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Page 4 of 43

Added type hints to scory.py and some to reads.py.

Removed `bin/find-hits.py`. Fixed matplotlib deprecation warnings. Ran black.

Backed out 4.0.59 and 4.0.60 changes.

More index checking in `bin/sam-coverage-depth.py`.

Subtract one from `stop` arg to pysam.pileup because, despite being
0-based, pysam apparently includes the final index.

Make `bin/download-refseq-viral-gbff.sh` exit non-zero if no viral genome
files are downloaded.

Has known vulnerabilities

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