Added `--percentageIdenticalCutoff` argument to `alignment-panel-civ.py` and `noninteractive-alignment-panel.py` and all that implies, down to reading DIAMOND output with the `pident` value, storing it, restoring it, and filtering on it in `dark.alignments.ReadsAlignmentsFilter`, plus tests.
3.1.21
Not secure
Minor changes to HTML output.
3.1.20
Not secure
Allow multiple `--preamble` args to `proteins-to-pathogens-civ.py`. Tiny cosmetic adjustments to output HTML.
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`.