refine: warn if doing timetree and there's apparent mismatch between metadata and sequence ids#1902
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corneliusroemer wants to merge 7 commits intomasterfrom
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refine: warn if doing timetree and there's apparent mismatch between metadata and sequence ids#1902corneliusroemer wants to merge 7 commits intomasterfrom
corneliusroemer wants to merge 7 commits intomasterfrom
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When building a time tree, warn users if sequence IDs in the tree don't match the metadata IDs. This helps identify when --metadata-id-columns needs to be set explicitly, especially when the strain column exists but contains different values than the sequence IDs, causing time tree inference to fail. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
corneliusroemer
commented
Oct 10, 2025
corneliusroemer
commented
Oct 10, 2025
corneliusroemer
commented
Oct 10, 2025
- Unified the warning message for both 0% and <50% match cases - Improved message clarity: "For X sequence IDs, only Y corresponding metadata rows could be matched" - Added functional CRAM test to verify the warning appears with mismatched IDs and disappears when using --metadata-id-columns - Added test metadata file with mismatched IDs in strain column 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
Instead of adding a new metadata_mismatch.tsv file, generate the mismatched metadata inline in the CRAM test using awk. This reduces the number of new files and makes the test self-contained. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
CRAM requires blank lines in expected output to have exactly 2 spaces of indentation. Updated the test to properly match the actual stderr output including the TreeTime error messages. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## master #1902 +/- ##
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+ Coverage 74.09% 74.26% +0.16%
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Files 82 82
Lines 8972 8980 +8
Branches 1823 1824 +1
==========================================
+ Hits 6648 6669 +21
+ Misses 2019 2011 -8
+ Partials 305 300 -5 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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| * `augur refine` will now warn when building a time tree if sequence IDs in the tree don't match metadata IDs, suggesting the use of `--metadata-id-columns` to explicitly set the correct ID column. [#1902][] (@corneliusroemer) |
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Suggest we make more explicit, something like "if more than half of the tip names are missing corresponding metadata"
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(Otherwise PR looks good!)
victorlin
reviewed
Oct 17, 2025
| terminal_names = {n.name for n in T.get_terminals()} | ||
| matched_ids = terminal_names & set(dates.keys()) | ||
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| if len(matched_ids) < len(terminal_names) * 0.5: |
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Suggestion: warn on any missing metadata. That would match the expectation for typical Augur workflows. augur filter drops data on either side if it's missing on the other side.
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Description of proposed changes
We don't warn very explicitly when there's a mismatch between metadata and sequence ids. I helped @aleskunder debug a situation where a more explicit warning would have helped him save quite some time. This PR adds such a warning. If a timetree is done and less than half of sequences have a corresponding row in the metadata, an informative warning is printed.
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