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Version 0.10.0
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@martinghunt martinghunt released this 30 Jun 11:33
v0.10.0
6a7e7f6

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].
Assets 12
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