Nextstrain-augur

Bug Fixes

* filter: Fix parsing of missing data in metadata [758][] (huddlej)
* filter: Fix probabilistic sampling with small values [759][] (huddlej)

[758]: https://github.com/nextstrain/augur/pull/758
[759]: https://github.com/nextstrain/augur/pull/759

Features

* export: Add support for custom legend and color scale specifications in Auspice config files [727][] (jameshadfield)
* utils: Add support for compressed strain name files (e.g., "include.txt.gz") [730][] (benjaminotter)
* filter: Rewrite internal logic to use pandas DataFrames ([743][]), define filters and subsampling logic as individual functions ([745][] and [746][]), and iterate through chunks of metadata instead of loading all records into memory at once ([750][]) (tsibley, huddlej)

Bug Fixes

* distance: Change numeric type of distance output to float [729][] (benjaminotter)
* filter: Disable probabilistic sampling when users provide `--sequences-per-group` [737][] (benjaminotter)
* export: Provide correct missing file error messages for metadata and node data JSON inputs [752][] (benjaminotter)

[727]: https://github.com/nextstrain/augur/pull/727
[729]: https://github.com/nextstrain/augur/pull/729
[730]: https://github.com/nextstrain/augur/pull/730
[737]: https://github.com/nextstrain/augur/pull/737
[743]: https://github.com/nextstrain/augur/pull/743
[745]: https://github.com/nextstrain/augur/pull/745
[746]: https://github.com/nextstrain/augur/pull/746
[750]: https://github.com/nextstrain/augur/pull/750
[752]: https://github.com/nextstrain/augur/pull/752

Major Changes

* filter: Date bounds (`--min-date` and `--max-date`) are now inclusive instead of exclusive such that records matching the given dates will pass date filters [708][] (benjaminotter)

Bug Fixes

* refine: Recommend an alternate action when skyline optimization fails [712][] (huddlej)

Features

* distance: Count insertion/deletion events once in pairwise distances [698][] (huddlej, benjaminotter)
* distance: Optionally ignore specific list of characters defined in a distance map's top-level `ignored_characters` list [707][] (benjaminotter)
* filter: Allow `--subsample-max-sequences` without `--group-by` [710][] (benjaminotter)
* tree: Prefer `iqtree2` binary over `iqtree` when possible [711][] (benjaminotter)

[698]: https://github.com/nextstrain/augur/pull/698
[707]: https://github.com/nextstrain/augur/pull/707
[708]: https://github.com/nextstrain/augur/pull/708
[710]: https://github.com/nextstrain/augur/pull/710
[711]: https://github.com/nextstrain/augur/pull/711
[712]: https://github.com/nextstrain/augur/pull/712

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