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Change Log

All notable changes to this project will be documented in this file. This project adheres to Semantic Versioning.

About changelog here

Please add a new candidate release at the top after changing the latest one. Feel free to copy paste from the "squash and commit" box that gets generated when creating PRs

Try to use the following format:

[unreleased]

Fixed

  • Sorting command more inclusive for e.g. BusyBox sort for containers built with Bioconda (#198)

[3.10.2]

Fixed

  • Add scoring normalisation for flag lookup mode (#177)
  • Fix crash on test for missing annotation key for phased mode (#178)
  • Bugfixes related to multiprocessing stability and error handling (#183 and #186)
  • Removed unused dependency (#182)

[3.10.1]

Fixed

  • Documentation formatting for more modern mkdocs (pages to nav) (#168)
  • Stable sort in bioconda (BusyBox sort) not recognizing long options (#170)
  • Unstable Annotation= order in genmod annotate --regions (#173)

[3.10]

Changed

  • Use uv with hatchling to build and publish (#104)
  • Automation for Docker publish and mkdocs githubio (#161)

Fixed

  • The optional fields Source and Version are allowed in the VCF header(#106)
  • Released the constraint on Python 3.8 (collections, pkg_resources to importlib, tests) (#142)
  • Update annotation examples (#144)
  • Updated documentation with warning about compounds only being scored within the first family in the VCF (#151)
  • Fixed sorting of variants (#152)
  • genmod annotate for mitochondrial variants when using the chrM notation (#157)
  • Fix linting issues (#154)
  • genmod models adds headers to VCF even if it contains no variants (#160)

[3.9]

  • Fixed wrong models when chromosome X was named chrX and not X (#135)
  • Added GitHub Actions workflows for automatic publishing to PyPI on release, and keep a changelog reminder (#136)
  • Optional user defined threshold and penalty for compound scoring (#138)
  • Update README with current github.io docs page (#140)

[3.8.3]

  • Fixed unstable compounds order in models output (#134)
  • Added six to requirements.txt and setup.py (#134)

[3.8.0]

  • Rank score normalisation

[3.7.4]

Fixed

  • OSError crashes due to socket address conflicts when using containers

[x.x.x]

Changed

  • Adds support for escaped characters in FORMAT description header strings

Fixed

  • Documentation about cli options strict and phased