Poppunk

New features:
* Cluster IDs now start from 1 rather than 0 (26)
* Added various error checking (27)
* Report merged clusters when using `--assign-query`
* Sort `_clusters.csv` by cluster ID, rather than sample name

Bug fixes:
* `--update-db` works with reference only databases (28)

Bug fixes:
* An error in stderr writing `models.py` which causes problems with some versions of python

Bug fixes:

- Use the relative and not absolute path, allowing `--assign-query` to work with inputs from non-writable directories, or directories in other locations.
- Corrected model copying with `poppunk_references`

Code:

- Move many functions from `mash.py` to `utils.py`

Added features:
* Added program `poppunk_references` to perform clique-based reference selection, if `--full-db` was run first time round.
* If core or accessory refined models have been created, also write out their networks when using `--cytoscape`.

Bug fixes:
* When picking references, remove the non-reference isolates from the distance file

Added features:
* Ability to write output for [GrapeTree](https://github.com/achtman-lab/GrapeTree)
* Ability to write output for [Phandango](http://jameshadfield.github.io/phandango/)
* Ability to re-run t-SNE with different perplexity without rerunning everything (`poppunk_tsne`)

Bug fixes:
* Pasting epi information into Microreact output (24)
* Storing accessory distances with `--assign-query`

First public version