Dark-matter

* Added `--color` option to `fasta-identity-table.py`.

* Changed `Makefile` `upload` target rule.

* Moved all GOR4 amino acid structure prediction code into its own repo,
at [https://github.com/acorg/gor4](https://github.com/acorg/gor4).
* As a result, the `gor4` method on the `dark.reads.AAread` class has been
removed. This could be re-added by including `gor4` as a requirement but
for now if you want that functionality you'll need to install `gor4`
yourself and write a trivial function to call the `gor4` method on the
read (or make a subclass of `AARead` that adds that method). I've done it
this way because we have someone using the code who does not have a
working C compiler and this was causing a problem building dark matter.
Not a good reason, I know, but the GOR4 code makes for a good standalone
code base in any case.

* Added `--sampleIndexFilename` and `--pathogenIndexFilename` to
`proteins-to-pathogens.py`. These cause the writing of files containing
lines with an integer index, a space, then a sample or pathogen name.
These can be later used to identify the de-duplicated reads files for a
given sample or pathogen name.

* Added number of identical and positive amino acid matches to BLAST and
DIAMOND hsps.

* The protein grouper now de-duplicates read by id, not sequence.