Cgbeacon2

Latest version: v4.5.1

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1.2

Fixed
- Added an init file inside the demo resources folder
- Accept variants annotated with build GRCh37 and GRCh38 (`chrN`) instead of just `N` (as in hg19)
- Improved calculation of structural variants end coordinates

Changed
- Renamed SNV and SV demo VCF files
- Coordinate Range queries allowing fuzzy positions

Added
- Demo VCF file containing BND SV variants
- Save BND variants to database (introduced additional mateName key/values)
- Query BND variants using mateName
- Documentation using `MkDocs`.
- Populate database with genes downloaded from Ensembl Biomart
- Function to create a VCF Bedtool filter from a list of genes HGNC ids or Ensembl ids
- API endpoint to add variants using a POST request
- API endpoint to remove variants using POST request

1.1

Fixed
- Revert to previous code, since cyvcf2 returns 0-based coordinates
- Updated README
- Added missing `requests` lib in requests
- Freezes pysam in requirements file
- Sets pytest requirement to >4.6 because of lack of backward compatibility of new version of pytest-cov
- Remove redundant text from cli docstrings
- Modified colors of 2 big checkboxes in the query form html page

Added
- Check that all requested samples are in VCF samples before uploading any variant
- Registering events whenever datasets and/or variants are added or removed
- Beacon info endpoint now returns beacon createDateTime and updateDateTime

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