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v4.0.1

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@Cloufield Cloufield released this 29 Dec 17:36
· 72 commits to main since this release
v4.0.1
8182efc

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
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