Code

Add automatic detection of datasets#1244

Code

Merged

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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  a224aaf

• feat(cli): implement ref search

  ivan-aksamentov

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  16cf181

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

  ivan-aksamentov

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  0cf48f9

• feat(cli): improve error message text

  ivan-aksamentov

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  dfa63a6

• fix(cli): version warning false positive

  ivan-aksamentov

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  d327c77

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

  ivan-aksamentov

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  8940bbb

Commits on Sep 4, 2023

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

  ivan-aksamentov

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  b6b4fe8

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

  ivan-aksamentov

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  5b6bc87

• feat(cli): write sorted fasta files

  ivan-aksamentov

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  1b90f1b

• fix(web): dataset equality

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  db37dd3

Commits on Sep 5, 2023

• feat(web): add sequence sorting prototype

  ivan-aksamentov

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  8ac3f67

• fix: move wasm module into webworker

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  bb5aa6a

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

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  d60ced5

• fix(web): parentheses in the conditional

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  9b31210

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

  ivan-aksamentov

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  603ffa0

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

  ivan-aksamentov

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  23cb227

• fix(web): non-unique atom key

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  7c9e5cc

Commits on Sep 6, 2023

• refactor: lint

  ivan-aksamentov

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  8ec4530

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

  ivan-aksamentov

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  32f6ee5

Commits on Sep 7, 2023

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

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  5bcc43f

• feat(web): prototype new dataset autodetect ui

  ivan-aksamentov

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  816e727

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

  ivan-aksamentov

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  638da57

• perf: serialize directly to jsvalue to avoid json parsing

  ivan-aksamentov

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  94578f4

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

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  2a97561

• fix(web): duplicate id and label misalignment

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  c52e8d8

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

  Show description for 7c2a305
  ivan-aksamentov

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  7c2a305

Commits on Sep 8, 2023

• refactor: extract function

  ivan-aksamentov

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  ac91ecc

• refactor: lint

  ivan-aksamentov

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  af4841e

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

  ivan-aksamentov

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  d136b84

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

  ivan-aksamentov

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  e33c04f

• refactor: remove unused import

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  bfa0e9b

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

  ivan-aksamentov

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  1a7c48e

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

  ivan-aksamentov

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  e30adc0

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

  ivan-aksamentov

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  619aab4

• feat(cli): prettify help

  ivan-aksamentov

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  ac7c2d5

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

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  61eef71

Commits on Sep 12, 2023

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

  ivan-aksamentov

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  118f36b

• feat: filter datasets in wasm to speedup web ui

  ivan-aksamentov

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  eb15094

• feat: remove list animations to speed things up

  ivan-aksamentov

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  c4d2763

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

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  5dfb741

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

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  07526b8

• fix: typing

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  79a44fc

• fix: sorting of dataset list

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  f17cf32

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

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  407921c

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

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  a81bc88

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

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  d4efb62

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

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  99fb0c8

Commits on Sep 14, 2023

• feat(web): reimplement main page

  ivan-aksamentov

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  131fedd

Commits on Sep 15, 2023

• feat(web): prettify nav bar

  ivan-aksamentov

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  cabb824

• fix(web): small styling

  ivan-aksamentov

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  55093f9

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

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  68438ff

Commits on Sep 18, 2023

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

  ivan-aksamentov

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  01f3449

• refactor: simplify list scrolling setup

  ivan-aksamentov

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  453cf3b

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

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  f0e0cdf

• refactor: lint

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  a002c12

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

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  996980d