Label all the things

• Updated databases for May 2018
• New --label feature for column 1 instead of the filename
• New --check option to ensure dependencies are installed
• New scoring system to help break previous ties
• Inform users to also cite Jolley et al (PubMLST DB) when using this tool
• Remove need for File::Slurp
• Nicer --help layout

The best reads are contigs

• Updated PubMLST to Feb 2018 inc. 3 new schemes
• Nicer --help output
• Documentation for --minscore scoring system
• Added ST call to scoring system to break ties when depending on alleles only
• Documentation for adding a new custom scheme
• Bug fix with --minscore out-by-one error
• Experimental --json <file.json> output format

Clear out the issues

• Updated databases for April 2017
  • Removed dodgy homopolymer vcholerae alleles
  • New edwardsiella scheme
• Made it more obvious that we support .gbk and .gz files too
• Documentation on how to update the databases yourself
• New scheme_species_map.tab file
• Explained allele matching system better
• Fixed Markdown headings in docs

💖 Valentine edition

• Improved scoring system to not report schemes when insufficient alleles
• Added --minscore option
• Fixed bug when --scheme specified from --exclude list
• Removed culling limit option in BLAST to avoid side-effect bug with new --exclude option.

Exclude ALL the crappy schemes

• New --exclude option to ditch ecoli_2 etc.
• Updated databases

Oxford vs Pasteur

• Updated database
• Bug fixes with dual schemes
• Better scoring
• Coverage option

It's ominous we have S.hominis

Added new S.hominis scheme - thank you to Keith Jolley for the heads up!

Let there be haem.

New scheme for https://en.wikipedia.org/wiki/Staphylococcus_haemolyticus

O.sutsugamushi driving me batty

• Bug fix for otsutsugamushi scheme - thank you @embatty for the report
• Better alllele calling
• Improved --debug output

Never trust a zero point release!

Of course there was a bug in 2.0 release - I was legally bound by the Coder Laws of 1970 to make that happen.

So here is 2.1 with essentially a 1 character difference, but a big difference it makes to weird recombinant genomes like E.faecium.

I'll update the Brew package too.

Enjoy!