Releases: Cloufield/gwaslab
Releases · Cloufield/gwaslab
v4.0.2
v4.0.2
- Fixed log message accuracy issues: < or <=
- Fixed log message accuracy issues: corrected typos ("macthes" → "matches", "will will" → "will") and improved grammar in log messages across harmonization and QC modules
- Fixed bugs in _parallelize_check_af() and _parallelize_infer_af(): added missing else clause for force=True case to prevent NameError
- Fixed bug in _fix_ID(): corrected redundant column check (nea in sumstats.columns) and (nea in sumstats.columns) to properly check both nea and ea columns
- Fixed log message placement in _infer_strand_with_annotation(): moved renaming log message inside conditional block to only log when renaming actually occurs
- Added type hints to improve code documentation and IDE support
- Added missing dependencies to pyproject.toml: requests, pyyaml, bitarray, platformdirs
v4.0.1
v4.0.1
- Added ChromosomeMapper with numeric middle layer architecture: unified chromosome format conversion system supporting numeric, string, chr-prefixed, and NCBI RefSeq formats across 12+ species
- ChromosomeMapper supports automatic format detection from sumstats and reference files (VCF, FASTA, GTF, Chain files)
- ChromosomeMapper can auto-detect genome build from NCBI RefSeq notation in reference files (hg19/hg38)
- Removed legacy chr_dict in favor of ChromosomeMapper
- Fixed infer_strand bug: added FREQ_COMPARISON_EPSILON constant (1e-6) for floating-point precision in allele frequency comparisons to handle edge cases at threshold boundaries
- Added comprehensive test cases for floating-point precision edge cases in strand inference (e.g., EAF=0.4000003453, VCF AF=0.4000000059604645)
- Enhanced P-value consistency checking in check_data_consistency(): now uses fold change as primary metric for better interpretability with small P-values (reports "10.23x" instead of absolute difference)
- Improved handling of P-values spanning many orders of magnitude and NaN values
- Added comprehensive test suite for P-value consistency checks
- Created ChromosomeHandling.md documentation covering architecture, formats, species support, and usage examples
GWASLab v4.0.0
GWASLab v4.0.0
Major update release celebrating our 4th anniversary!
- Performance improvements: Optimized algorithms and data structures for faster processing and improved memory usage
- API consistency: Standardized parameter naming across functions
- Command Line Interface: New CLI for processing GWAS summary statistics from the terminal
- Enhanced documentation: Improved documentation with practical examples
- Test modules: Comprehensive test suite with expanded coverage across core functionality