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.
3.0.39
The fix to solve [630](https://github.com/acorg/dark-matter/issues/630) was insufficient. That's fixed in this release, hopefully!
3.0.38
Not secure
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.
3.0.37
Not secure
Add a `--titlesJSONFile` option to `noninteractive-alignment-panel.py`.
3.0.36
Not secure
Added `whitelistFile` and `blacklistFile` to `ReadsAlignmentsFilter` class in `dark/alignments.py`.
3.0.35
Not secure
Fixed small bug in `filter-hits-to-fasta.py`.
Added flushing of intermediate output in `noninteractive-alignment-panel.py`.