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CHANGELOG.md

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Change log

Version 1.4.0

v1.4.0 New Features

  • Replaced Ray with HydraMPP
    • Reduced number of dependencies making install easier

v1.4.0 Improvements

  • Removed a redundant hmm search when using KOFam
  • Organized output files

v1.4.0 Bug Fixes

  • Fixed resume feature for hmm step
  • Fixed counting conflict between parser and filter steps

Version 1.3.2

v1.3.2 Bug Fixes

  • Fixed Ray dependency issue for MetaCerberus-lite, or when Ray is not available.

Version 1.3.1

v1.3.1 New Features

  • created "lite" version.
    • removed hard dependency requirements, failing more gracefully to make some dependencies optional
    • added linear override for Ray when Ray is not found
  • Implemented PyHMMER
  • Implemented Pyrodigal
  • Implemented Pyrodigal-gv
  • Added ORF start and end to output summary files
  • Improved speed in creating final GFF files
  • Fixed dependency checking for lite version
  • Made N removal optional
  • Improved Genbank output

v1.3.1 Bug Fixes

  • Fixed prodigal-gv GFF
  • Fixed some Phanotate bugs
  • Fixed bug with --protein option
  • Fixed crash when GFF is not present
  • Other minor bug fixes

Version 1.3.0

v1.3.0 New Features

  • Custom download location for databases
  • Ability to download individual databases
  • Update downloaded databases (currently re-downloads the database)
  • List available databases
  • Custom database support -HMM file with .hmm extension (also supports .hmm.gz) -A TSV file is also required with minimum columns: ID, Function -The ID field must match the NAME field of the HMM file, one row per HMM entry
  • Output files -reworked output directories to separate graphs/stats from annotation files -Final folder with annotation summary and files in GTF, genbank, GFF, .FAA, .FNA, .FFN
  • Other improvements -Performance improvements -Improved some error handling and reporting

v1.3.0 Bug Fixes

  • Multi-domain in summary files -Individual database summary files contain a line per match found -The combined summary file lists only the best match based on e-value
  • Slurm on cluster with multiple nodes now working
  • Filtering algorithm fix (on rare circumstances it would enter an infinite loop)