5.1.0

5.1.0 (29 May 2019)

Documentation

• Documentation is now available online for the augur CLI and Python API via
  Read The Docs: https://nextstrain-augur.readthedocs.io. The latest
  version on RTD points to the git master branch, and the stable version to
  the most recent tagged release. Instructions for building the docs locally
  are in the README.

5.0.0

5.0.0 (26 May 2019)

Features

• ancestral: New option to --keep-ambiguous, which will not infer nucleotides at
  ambiguous (N) sites on tip sequences and instead leave as 'N'
  See PR 280.
• ancestral: New option to --keep-overhangs, which will not infer nucleotides for
  gaps on either side of the alignment and instead leave as '-'.
  See PR 286.
• clades: This module has been reconfigured to identify clade defining mutations on
  top of a reference rather than identifying mutations along the tree. The command
  line arguments are the same except for the addition of --reference, which
  explicitly passes in a reference sequence. If --reference is not defined, then
  reference will be drawn from the root node of the phylogeny by looking for
  sequence attribute attached to root node of --tree.
  See PR 288.
• refine: Revise rooting behavior. Previously --root took 'best', 'residual', 'rsq'
  and 'min_dev' as options. In this update --root takes 'best', least-squares',
  'min_dev' and 'oldest' as rooting options. This eliminates 'residual' and 'rsq'
  as options. This is a backwards-incompatible change. This requires updating
  TreeTime to version 0.5.4 or above.
  See PR 263.
• refine: Add --keep-root option that overrides --root specification to preserve
  tree rooting.
  See PR 263.
• refine: Add --covariance and --no-covariance options that specify TreeTime
  behavior.
  See PR 263.
• titers: This command now throws an InsufficientDataException if there are not
  sufficient titers to infer a model. This is paired with a new --allow-empty-model
  flag that proceeds past the InsufficientDataException and writes out a model
  JSON corresponding to an 'empty' model.
  See PR 281.
• By default JSONs are written with index=1 to give a pretty-printed JSON. However,
  this adds significant file size to large tree JSONs. If the environment variable
  AUGUR_MINIFY_JSON is set then minified JSONs are printed instead. This mirror the
  explicit --minify-json argument available to augur export.
  See PR 278.

Bug fixes

• export: Cast numeric values to strings for export.
  See issue 287.
• export: Legend order preserves ordering passed in by user for traits that have
  default colorings ('country' and 'region').
  See PR 284.
• refine: Previously, the --root argument was silently ignored when no timetree
  was inferred. Re-rooting with an outgroup is sensible even without a timetree.
  See PR 282.

4.0.0

4.0.0 (24 April 2019)

Features

• distance: New interface for specifying distances between sequences. This is
  a backwards-incompatible change. Refer to augur distance --help for
  all the details.

• export: Add a --minify-json flag to omit indentation in Auspice JSONs.

Bug fixes

• frequencies: Emit one-based coordinates (instead of zero-based) for KDE-based
  mutation frequencies

Data

• Include additional country lat/longs in base data

3.1.8

3.1.8 (13 February 2019)

Bug fixes

• titers: fix calculation of mean_potentency for model export

3.1.7

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

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

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

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

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

• Remove non-modular measles build in favor of nextstrain/measles repo.

3.1.2

3.1.2 (21 December 2018)

Bug fixes

• Update dependencies