v0.0.5 release

v0.0.5 (2025-12-11)

This is a patch release focused on fixing coordinate-related bugs in the predict and variant subcommands and adding a helper script for custom annotations.

Bug fixes

• Correct BED coordinates in predict output

  • Donor and acceptor sites are now reported as single-nucleotide positions (the actual splice site) instead of the 2-bp dimer.
  • This fixes the previous 1-bp shift in reported sites and eliminates cases where chromStart > chromEnd could appear in the BED output.
  • Thanks to @cooketho for the detailed report and test case.

• Correct delta position reporting in variant output

  • Fixed a cropping bug where the model outputs were not trimmed to the variant-centered distance window (e.g. ±50 bp) before extracting delta positions.
  • Delta indices are now computed relative to the correctly cropped window, so reported delta positions match the variant-centered window rather than the full flanking region.
  • Thanks to @kasia-te and @conbward for identifying and documenting this issue.

New utilities / documentation

• GFF → OpenSpliceAI annotation helper script
  • Added a script and example resources to help convert generic GFF files into the annotation format required by OpenSpliceAI.
  • See the data/ directory for the script and usage instructions:
    https://github.com/Kuanhao-Chao/OpenSpliceAI/tree/main/data

PyPI release

• OpenSpliceAI v0.0.5 is available on PyPI:
  https://pypi.org/project/OpenSpliceai/