Dark-matter

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Page 6 of 44

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.

Use `[0-9]' instead of `\d` in `bin/download-refseq-viral-gbff.sh` so that
`egrep` works with the brew-installed GNU egrep on OS X.

Make `utils.py` `asHandle` work when passed a `pathlib.Path` argument.

Added `--includeAmbiguousMatches` and `--includeNonGapMismatches` options to
`bin/compare-sequences.py`.

Added `includeAmbiguousMatches` and `includeNonGapMismatches` options to
`matchToString` in `dark/dna.py`.

Has known vulnerabilities

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