github.com/nextstrain/augur/pull/671

Major Changes

* filter: Use probabilistic sampling by default when requesting a maximum number of sequences to subsample with `--subsample-max-sequences`. Adds `--no-probabilistic-sampling` flag to disable this default behavior and prevent users from requesting fewer maximum sequences than there are subsampling groups. [659][]

[659]: https://github.com/nextstrain/augur/pull/659