Dark-matter

Latest version: v4.0.89

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4.0.77

Prevent an `IndexError` in `bin/sam-reference-read-counts.py` when there
are no matching reads.

4.0.76

Fixed (hopefully!) a bug in `bin/fasta-identity-table.py` that could cause
a `KeyError` when producing a non-square table,
[as described here](https://github.com/acorg/dark-matter/issues/780).

4.0.75

Moved `getNoCoverageCounts` from `bin/fasta-identity-table.py` into
`dark/reads.py`. Made it handle an empty set of no-coverage chars. Added
tests.

4.0.74

Added `allowedTaxonomicRanks` argument to the `SqliteIndexWriter` class for
building a protein database, and corresponding command line argument to
`bin/make-protein-database.py`.

4.0.73

Wrap the `savefig` call to make the pathogens panel (in
`dark/civ/proteins.py`) in a `try/except` to catch the `ValueError` that
results if the image has a dimension exceeding 2^16.

4.0.72

Made `aa-info.py` slightly more useful by identifying stop codons. Added
`--details` option to request printing of amino acid property numeric
details.

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