Dark-matter

Added printing of transversion and transition counts to
`bin/codon-distance.py`. Output is sorted first by distance, then by number
of transitions (highest to lowest) then by codon DNA. The idea being to
present the possible codon changes to get from one amino acid to another in
the order that requires the least change to the most.

The lists in the values in the dict returned by `codonInformation` now
contain 2-tuples instead of lists of length 2. If you pass
`countTransitions=True` to that function it will also put the count of the
number of transitions (as opposed to transversions) into the tuple. See the
tests in `test/test_codonDistance.py`.

Added `--reference` option to `sam-coverage-depth.py`.

Return an empty list of reads from mafft and needle when dryRun is True.

Added optional `executor` and `dryRun` arguments to MAFFT and needle
aligners to allow the caller to pass in a pre-existing process
executor. Added `--format` option to `newick-to-ascii.py` tree printing to
allow loading a wider range of Newick files.

Improve output of `compare-aa-sequences.py` to show the percentage of
matches in regions that do not involve a gap in either sequence.

Bump mysql connector version due to security issue with 8.0.13