Dark-matter

* 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.

* Fixed HTML tiny formatting error in `toHTML` method of `ProteinGrouper`
in `dark/proteins.py`.

* The `--indices` option to `filter-fasta.py` was changed to accept a
string range (like 10-20,25-30,51,60) instead of a list of single
integers. It is renamed to `--keepSequences` and is also now 1-based not
0-based, like its friends `--keepSites`.
* `--removeSequences` was added as an option to `filter-fasta.py`.
* The options `--keepIndices`, `--keepIndicesFile`, `--removeIndices`, and
`removeIndicesFile` to `filter-fasta.py` are now named `--keepSites`,
`--keepSitesFile`, `--removeSites`, and `removeSitesFile` though the old
names are still supported for now.
* The `indicesMatching` methods of `Reads` is renamed to `sitesMatching`.
* `removeSequences` was added to read filtering in `ReadFilter` and as a
`--removeSequences` option to `filter-fasta.py`.