Step 1 of ST establishment - Githubissues

Clinical-Genomics / microSALT

Microbial Sequence Analysis and Loci-based Typing pipeline for use on NGS WGS data.

GNU General Public License v3.0

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Step 1 of ST establishment #43

Closed sylvinite closed 5 years ago

sylvinite commented 5 years ago

Major changes:

Proper novel alleles are now categorized with a running number at -10 and below
Resistance type now works 100% of the time, falling back on file name
Indexing of resistance databases will now never fail
Novel alleles moved to error code -2
File checker now also checks for invalid symlinks
MLST is no longer established on prior BLAST filter

Minor integrations from master:

Novel (x alleles) no longer display debug info
Expanded ctrl category, orgs w/o pubmlst ref marked as unavailable

sylvinite commented 5 years ago

Unknown organisms should now also be written out, as opposed to "control"