Stringmlst

stringMLST is licensed and distributed under [CC Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)](https://creativecommons.org/licenses/by-nc-sa/4.0) and is free for academic users and requires permission before any commercial use for any version of this code/algorithm.


If you are a commercial user, please contact "king.jordan <AT> biology.gatech.edu" for permissions

Fix for weighted dictionaries when alleles are dash ('-') delimited instead of underscore ('_')

This version fixes several cosmetic issues with v0.3.4 and brings stringMLST to the masses via PyPI

_No new typing features or fixes_
1. stringMSLT now comes bundled with all the pubMLST profiles available as of **Feb 15, 2017**.
2. PubMLST schemes can now be downloaded using the `--getMLST` module

1. Fixes for fuzzy reporting when using definitions with weighted dicts
2. Add Listeria monocytogenes and E coli MLST databases

A new `--coverage` option is introduced in this version, and we now require the pyfaidx module be installed (`pip install pyfaidx`) and that `bwa`, `samtools` and `bedtools` are in PATH. `--coverage` turns on read file generation (`-r`) and turns off fuzziness (`-z 1`). It reports allele (coverage) for the entire allele.


Hanging indent fixed on line 250