fix: fix metadata format and sequence processing#15
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gp201 merged 2 commits intoandersen-lab:mainfrom Dec 9, 2025
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Pull request overview
This PR fixes two issues: a bug in the lineage processing logic and updates the metadata output format documentation to reflect the actual TSV format used.
- Fixed a critical bug where the lineage processing would stop at the first missing sample instead of continuing to process remaining samples
- Updated CLI help text and default filename to correctly indicate TSV format for metadata output (aligning with actual implementation)
Reviewed changes
Copilot reviewed 2 out of 2 changed files in this pull request and generated no comments.
| File | Description |
|---|---|
| barcodeforge/ref_muts.py | Fixed bug by changing break to continue to ensure all samples are processed even when some are missing from FASTA |
| barcodeforge/cli.py | Updated default metadata filename from .csv to .tsv and corrected help text to reflect TSV format |
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This pull request makes two fixes: it updates the output metadata file format to TSV and fixes a bug in the lineage processing logic to ensure as many samples are processed.
Output format update:
barcodeCLI command to reflect this change.Bug fix in lineage processing:
breakwithcontinuein theprocess_and_reroot_lineagesfunction so that all missing samples are skipped individually, rather than stopping at the first missing sample.