Moved some code out of dark/civ/proteins.py into dark/genbank.py to make it more useful to others.
4.0.8
Not secure
Added `DistanceMatrix` class to `dark/sam.py` for computing distances between references according to which reads match both (and how well, if an alignment score tag is given).
4.0.7
Not secure
Color overall number of reads per pathogen in HTML output.
4.0.6
Not secure
Fixed subtle bug introduced into `bin/filter-fasta.py` due to a code reordering.
4.0.5
Not secure
Added printing of reference lengths to `bin/sam-reference-read-counts.py`. Changed the `--sort` option of that script to `--sortBy`. Added options to stop printing references once they either have no reads mapped to them or the number of new reads mapped to them ("new" as in not already mapping to an earlier reference) falls to zero.
4.0.4
Added `fasta-split.py` command to split a FASTA/Q file into multiple files, each containing a given number of sequences. Added `dark/utils.py` function `take` to repeatedly yield lists of a given number of things from an iterable.