Dark-matter

[Pysam issue 716](https://github.com/pysam-developers/pysam/issues/716)
wasn't solved the way we hoped it would be, so now the `filter-sam.py`
command always passes the template of the original SAM file to the
constructor for the new file. As a result, the new file will have `SN`
entries for all the original sequences, even when `--referenceId` is passed
to `filter-sam.py` to restrict output to a specific set of reference ids.

Added `--showDiffs` option to `bin/compare-sequences.py`.

Force use of `mysql-connector-python` version `8.0.11` in
`requirements.txt` due to segmentation fault running tests using TravisCI.
Set version `0.5.0` of `pyfaidx` to avoid error in `pyfaidx/__init__.py`
line 711 (AttributeError: 'str' object has no attribute 'decode') in later
`pyfaidx` version. Removed some deprecation warnings when running tests.

The fix to solve [630](https://github.com/acorg/dark-matter/issues/630)
was insufficient. That's fixed in this release, hopefully!

Fixed [630](https://github.com/acorg/dark-matter/issues/630) to deal with
non-hard-clipped queries that have a CIGAR string that indicates they have
been clipped.

Add a `--titlesJSONFile` option to `noninteractive-alignment-panel.py`.