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v0.8.0

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@jamesli124 jamesli124 released this 05 Dec 01:29
· 231 commits to main since this release
b814de7

Removed

  • finaletoolkit.frag.frag_length_bins no longer has the contig_by_contig
    option. This never had any functionality.
  • finaletoolkit.frag.frag_length_bins no longer generates a text-based
    histogram.

Fixed

  • contig_sizes option included for cleavage-profile CLI command.
  • normalize option for coverage fixed so it no longer normalizes twice
  • normalize=False for coverage runs much faster
  • misc typehints and docstrings

Changed

  • finaletoolkit.frag.frag_length_bins uses a dict based implementation
    that is more memory efficient.
  • finaletoolkit.frag.frag_length_bins and
    finaletoolkit.frag.frag_length_intervals now take min_length and
    max_length keyword args to only consider fragments of certain lengths.
  • flags for frag-length-bins and frag-length-intervals CLI commands updated to match Python API
  • coverage default argument for normalize changed to False
  • coverage default argument for scale_factor changed to 1.

Added

  • finaletoolkit.frag.frag_length_bins can generate a histogram figure
  • tests for frag_length module