Ngmaster

NEWS

- `isPcr` has been replaced by `mlst` (https://github.com/tseemann/mlst) with a custom allele database
- [ng-mast.net](http://www.ng-mast.net/) is no longer online or maintained, so this version has been migrated to use the [pubMLST database](https://pubmlst.org/bigsdb?db=pubmlst_neisseria_seqdef&page=schemeInfo&scheme_id=71) instead.
- Updating of the database is done via pubMLSTs API, replacing the need for web-scraping.
- [NG-STAR](https://pubmlst.org/bigsdb?db=pubmlst_neisseria_seqdef&page=schemeInfo&scheme_id=67) is now integrated into `ngmaster`. NG-STAR is an AMR typing scheme for _N. gonorrhoeae_, using seven resistance alleles. `--comments` function is also implemented which allows to download free-text fields from pubMLST for each allele.
- Code has been refactored

NEWS

* Added support for `bumpversion` to make it easier to update
* Moved utilities from `__init__.py` to `utils.py`
* Renamed `ngmaster.py` to `run_ngmaster.py` to avoid any confusion when importing
* Pushed to `pypi`
* Updated documentation on how to install (now from `pypi`). `Conda` and `Brew` will also be available.
* Added TravisCI support
* Added `__version__` to `__init__.py`

NEWS
* Added option to force DB update without requesting user blessing (`ngmaster --dbupdate --assumeyes`), which makes it possible to do it programmatically

BUGS
* Fixed bug with reading the README file when pip installing in some systems
* Fixed bug in parsing user response when double checking request to update DB.

NEWS
* Code has been updated to work under Python3
* README has been updated to reflect changes to code
* Mark Schultz added as author

Working version with bug fix for 22 to detect multiple alleles.
Thanks to Simon Harris for picking up the bug.