Dark-matter

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Page 40 of 43

Not secure

Made `dark/sam.py` properly deal with secondary alignments that are missing
a SEQ.

Not secure

Added `sam-reference-read-counts.py` script.

Not secure

Updated ViralZone search URL in `dark/proteins.py`.

Not secure

Added `--sites` argument to `compare-dna-sequences.py` and corresponding
`offsets` argument to the underlying function.

Not secure

Fixed bug that got introduced when doing `3.0.17 June 14, 2018`.

Not secure

Fixed bug that got introduced when doing `3.0.16 June 14, 2018`.

Has known vulnerabilities

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