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GFFx v0.3.0

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@Baohua-Chen Baohua-Chen released this 22 Aug 13:08
· 53 commits to main since this release
v0.3.0
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GFFx v0.3.0 Release Notes

This is a major release of GFFx, introducing important changes to default behavior, performance improvements, and bug fixes.

Breaking Changes

  • Default extraction/intersection mode changed:
    Non Full-Model Mode is now the default. To preserve the previous behavior (returning the entire gene model), users must explicitly pass the -F / --full-model flag.
    Non Full-Model Mode and Full-Model Mode have comparable runtime performance.

New Features

  • Non Full-Model Mode for extract and intersect
    Added support for a new mode where these commands return only the features that directly match the queries, instead of always returning the entire gene model.

Changes

  • Default Behavior Update
    Non Full-Model Mode is now the default (see Breaking Changes).
  • Threading Default Update
    The default number of threads has been changed from 4 to 12 CPU cores to improve the performance under default settings.

Improvements

  • Refactored code to increase cohesion and function reusability.

Bug Fixes

  • Fixed several minor issues to improve stability and correctness.
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