v0.13.0

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".

v0.12.2

Command-line only release, GUI files are not included

Windows and Mac GUI programs are unavailable for this release.

Fixed

• Use all input files when -1/-i/--seq is passed multiple times [#168]
• When running on Staph, was throwing TypeError [#170]
• Windows build [#172]

v0.12.1

Command-line only release, GUI files are not included

Windows and Mac GUI programs are unavailable for this release.

Fixed

• output from --version flag (version 0.12.0 was reporting version 0.11.0)

v0.12.0

Command-line only release, GUI files are not included

Windows and Mac GUI programs are unavailable for this release.

Added

• This version is required to use the latest panel which combines the 2021 WHO
  catalogue (doi:10/h298) with the previous default mykrobe
  catalogue, as constructed in doi:10/h299.

• Latest panel also calls BCG lineage correctly

Changed

• Loading JSON files will now handled (gzip) compressed files.
• When an X mutation resolves to an existing variant in the panel, instead of
  raising an error, do not output the X mutation. This means can still use
  Walker-2015 panel.

v0.11.0

Command-line only release, GUI files are not included

Windows and Mac GUI programs are unavailable for this release.

Added

• Support for including stop codons in the panel with the * character.
• Panel version is now included in JSON output [#119]
• Shorthand CLI versions for common/long options:
  • -D: --min_proportion_expected_depth
  • -P: --custom_probe_set_path
  • -R: --custom_variant_to_resistance_json
  • -L: --custom_lineage_json
  • -O: --format
• Singularity container automatically built and added to each new release.

Changed

• Default kmer size (21) made consistent across all subcommands [#141]
• Nanopore preset --ont defaults to an expected error rate of 0.08 and ploidy
  'haploid' [#134]
• VCF interface from pyvcf to pyvcf3
• Automated tests/builds all (ie linux, windows, mac) moved to github actions.
  Turned off travis and appveyor.

Fixed

• Improved error messaging when an X amino acid resolves to a mutation already present
  in the panel.
• Do not assume reference fasta file name is the same as the chromosome [#140]

Version 0.10.0

Added

• -o as another option for --output
• -i as another option for -1,--seq
• -A as another option for --report_all_calls
• -e as another option for --expected_error_rate
• new species typhi

Changed

• If --tmp is not specified now, it is set to tempfile.mkdtemp(). By
  default, this is a directory that is created within the $TMPDIR. The reason for this
  is that currently, when mykrobe cleans up temporary files, it doesn't remove the
  temporary directory (#113). I wasn't really comfortable with removing the
  temporary directory in case the user had set it to something like the current
  directory. At least with this default now the temporary directory won't clog up the
  current directory after mykrobe is finished and the OS should clean it up
  periodically.
• Ensure --memory and --threads are passed on to mccortex [#114].
• Positional arguments species and sample are now options -S,species and
  -s,--sample respectively.

Fixed

• Bug where the --ont flag resulted in mykrobe predict crashing if the panel
  contained any presence/absence genes [#123].
• Bug reporting variants that are "amino acid to any other amino acid" changes,
  eg katG_S315X. If gene is on reverse strand, then the wrong new amino
  acid change was being reported [#127].

v0.9.0

• panel data is now handled differently. Please check the documentation for how to install mykrobe panel data.
• new lineage calling model added
• updated TB lineage calling to use Chiner-Oms 2020 lineage scheme
• new Shigella sonnei panel added from Hawkey 2020
• app supports drag + drop more than one file (useful for paired FASTQ files)
• mykrobe genotype removed. Same functionality is now available from mykrobe predict
• Fix report so amino acid changes to "X" are now reported as the actual amino acid change (eg H445X is now something like H445Y)
• various other small changes, including tidying up logging to terminal

v0.8.2

New release for changes to the app. Command line unchanged.

v0.8.1

• Bug fix where options to use custom panel were ignored when species was staph.
• Releases now include GUI versions for Windows and Mac.

v0.8.0

• Improvements to packaging:
  • no longer need to manually download data as part of install process
  • pip3 install . works when not using virtual environment
  • mccortex installed in same place as mykrobe, not centrally in /usr/bin/
• Automated builds of mac and windows binaries for GUI