v0.3.1

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

v0.3.4

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

v0.3.2

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

v0.2.2

stringMLST will now report best/closest match alleles in SRST2 format #3

The threshold for new allele is based on the difference in counts between max and second best support and is configurable via a new option, -z|--fuzzy.

v0.2.1

This version brings minor cosmetic changes to the manuscript version (v0.2) as well as refinements in output.

Thanks @Takadonet