Nextstrain-augur

Bug fixes

* titers: fix calculation of `mean_potentency` for model export

Bug fixes

* Update to TreeTime 0.5.3
* tree: Fix bug in printing causing errors in Python versions <3.6
* tree: Alter site masking to not be so memory intensive

Features

* filter: Allow negative matches to `--exclude-where`. For example,
`--exclude-where country!=usa` would exclude all samples where metadata `country` does
not equal `usa`.
* tree: Allow `--exclude-sites` to work with FASTA input. Ensure that indexing of input
sites is one-based.

Bug fixes

* fix loading of strains when loading titers from file, previously strains had not been
filtered to match the tree appropriately

Features

* frequencies: Add `--ignore-char` and `--minimal-clade-size` as options.
* frequencies: Include `--stiffness` and `--inertia` as options.
* titers: Allow multiple titer date files in `--titers` import.

Bug fixes

* filter: Fix `--non-nucleotide` call to include `?` as allowed character.
* tree: Fix `--method raxml` to properly delimit interim RAxML output so that
simultaneous builds don't conflict.

Data

* Include additional country lat/longs in base data

Bug fixes

* frequencies: Include `counts` in `augur frequencies` output JSON to support
downstream plotting.

Data

* Include additional country lat/longs in base data

Features

* filter: Add `--non-nucleotide` option to remove sequences with non-conforming
nucleotide characters.

Bug fixes

* Revise treatment of `-`, ` ` in `augur parse` to leave `-` as is and remove white
space. Also delimit `[` and `]` to `_`.
* Fix bug in naming of temp IQTREE fixes to prevent conflicts from simultaneous builds.

Data

* Include additional country lat/longs in base data

Development

* Remove non-modular measles build in favor of [nextstrain/measles](https://github.com/nextstrain/measles) repo.