Fix silent parse bug #1712
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Fix silent parse bug #1712
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## master #1712 +/- ##
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Coverage 72.90% 72.90%
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Files 79 79
Lines 8299 8299
Branches 1694 1694
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Hits 6050 6050
Misses 1961 1961
Partials 288 288 ☔ View full report in Codecov by Sentry. |
genehack
approved these changes
Jan 9, 2025
victorlin
approved these changes
Jan 11, 2025
Modifies the existing functional tests for parse by adding invalid
characters (spaces and parentheses) which augur parse converts to either
nothing or underscores, respectively. Since parse only transforms strain
names in the sequence output and not the metadata, this change to the
input data causes the functional test to fail. This commit adds a
parallel copy of the metadata ("other") for use in the test where the id
column is an accession and not the strain name and we don't expect the
strain name to get transformed.
Transforms the strain name in the metadata, fixing a bug where augur parse only transformed invalid characters in the sequence output and not the metadata output, causing records with those characters to become unlinked in downstream analyses. Fixes #1427 Co-authored-by: Victor Lin <[email protected]>
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Description of proposed changes
Transforms the strain name in the metadata, fixing a bug where augur parse only transformed invalid characters in the sequence output and not the metadata output, causing records with those characters to become unlinked in downstream analyses.
Related issue(s)
Closes #1427
Checklist