Capice

Latest version: v5.1.2

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4.0.0rc2

What's Changed
* feat: Updated libraries by SietsmaRJ in https://github.com/molgenis/capice/pull/131


**Full Changelog**: https://github.com/molgenis/capice/compare/v4.0.0-rc1...v4.0.0-rc2

4.0.0rc1

What's Changed
* feat: No Imputing by SietsmaRJ in https://github.com/molgenis/capice/pull/130


**Full Changelog**: https://github.com/molgenis/capice/compare/v3.3.0...v4.0.0-rc1

3.3.0

What's Changed
* fix: Allele frequency support by SietsmaRJ in https://github.com/molgenis/capice/pull/133


**Full Changelog**: https://github.com/molgenis/capice/compare/v3.2.1...v3.3.0

3.2.1

What's Changed
* fix: raw train file by SietsmaRJ in https://github.com/molgenis/capice/pull/122
* fix: Index in train TSV by SietsmaRJ in https://github.com/molgenis/capice/pull/124
* fix: README VEP duplicate flag by SietsmaRJ in https://github.com/molgenis/capice/pull/129
* fix: Train input raw by SietsmaRJ in https://github.com/molgenis/capice/pull/132


**Full Changelog**: https://github.com/molgenis/capice/compare/v3.2.0...v3.2.1

3.2.0

New:

- Added `explain` module. This module takes any CAPICE model, using v3.0.0 or greater, and exports the feature importance of said model with importances: `gain`, `total_gain`, `weight`, `cover` and `total_cover`, ordered by `gain`.
- Added `-t/--threads` flag to train to specify how many computing cores can be used during training.

Changes:

- Changed behaviour of VEP processor `consequence.py`. Added 3 missing possible consequences that could be within the output of VEP but were not processed yet. The processor will now also throw a warning if it encounters a consequence it does not support.
- Code refactoring to `main_train.py`
- Changed feedback to user for exports. Now if a user supplies an output argument that is a full path including filename, it will not print where the file is placed. In any other case, such as no supplied output, only a path as output or only a filename as output, CAPICE will now print where the file is placed. This change is implemented for `predict`, `train` and `explain`.
- Increased strictness of the output argument. CAPICE will no longer add a `.gz` extension to the output, it is required to be supplied by the user.
- Fixed data types errors that would only be raised on Windows machines.
- Fixed the VEP command.

3.1.2

Changes:

- Bumped Numpy to version 1.22.0 due to security vulnerability.

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