Added
Fixed
- Bug fixes to handle new CGI wildtype biomarkers
- civicpy cache will only be updated when civic is queried
Dependencies
Deprecated
Added
Fixed
- Bug fixes to include all evidence of CIViC
Dependencies
Deprecated
Added
Fixed
- Fixed functionality for new CGI file structure
- Fixed case when CIViC has no hits
Dependencies
Deprecated
Added
Fixed
- Fixed API docs
Dependencies
Deprecated
Added
Fixed
- Fixed version bump
Dependencies
Deprecated
Added
Fixed
- Fixed import of site-packages in setup.py
Dependencies
Deprecated
Added
- Added functionality to combine the results of the Knowledgebases in an HTML report
- Added possibility to have non-numerical chromosome columns in the input vcf
- Added deletion of CGI jobs from CGI Server after completion
Fixed
Dependencies
Deprecated
Added
- Optional VEP annotation based filtering
- Additional metadata
- Usage of pyVCF3 to read vcf files
- Querynator ID added for filtered vcf files
- All possible reference genomes for CIViC
Fixed
Dependencies
Deprecated
- Usage of pysam to read vcf files
Added
Fixed
- Rendering API docs
Dependencies
Deprecated
Added
- Added functionality to query the Clinical Interpretation of Variants in Cancer (CIViC) Knowledgebase
- Added possibility to query bgzipped files
Fixed
Dependencies
Deprecated
Added
Fixed
- Fix including module
Dependencies
Deprecated
Added
Fixed
- Fix installing requirements
Dependencies
Deprecated
Added
Fixed
- Github Actions publishing to PyPI
- Fix docs
Dependencies
Deprecated
Added
- First release on PyPI
- Created the package template with cookiecutter
- Functions to query the cancergenomeinterpreter REST API
Fixed
Dependencies
Deprecated