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Add automatic detection of datasets#1244

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ivan-aksamentov merged 56 commits intomasternextstrain/nextclade:masterfrom feat/ref-minimizernextstrain/nextclade:feat/ref-minimizerCopy head branch name to clipboardSep 18, 2023

+3,044-771

Commits

Commits on Sep 1, 2023

• feat(cli): scaffold seq sort cli command, input parsing and main loop

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• feat(cli): implement ref search

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• feat(cli): allow external minimizer index JSON file

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• feat(cli): improve error message text

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• fix(cli): version warning false positive

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• feat(cli): add cli params for minimizer search algo

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Commits on Sep 4, 2023

• Merge remote-tracking branch 'origin/master' into feat/ref-minimizer

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• fix(cli): allow minimizer index to be absent

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• feat(cli): write sorted fasta files

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• fix(web): dataset equality

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Commits on Sep 5, 2023

• feat(web): add sequence sorting prototype

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• fix: move wasm module into webworker

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• fix(web): prioritize dataset-server URL param

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• fix(web): parentheses in the conditional

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• feat(web): only show "Autodetect" entry when minimizer data is available

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• feat(web): improve message in GitHub URL errors

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• fix(web): non-unique atom key

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Commits on Sep 6, 2023

• refactor: lint

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• feat(web): display multiple relevant auto-detected refs

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Commits on Sep 7, 2023

• Merge remote-tracking branch 'origin/master' into feat/ref-minimizer

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• feat(web): prototype new dataset autodetect ui

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• feat(web): animate list updates to prevent flickering

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• perf: serialize directly to jsvalue to avoid json parsing

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• perf: batch updates from wasm to reduce main thread blocking

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• fix(web): duplicate id and label misalignment

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• feat: count detections for all datasets, not just the top one

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Commits on Sep 8, 2023

• refactor: extract function

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• refactor: lint

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• refactor(cli): simplify check for completions cli args

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• feat(cli): rename 'seq sort' subcommand to 'sort'

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• refactor: remove unused import

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• Merge remote-tracking branch 'origin/master' into feat/ref-minimizer

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• feat(cli): write sorted sequences to all common path prefixes

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• Merge remote-tracking branch 'origin/master' into feat/ref-minimizer

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• feat(cli): prettify help

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• feat(cli): print all dataset detections in terminal output

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Commits on Sep 12, 2023

• Merge remote-tracking branch 'origin/master' into feat/ref-minimizer

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• feat: filter datasets in wasm to speedup web ui

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• feat: remove list animations to speed things up

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• fix: styled-components warning about updates being too frequent

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• feat: make batch flushes more frequent for faster visible response

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• fix: typing

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• fix: sorting of dataset list

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• feat(cli): add dataset statistics into sort command printout

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• feat(cli): print results of sort command only in verbose mode

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• feat(cli): add output tsv file for sort command

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• fix(cli): add undetected entries into sort tsv

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Commits on Sep 14, 2023

• feat(web): reimplement main page

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Commits on Sep 15, 2023

• feat(web): prettify nav bar

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• fix(web): small styling

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• fix(web): use unique files ids as react keys

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Commits on Sep 18, 2023

• feat(web): scroll current dataset list item into view

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• refactor: simplify list scrolling setup

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• feat(web): preselect top dataset after suggestion is complete

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• refactor: lint

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• fix(web): text of example entry in query sequence list

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