Issues
- 2
Augur index may always report sequence file is missing even if output dir is missing?
#1644 opened by emmahodcroft - 2
filter: Prefer "output sequences" over "output"?
#1607 opened by victorlin - 0
Add examples for weighted sampling with multiple columns including month/week
#1645 opened by victorlin - 10
merge: Support sequences
#1579 opened by tsibley - 0
Improve rendering of CLI documentation
#1642 opened by victorlin - 1
- 2
Add escape hatch for the "Augur version incompatibility detected" error
#1635 opened by corneliusroemer - 3
Improve help text of CLI options
#1630 opened by victorlin - 5
Set pipefail for cram tests
#1627 opened by victorlin - 0
CI/release: Run tests on build artifacts
#1638 opened by victorlin - 2
- 10
Pick a meaning of TSV and use it consistently
#1566 opened by tsibley - 0
filter: `--output-sequences` silently allows duplicates
#1602 opened by victorlin - 2
Augur traits error
#1626 opened by vanessazubach - 2
- 0
`augur merge` is slow to read in metadata
#1628 opened by tsibley - 0
merge: Import metadata files concurrently?
#1617 opened by tsibley - 4
Release: changelog can be out-of-sync
#1620 opened by victorlin - 4
- 1
CI: codecov artifact download failing
#1616 opened by victorlin - 2
Simplify probabilistic sampling calculation
#1588 opened by victorlin - 3
Subsample has uncaught assertion in ncov
#1598 opened by corneliusroemer - 1
Spaces in BEAST annotations cause error
#1609 opened by watronfire - 0
Align fractional sequences per group conversion methods
#1614 opened by victorlin - 0
Legacy editable installs are deprecated
#1611 opened by genehack - 1
merge: Uncaught error with user-defined `.sqliterc`
#1603 opened by victorlin - 0
- 2
filter: Confusing warning and error combination when query contains a missing column
#1592 opened by victorlin - 0
CI failing on JSON diff
#1605 opened by victorlin - 0
- 0
Use identical help text for shared options
#1597 opened by victorlin - 0
filter: Make under-sampling more apparent
#1590 opened by victorlin - 1
augur curate format-host
#1586 opened by joverlee521 - 2
CLI docs have incorrect default values for options using `store_false` action
#1585 opened by victorlin - 1
Missing trait literals are converted to lower case in augur export stderr output
#1584 opened by corneliusroemer - 0
Fix broken links in docs
#1569 opened by genehack - 0
Update language around snakemake install
#1582 opened by genehack - 9
Uncaught error when root not in tree.
#1580 opened by vanessazubach - 2
Command descriptions mangled in `--help` output
#1576 opened by tsibley - 1
Speed up augur filter by replacing Pandas
#1574 opened by victorlin - 0
Speed up augur filter
#1575 opened by victorlin - 0
Speed up augur filter without replacing Pandas
#1573 opened by victorlin - 1
Poorly formatted metadata TSV leads to KeyError
#1572 opened by joverlee521 - 7
No standard test environment
#1557 opened by tsibley - 0
Add sqlite3 cli to augur's bioconda recipe once augur merge PR is merged
#1567 opened by corneliusroemer - 0
tree: Update Cram tests
#1558 opened by victorlin - 3
[traits] cmd should warn when metadata is completely missing for a given node
#1556 opened by genehack - 1
augur curate: improve metadata header parsing
#1553 opened by joverlee521 - 0
- 0
`augur curate` could have a more helpful error message
#1539 opened by genehack