v0.8.0

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

v0.7.8

First release using GitHub!

Fixed

• update docs, docstring, and help message for wps to mention that
  site_bed must be sorted. (#107)

Added

• normalize keyword argument and --normalize flag to finaletoolkit.frag.coverage function and finaletoolkit coverage subcommand, respectively. Setting this argument/flag to true results in the output
  being normalized by the total coverage, ignoring scale_factor if specified. (suggested by @ravibandaru-lab )
• --intersect-policy or -p flag added to finaletoolkit coverage subcommand. (suggested by @ravibandaru-lab )