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Pull requests: nextstrain/augur

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Pull requests list

fix: explicitly specify how the root and ambiguous states are handled…
#1690 opened Nov 25, 2024 by rneher Loading…
3 of 4 tasks
1
14
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…
3 of 5 tasks
1
@victorlin
7
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
filter: Rewrite using SQLite3
#1242 opened Jun 17, 2023 by victorlin • Draft
1 of 7 tasks
@victorlin
6
ProTip! Exclude everything labeled bug with -label:bug.