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]