Ivan Aksamentov

react-app

1

A complete rewrite of the visualization using React and other tools form the modern web stack. Resolves: https://github.com/neherlab/pan-genome-visualization/issues/6, https://github.com/neherlab/pan-genome-visualization/issues/7, https://github.com/neherlab/pan-genome-visualization/issues/11, https://github.com/neherlab/pan-genome-visualization/issues/15, https://github.com/neherlab/pan-genome-visualization/issues/16 others.

feat(cli): add "sort-and-run" subcommand

1

Combination of `sort` and `run` subcommands. Analyzes each sequence using the most likely dataset. ``` cargo run --bin=nextclade -- sort-and-run -O tmp/ -r tmp/sort/sort.tsv sequences.fasta ```

A snippet from the GISAID ingest log: ``` + ./bin/check-locations data/gisaid/metadata.tsv data/gisaid/location_hierarchy.tsv gisaid_epi_isl sys:1: DtypeWarning: Columns (9,28,37,39,43) have mixed types.Specify dtype option on import or set low_memory=False ``` This is...

Support subcommands

1

From readme: > Note: there's no support for subcommands, create an issue if you need it. So, here we go, creaing an issue :) This is a very valuable crate...

feat: use Auspice JSON as a dataset

3

Slack threads: - https://bedfordlab.slack.com/archives/C01LCTT7JNN/p1715225548823919 - https://bedfordlab.slack.com/archives/C01LCTT7JNN/p1716475486151749 This allows to use Auspice JSON v2 as input dataset. In this case we attempt to read not only tree, but also ref sequence,...

feat: make `clade_membership` node attribute optional

1

Not all trees have `clade_membership` attribute on the nodes. Here I made this attribute optional in Nextclade. If `clade_membership` is not present: - output JSON/NDJSON result entries will not contain...

docs: document nextalign-like use-case

1

Related: https://github.com/nextstrain/seasonal-cov/issues/2 After release of Nextclade v3 and removal of a standalone `nextalign` binary, some older workflows relying on Nextalign are left in an awkward state. There is a [migration...

feat: mutations relative to arbitrary node

1

This extends concept of private mutations (private mutations are mutations relative to the parent node on the ref tree) to a more general concept of mutations relative to an arbitrary...

Avoid hardcoded UID and GID in docker build

4

### Description of proposed changes The [Dockerfile](https://github.com/nextstrain/docs.nextstrain.org/blob/1da467787db9a8f9b43724f3c41264fa30ff4db6/Dockerfile) uses `UID` and `GID` args to create a user inside the container. Files are then written during build on behalf of this user,...

Test data for https://github.com/nextstrain/nextclade/pull/1455 DO NOT MERGE