Releases: tseemann/mlst
Releases · tseemann/mlst
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
- Removed dodgy homopolymer
- 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 ditchecoli_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.
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!