Nextstrain-augur

Bug fixes

* Update dependencies

Bug fixes

* filter: Fix `--include-where`. Adds an `all_seq` variable needed by the logic to
include records by value. This was previously working for VCF but threw an exception
for sequences in FASTA format.
* Update flu reference viruses and lat longs.
* Update dependencies

Features

* reconstruct-sequences: Include `augur reconstruct-sequences` module that reconstructs
alignments from mutations inferred on the tree
* distance: Include `augur distance` module that calculates the distance between amino
acid sequences across entire genes or at a predefined subset of sites
* lbi: Include `augur lbi` module that calculates local branching index (LBI) for a
given tree and one or more sets of parameters.
* frequencies: Include `--method kde` as option to `augur frequencies`, separate from the
existing `--method diffusion` logic. KDE frequencies are faster and better for smaller
clades but don't extrapolate as well as diffusion frequencies.
* titers: Enable annotation of nodes in a tree from the substitution model

Bug fixes

* translate: Nucleotide ("nuc") annotation for non-bacterial builds starts at 0
again, not 1, fixing a regression.

Documentation

* Schemas: Correct coordinate system description for genome start/end
annotations.

Bug fixes

* validate: Fix regression for gene names containing an asterisk.

Development

* Fix Travis CI tests which were silently not running.

Features

* refine: Add a `--clock-std-dev` option

* traits: Add a `--sampling-bias-correction` option for mugration model

* validate: Gene names in tree annotations may now contain hyphens. Compatible
with Auspice version 1.33.0 and later.

* All JSON is now emitted with sorted keys, making it easier to diff and run
other textual comparisons against output.

Bug fixes

* filter: Only consider A, T, C, and G when calculating sequence length for the
`--min-length` option.

* filter: Allow comments in files passed to `--exclude`.

* filter: Ignore case when matching trait values against excluded values.

* Normalize custom geographic names to lower case for consistent matching.

Data

* Fix typo in geographic entry for `netherlands`.

* Schemas: Reconcile naming patterns used in gene definitions and tree
annotations.

Development

* Upgrade TreeTime dependency to 0.5.x and at least 0.5.1.

* Add an `environment.yml` file for use with `conda env create`.

* Stop testing under Python 2.7 on Travis CI.