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CHANGELOG.md

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Change Log

1.2.3rc4

  • [2024.12.16] - Added --graph auto and --paths auto to try and automatically detect files
  • [2024.12.16] - Added alias for key command line arguments

1.2.3rc3

  • [2024.12.13] - Added support for Python v3.8.x

1.2.3rc2

  • [2024.12.12] - Added --assembler auto to automatically detect assembler used

1.2.3rc1

  • [2024.12.12] - Added support for Pyrodigal and PyHMMSearch instead of FragGeneScan and HMMSearch
  • [2024.12.12] - Added support for precomputed genes via --proteins and --proteins_to_contigs arguments
  • [2024.12.11] - Changed .fasta to .fa extension
  • [2024.12.11] - Removed --prefix argument
  • [2024.12.11] - Removed --no_cut_tc and --mg_threshold because PyHMMSearch does not use coverage filter at the moment
  • [2024.12.11] - Changed output_path to output_directory with intermediate files being added in this directory only

Pending:

  • Add precomputed PyHMMSearch results
  • Check abundance tables to make sure there are 2 columns
  • If --graph auto or --paths auto do not find files in --contigs directory then look in BAM directory (useful for VEBA when using unbinned.fasta)