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nextstrain
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augur
Pipeline components for real-time phylodynamic analysis
https://docs.nextstrain.org/projects/augur/
GNU Affero General Public License v3.0
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Subsample has uncaught assertion in ncov
#1598
corneliusroemer
closed
1 month ago
3
Use identical help text for shared options
#1597
victorlin
opened
1 month ago
0
Use ngettext to handle plurality
#1596
victorlin
closed
1 week ago
1
Update changelog entry for weighted sampling
#1595
victorlin
closed
1 month ago
0
merge: Support table-specific id columns and delimiters
#1594
tsibley
closed
1 month ago
4
merge: Avoid overwriting the output id column with non-id columns
#1593
tsibley
closed
1 month ago
2
filter: Confusing warning and error combination when query contains a missing column
#1592
victorlin
closed
1 month ago
2
merge: polish
#1591
tsibley
closed
1 month ago
3
filter: Make under-sampling more apparent
#1590
victorlin
opened
1 month ago
0
Test new CI workflow
#1589
genehack
closed
1 month ago
1
Simplify probabilistic sampling calculation
#1588
victorlin
closed
1 month ago
2
`AUGUR_DEBUG` documentation
#1587
tsibley
closed
1 month ago
0
augur curate format-host
#1586
joverlee521
opened
1 month ago
1
CLI docs have incorrect default values for options using `store_false` action
#1585
victorlin
opened
1 month ago
2
Missing trait literals are converted to lower case in augur export stderr output
#1584
corneliusroemer
opened
1 month ago
1
Update language around snakemake install
#1582
genehack
opened
1 month ago
0
merge: polish
#1581
tsibley
closed
1 month ago
2
Uncaught error when root not in tree.
#1580
vanessazubach
opened
1 month ago
9
merge: Support sequences
#1579
tsibley
opened
1 month ago
10
`parse-genbank-location` should warn about region/locality mix ups
#1578
joverlee521
opened
1 month ago
2
Add a debugging mode controlled by AUGUR_DEBUG
#1577
tsibley
closed
1 month ago
5
Command descriptions mangled in `--help` output
#1576
tsibley
closed
1 month ago
2
Speed up augur filter
#1575
victorlin
opened
1 month ago
0
Speed up augur filter by replacing Pandas
#1574
victorlin
opened
1 month ago
1
Speed up augur filter without replacing Pandas
#1573
victorlin
opened
1 month ago
0
Poorly formatted metadata TSV leads to KeyError
#1572
joverlee521
closed
1 month ago
1
Simplify Python version config for mypy/pyright
#1571
victorlin
closed
1 month ago
0
Fix broken links [#1569]
#1570
genehack
closed
1 month ago
3
Fix broken links in docs
#1569
genehack
closed
1 month ago
0
Fix broken links [nextstrain/docs.nextstrain.org#14]
#1568
genehack
closed
1 month ago
2
Add sqlite3 cli to augur's bioconda recipe once augur merge PR is merged
#1567
corneliusroemer
opened
2 months ago
0
Pick a meaning of TSV and use it consistently
#1566
tsibley
opened
2 months ago
10
Fix curate internal quotes take 2
#1565
joverlee521
opened
2 months ago
5
Fix newline handling when reading CSV/TSV
#1564
tsibley
closed
2 months ago
2
augur merge
#1563
tsibley
closed
1 month ago
11
augur {read,write}-file
#1562
tsibley
closed
2 months ago
3
io.metadata: Fix newline handling when reading CSV/TSV
#1561
tsibley
closed
2 months ago
0
dev: Rename pytest.python3.ini → pytest.ini so it's used by default
#1560
tsibley
closed
2 months ago
0
tree: Update Cram tests
#1559
victorlin
closed
2 months ago
0
tree: Update Cram tests
#1558
victorlin
closed
2 months ago
0
No standard test environment
#1557
tsibley
opened
2 months ago
7
[traits] cmd should warn when metadata is completely missing for a given node
#1556
genehack
opened
2 months ago
3
Fix titer substitution model tree annotations
#1555
huddlej
closed
2 months ago
1
Update lassa CI
#1554
joverlee521
closed
2 months ago
0
augur curate: improve metadata header parsing
#1553
joverlee521
opened
2 months ago
1
Update avian-flu CI
#1552
jameshadfield
closed
2 months ago
1
Update sphinx-argparse pin to !=0.5.0
#1551
victorlin
closed
2 months ago
0
curate: Accept Excel and OpenOffice metadata files
#1550
tsibley
closed
2 months ago
2
CI: Update pathogen-repo-ci
#1549
joverlee521
closed
2 months ago
1
io.json: Serialize date objects as ISO 8601 too
#1548
tsibley
closed
2 months ago
1
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