Loqusdb

Added
- Basic cli tests touching fixed deprecated code
Changed
- Unfreezed PyMongo in requirements.txt
- Replaced deprecated pymongo `.count()` function with `count_documents()` in code.

Fixed
- `Deprecated config in setup.cfg` error when installing the package

Added
- Script to correct contig name
- Expanded instructions on how to set up an instance and load data into database
Changed
- GitHub actions run tests using MongoDB versions 3.2, 4.4 and 5.0
Fixed
- Restore command accepts custom database name
- Restore command uses either database URI or host:port params

Changed
- Convert version to string
- Use Github Actions for running CI instead of Travis

Added
- Option to add observation frequencies to exported VCF (--freq)

Added
- Profiling feature added. Each sample gets a profile based on the genotypes for
a set of high maf variants.
- High maf variants used in profiling is loaded into DB via CLI
- Reject loading a case if a similar profile already exists for any of the samples
- Statistics of the profiles in DB can be generated through CLI
- use bulk operations when deleting variants
- Compatible with GRCh38
- Option to include case count when querying for a variant

Fixed
- Use correct fields in index