Skip to content

v0.13.0

Latest
Latest
Compare
Choose a tag to compare
@github-actions github-actions released this 28 Sep 12:26
· 4 commits to master since this release
v0.13.0
7f9a500
This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
GPG key ID: 4AEE18F83AFDEB23
Expired
Learn about vigilant mode.

Command-line only release for Linux and Mac, GUI files are not included

This release only includes command line for Linux and Mac. Windows and Mac GUI programs are unavailable for this release.

Mtb panel updated

The default panel for species tb is now 202309. This release v0.13.0 (or later) is required to use panel 202309. Older panels continue to work as normal. The new panel has updated species calls. AMR and lineage calls remain unchanged.

Added

  • When using --debug flag, log species probe coverage/depth info and also each time a probe is rejected due to low coverage and/or depth.
  • Added flag --ncbi_names. This is for latest tb probes for species calling, where the JSON file will also report alternative NCBI taxon names, as well as the default GTBD names.
  • Added option --dump_species_covgs, to dump a JSON file of all the species probe coverage information. This includes the raw coverage info from mccortex, before it is aggregated into a single call that you see in the usual mykrobe output.

Changed

  • The tb species probes have been updated in a newpanel 202309. Code changed to handle these new probes, specifically where a node in the taxon tree has no probes. If a child node is called as present from the reads, then push that call up to the parent node. Code still works as normal on the old panels.
  • When reporting panel version in JSON file and stderr logging, only had the "main" version of the collection of panels, eg "20220705" for tb. Changed to also report the specific panel used, eg "20220705/202206".
Assets 4
Loading