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filter: Fix support for numerical IDs with both metadata and sequences #1256

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merged 3 commits into from Jul 10, 2023
Merged

filter: Fix support for numerical IDs with both metadata and sequences #1256

merged 3 commits into from Jul 10, 2023

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victorlin
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@victorlin victorlin commented Jul 10, 2023 •
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Description of proposed changes

See #667 (comment) and commit messages.

Related issue(s)

Fixes #667

Testing

  • Added a test to show change in behavior
  • Checks pass

Checklist

  • Add a message in CHANGES.md summarizing the changes in this PR that are end user focused. Keep headers and formatting consistent with the rest of the file.

@victorlin
Add test for numerical strain IDs
253a8f0
@victorlin
Read sequence index ID column as a string
7eda4bb 
This ensures proper matching with metadata IDs, which are always read as
string.
@victorlin victorlin self-assigned this Jul 10, 2023
@victorlin victorlin marked this pull request as ready for review July 10, 2023 19:15
@victorlin victorlin requested a review from a team July 10, 2023 19:15
joverlee521
joverlee521 approved these changes Jul 10, 2023
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Thanks for catching that this is still a bug in augur filter!

@victorlin victorlin merged commit 5eae388 into master Jul 10, 2023
27 checks passed
@victorlin victorlin deleted the victorlin/filter-numerical-ids branch July 10, 2023 20:31
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@joverlee521 joverlee521 joverlee521 approved these changes

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Successfully merging this pull request may close these issues.

augur tools do not recognize purely numeric strain IDs
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@victorlin @joverlee521