34.1.3

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Development

• subsample: Refactored helper functions to only validate config during run time. #2039 @victorlin
• Added a subsample config schema for workflows that use unaligned sequences. #2038 @victorlin

34.1.2

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Development

• Refactored JSON schema validation functions for external use. #2034 @victorlin

34.1.1

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Bug fixes

• filter: Fix unhandled ValueError with --group-by-weights when no sequences pass earlier filters. #2032 @victorlin

34.1.0

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Features

• distance: Add --output-edge-list argument to save pairwise distances between sequences to an edge list TSV file for better compatibility with MicrobeTrace. #2025 @huddlej
• Augur now automatically creates missing parent directories before writing output files. #2014 @victorlin

Bug fixes

• filter: Improved the speed and memory usage of subsampling with --group-by and --subsample-max-sequences by caching each record's group during the first pass instead of reading the metadata a second time. #2018 @trvrb
• filter: Improved the speed of computing groups for --group-by subsampling by replacing a row-wise pandas apply with a vectorized operation. #2018 @trvrb
• filter: Improved the speed of writing --output-metadata by streaming rows instead of building a dictionary per row. #2018 @trvrb
• Improved the error message for unrecognized arguments. #2028 @victorlin

34.0.0

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Major Changes

• A metadata column named id is now preferred as the identifier column when present. This applies to all commands that work with metadata id columns (parse, merge, filter, subsample, refine, traits, frequencies, export v2). Typical Augur usage should start with ensuring your metadata file has an id column instead of passing --metadata-id-columns to each command. Note this is a behavior change: metadata that already contains an id column but relied on strain/name being inferred will now use id; pass --metadata-id-columns strain name to restore the previous behavior. #1780 @victorlin

Features

• merge: Add --output-metadata-id-column to explicitly name the id column in the merged metadata output, overriding the default of using the first input's id column. #1780 @victorlin
• merge: Support a single --metadata or --sequences input, instead of requiring at least two. This allows augur merge to be used as a general entry point for standardization even when no actual merge is needed. #1974 @victorlin

Bug fixes

• Bump minimum xopen version to 2.1.0. This removes the indirect dependency on zstandard as there is built-in zstd support in Python 3.10 and an equivalent backport for older versions. #2009 @victorlin

33.4.1

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Bug fixes

• filter: Fix handling of date ranges with --group-by and --exclude-ambiguous-dates-by. #2007 @victorlin

33.4.0

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Features

• curate format-dates: Support date ranges in the formats YYYY/YYYY. #2005 @victorlin

33.3.0

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Features

• curate format-dates: Support date ranges in the formats YYYY-MM-DD/YYYY-MM-DD and [YYYY TO YYYY]. #2000 @victorlin

Bug fixes

• [export] Add sharing.screenshot to the auspice-config schema which was unintentionally omitted in the previous release. #1999 @jameshadfield

33.2.0

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Features

• Support treetime 0.12.* #1986
• Enable auspice config JSONs to define sharing, which controls which assets Auspice offers for download. See Auspice docs for more. #1993 @jameshadfield

Bug fixes

• Improved formatting of command line help text. #313, #1630 @victorlin

33.1.0

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Features

• proximity: Introduce a new augur proximity tool to find the k closest strains against a query set using hamming distance. #1962 @jameshadfield

• subsample: Allow subsampling schemes (YAML configuration) to perform hierarchical sampling where one sample depends on another, as well as proximal sampling where we use another sample as the query set. #1962 @jameshadfield

• Allow analyses of AA (protein) datasets. This includes changes to the following augur components: #1958 @jameshadfield

  • index: AA sequences can be indexed by using --seq-type aa. The column names of the resulting index will differ from those for nuc sequences.
  • filter: AA sequences now work with sequence based filters when using --seq-type aa.
  • filter: The --non-nucleotide argument is deprecated and has been replaced with --exclude-invalid.
  • subsample: AA sequences now work when using --seq-type aa.
  • subsample: The non_nucleotide sample keyword is deprecated and has been replaced with exclude_invalid.
  • refine: Addition of an --seq-type aa argument which will result in TreeTime using the JTT92 substitution model.
  • ancestral: Reconstruction to genes can now happen without a nucleotide sequence. We also allow AA root sequences to be provided (for AA-only or AA+nuc analyses).
  • export v2: Node-data JSONs with gene-only annotations are now valid and will be exported.
  • Schema changes to annotations and export_v2 to make the nuc key optional for (genome) annotations.

• ancestral: Add --report-inconsistent-translation argument to report where amino acid reconstruction differed from the translation of the reconstructed nuc sequence. #1975 @jameshadfield

Bug fixes

• ancestral: Fix potential bugs where 'N' could be used as the ambiguous character for AA sequences (this bug wasn't exposed if the provided translations came from Nextclade which was the usual path). Also includes fixes for nucleotide reconstructions involving the ambiguous 'X' character. #1975 @jameshadfield
• merge: Added a workaround for a bug in SQLite version 3.53.0. #1984 @victorlin