Staramr

* Add support for campylobacter from PointFinder database.
* Fix `read_table` deprecation warnings by replacing `read_table` with `read_csv`.
* Handling issue with name of `16S` gene in PointFinder database for salmonella.
* Refactoring and simplifying some of the git ResFinder/PointFinder database code.
* Added automated type checking with [mypy](https://mypy.readthedocs.io).

* Exclusion of `aac(6')-Iaa` from results by default. Added ability to override this with `--no-exclude-genes` or pass a custom list of genes to exclude from results with `--exclude-genes-file`.

* Fix issue where `staramr` crashes if an input contig id is a number.

* Minor
* Updating default ResFinder/PointFinder databases to version from July 2018.
* Fix regex extracting gene/variant/accession values from ResFinder/PointFinder databases.
* Fixing a few entries in table mapping genes to phenotypes.
* Print stderr for errors with `makeblastdb`

* Major
* Inclusion of predicted resistances to antimicrobial drugs thanks to gene/drug mappings from the NARMS/CIPARS Molecular Working Group. Resistance predictions are microbiological resistances and not clinical resistances (issue 4, 6).
* Adding a `staramr db restore-default` command to restore the default `staramr` database (issue 3).
* Switched to using BLAST Tabular data + pandas to read BLAST results (issue 10).
* Inverted direction of BLAST (we now BLAST the AMR gene files against the input genomes).
* Minor
* Less verbose messages when encountering errors parsing the command-line options.
* Able to support adding options after a list of files (e.g., `staramr search *.fasta -h` will print help docs).
* Switched to including negative AMR results (samples with no AMR genes) by default. Must now use parameter `--exclude-negatives` to exclude them (issue 2).
* Only print 2 decimals in Excel output (issue 5).
* Automatically adjust Excel cells to better fit text (issue 7).
* Many other coding improvements (issue 11, 13 and others).

* Initial release. Supports batch scanning against the ResFinder and PointFinder databases.