Skip to content

Pull requests: nextstrain/augur

New pull request New
55 Open 921 Closed
55 Open 921 Closed
Author
Filter by author
Loading
Label
Filter by label
Loading
Use alt + click/return to exclude labels
or ⇧ + click/return for logical OR
Projects
Filter by project
Loading
Milestones
Filter by milestone
Loading
Reviews
Filter by reviews
No reviews Review required Approved review Changes requested
Assignee
Filter by who’s assigned
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Pull requests list

fix: explicitly specify how the root and ambiguous states are handled…
#1690 opened Nov 25, 2024 by rneher Loading…
4 tasks
5
Fix type error in titer model cross-validation
#1688 opened Nov 21, 2024 by huddlej • Draft
4 tasks
1
feat(ancestral): make --genes optional when reconstructing translations, if omitted, translate all genes in annotation
#1668 opened Nov 10, 2024 by corneliusroemer • Draft
4 tasks
3
tests: add cram wrapper parallel_cram.sh that runs cram tests in parallel
#1667 opened Nov 9, 2024 by corneliusroemer Loading…
2 of 4 tasks
13
fix(tests): Fix false negative cram tests
#1666 opened Nov 9, 2024 by corneliusroemer Loading…
4 tasks done
1
18
feat(ancestral): Add optional Nextclade GFF3 compatibility mode
#1664 opened Nov 9, 2024 by corneliusroemer Loading…
2 of 5 tasks
11
CLI: Use raw descriptions
#1641 opened Sep 24, 2024 by victorlin • Draft
5 tasks
@victorlin
Register subparsers recursively
#1640 opened Sep 24, 2024 by victorlin • Draft
2 of 5 tasks
@victorlin
5
filter: Deprecate --output and -o
#1622 opened Sep 4, 2024 by victorlin Loading…
4 tasks done
1
@victorlin
1
merge: Support sequences with cross-checking
#1601 opened Aug 27, 2024 by victorlin Loading…
2 of 5 tasks
1
@victorlin
6
chore(deps): configure dependabot for pip deps
#1538 opened Jul 11, 2024 by corneliusroemer Loading…
4 tasks
5
chore(deps): allow numpy v2
#1533 opened Jul 11, 2024 by corneliusroemer • Draft
4 tasks
1
1
filter: Improve speed of --output-strains and --output-metadata
#1469 opened May 18, 2024 by victorlin • Draft
3 tasks
@victorlin
19
WIP [refine] unique internal node names
#1451 opened Apr 24, 2024 by jameshadfield • Draft
2
export multiple trees
#1450 opened Apr 24, 2024 by jameshadfield Loading…
2 tasks
12
DRAFT: add 'gene' feature capture when reading genbank files
#1435 opened Mar 8, 2024 by j23414 • Draft
3 tasks
5
filter: Split filtering and subsampling
#1432 opened Mar 7, 2024 by victorlin • Draft
3 tasks
@victorlin
6
filter: Improve help text
#1430 opened Mar 5, 2024 by victorlin • Draft
2 of 3 tasks
@victorlin
1
feat: complex CDSs within augur ancestral
#1333 opened Nov 4, 2023 by corneliusroemer • Draft
2 tasks
1
4
WIP: New clades subcommand that works like traits, using labeled tips rather than clades.tsv
#1329 opened Oct 26, 2023 by corneliusroemer • Draft
8
feat: support treetime ambiguous date format
#1305 opened Sep 4, 2023 by corneliusroemer • Draft
2 of 3 tasks
1
@victorlin
6
feat(mask): allow empty mask file, warn not error
#1287 opened Aug 19, 2023 by corneliusroemer Loading…
1 task done
1
feat(mask): Add --mask-gaps {all,terminals} option
#1286 opened Aug 19, 2023 by corneliusroemer Loading…
2 tasks done
7
Update annotation schema for strand changes
#1279 opened Aug 11, 2023 by victorlin • Draft
2 tasks
@victorlin
1
Feat/parse nextclade annotation
#1263 opened Jul 26, 2023 by rneher Loading…
1 task
ProTip! Mix and match filters to narrow down what you’re looking for.