Major Changes
-
Improved Handling of Partial Genes: Partial genes are now correctly processed in PPanGGOLiN, no longer treated as pseudogenes (PR #290). This update affects results, as new genes may be included.
⚠️ -
Filtered Non-ASCII Characters: Non-ASCII characters are now filtered out to resolve issues for users with genomes annotated by Bakta (PR #291).
Minor Changes
- Enhanced Memory Efficiency for
ppanggolin fasta: Optimized memory usage for handling large pangenome files (PR #283). - Added Black Linter: Integrated Black linter to maintain consistent code formatting across the project (PR #295).
- Adjusted Log Level for Missing Translation Warnings: Changed log level to DEBUG to prevent log clutter when translation information is absent in input genomes (PR #296).
Bug Fixes
- Corrected Chao Calculation Formula: Fixed a formula error in the Chao metric displayed on the u-curve (PR #284, Issue #281).
- Resolved Empty Metadata Tag in Annotation Files: Fixed issue with empty metadata tags in annotation files (PR #287, Issue #285).
Full Changelog: Compare v2.1.2...v2.2.0