Dark-matter

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3.1.19

Not secure
Added read count color levels indicator in HTML. Added
`--bootstrapTreeviewDir` to `proteins-to-pathogens-civ.py` and the `toHTML`
method of `dark.civ.proteins.ProteinGrouper`.

3.1.18

Not secure
Fix (again) newline in HTML summary output.

3.1.17

Not secure
Fix newline in HTML summary output.

3.1.16

Not secure
Fix tiny bug in print arguments in `dark/civ/proteins.py`.

3.1.15

Not secure
Added `--readCountColor` and `--defaultReadCountColor` to
`proteins-to-pathogens-civ.py` for differential coloring of read
counts. Added `citrus yellow` to plant-only virus name regex in
`dark/taxonomy.py`.

3.1.14

Not secure
Added a const value for `--pathogenPanelFilename` in `proteins-to-pathogens-civ.py`.

Page 27 of 43

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