Pipeline components for real-time virus analysis

NEXT

3.1.8 (13 February 2019)

Bug fixes

  • titers: fix calculation of mean_potentency for model export

3.1.7 (5 February 2019)

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

3.1.6 (29 January 2019)

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

3.1.5 (13 January 2019)

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

3.1.4 (1 January 2019)

Bug fixes

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

Data

  • Include additional country lat/longs in base data

3.1.3 (29 December 2018)

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

3.1.2 (21 December 2018)

Bug fixes

  • Update dependencies

3.1.1 (21 December 2018)

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

3.1.0 (18 December 2018)

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

3.0.5.dev1 (26 November 2018)

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.

3.0.4.dev1 (26 November 2018)

Bug fixes

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

Development

  • Fix Travis CI tests which were silently not running.

3.0.3.dev1 (26 November 2018)

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.

3.0.2.dev1 (27 September 2018)

Bug fixes

  • translate: Fix broken --help message

3.0.1.dev1 (27 September 2018)

Features

  • align and tree: The --nthreads option now accepts the special value "auto" to automatically set the number of threads to the number of CPU cores available.

  • Alias augur --version to augur version

Bug fixes

  • tree: The --nthreads option is now respected. Previously all tree builders were ignoring the value and using either 2 threads (RAxML, IQ-TREE) or as many threads as cores (FastTree, if the OpenMP version).

  • translate: Check for and, if necessary pad, nucleotide sequences which aren't a multiple of 3 earlier to avoid errors later.

  • export: Optionally write inferred nucleotide and amino acid sequences (or mutations) to a separate file.

  • export: Omit genes with no amino acid mutations.

  • validate: Allow underscores in gene names.

  • refine: Remove unused --nthreads argument.

  • ancestral, filter, tree, refine: Exit 1 instead of -1 on error.

  • Print the help message, instead of throwing an exception, when augur is run without arguments.

Documentation

  • Briefly describe each command in its --help output and in the global augur --help output.

  • Revamp README to emphasize new, modular augur and make it suitable for inclusion on PyPi.

  • Reconciled conflicting license declarations; augur is AGPLv3 (not MIT) licensed like the rest of Nextstrain.

  • Include URLs for bug reports, the change log, and the source on PyPi.

Data

  • Geographic coordinates added for the Netherlands and the Philippines.

Development

  • Reset the release branch when rewinding a failed local release process.

  • Refactor the augur program and command architecture for improved maintainability.

3.0.0.dev3 (4 September 2018)

Development

  • Use an allowed Topic classifier so we can upload to PyPi

  • Ignore distribution egg-info build files

3.0.0.dev2 (4 September 2018)

Features

  • Export: Add safety checks for optional annotations and geo data

  • Include more lat/longs in the default geo data

Development

  • Add release tooling

  • Document the release process and a few development practices

  • Travis CI: Switch to rebuilding the Docker image only for new releases

  • Remove ebola, lassa, tb, WNV, and zika builds now in their own repos. These builds are now available at URLs like https://github.com/nextstrain/ebola, for example.

3.0.0.dev1 (unreleased)

Development

  • Start versioning augur beginning with 3.0.0. A new augur version command reports the running version.