v0.4.0

What's Changed

cluster: Add --checkm2-quality-file. Fixes #28.
Update to clap command line parser v4
Use skani as the default genome comparison tool, instead of fastANI

New Contributors

• @AroneyS made their first contribution in #30

Full Changelog: v0.3.1...v0.4.0

v0.3.1

• Improve symlinking procedure for Windows (wwood/CoverM#50) - thanks @apcamargo
• Use updated coverm-rs to allow absolute paths in checkm file (reported by @rhysnewell )

v0.3.0

• Suggest solution for dashing install problem - Thanks Rafael Laso Pérez (https://github.com/wwood/CoverM/#45)
• cluster: Fix argument parsing for --precluster-ani - Thanks @apcamargo (#8)
• Update to bird_tool_utils v0.3.0

v0.2.0

• Overall full help for cluster mode, add man as a dependency.
• Aligned fraction is calculated by galah from fragment counts, rather than relying on FastANI's thresholds. See #7 and ParBLiSS/FastANI#70
• Update FastANI dependency version to 1.31 (#6)
• Add further output options e.g. --output-representative-fasta-directory-copy and --output-representative-list. (#3)
• Add ability to change quality formula with --quality-formula, and default to Parks2020_reduced.
• Rename the --prethreshold-ani argument to be --precluster-ani.

Thanks to Antônio Pedro Camargo (@apcamargo ) for help on a few of these issues.

v0.1.0

Initial release.