nextclade

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Upgrade rust lib deps

1

ivan-aksamentov

chore(deps): bump auspice from 2.51.0 to 2.52.0 in /packages_rs/nextclade-web

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Bumps [auspice](https://github.com/nextstrain/auspice) from 2.51.0 to 2.52.0. Release notes Sourced from auspice's releases. Auspice 2.52.0 Sidebar filtering now contains all non-continuous metadata defined across the tree (i.e. all data within node.node_attrs)....

dependabot[bot]

feat: add dataset info to output json [wip]

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I'd like to add input dataset info into the output JSON.

ivan-aksamentov

feat(web): handle rust panics in wasm module gracefully [wip]

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The `console_error_panic_hook` prints details of Rust panics in wasm module into dev console, and triggers a "null pointer" error message in UI. I would like to display a nice error...

ivan-aksamentov

feat(gff): pick gene/cds/protein preferentially from "nextclade_name"

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This change means that we don't need to communicate the exact complicated order of preference for gene/cds/protein name to end users Instead, we can simply say: "If you want to...

corneliusroemer

feat: Reduce kmer spacing for short sequences

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This is a good heuristic to avoid lack of seed matching in short sequences (~1% of RSV A is only ~200bp long) If default kmer spacing is 50, a sequence...

corneliusroemer

feat/better seed debug logging

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- feat: log basic seed and align stats at debug level We're currently not really using `debug` level logging for anything. I think it'd be useful to output some basic...

corneliusroemer

fix: reimplement alignment stripes on top of signed ranges

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This reimplements `Stripe` struct to contain a `Range` instead of a pair of `usize`s. This way it's easier to catch integer bugs and we get all existing checks and fixes...

ivan-aksamentov

feat: add detailed version information

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This adds CLI args to display more information about Nextclade version and build environment. - `--version-detailed` (`-W`) shows single-line detailed information, for example: ``` 2.14.0 (Debug; Dirty; Commit d532ea3a; Branch...

ivan-aksamentov

refactor: inline pieces of bio-rust crate related to FM-index

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ivan-aksamentov