v0.9.0

Removed

• strand_location arg from agg_bigwig
• cli_hist module

Fixed

• fixed bug involving tqdm progress bar in frag_length_intervals
• some code formatting
• fixed bug involving arg names in filter-bam
• add some missing args to CLI
• issues with running cleavage-profile (#115)
• issues with writing to bigwig with wps

Changed

• change default of arg both_strands of end_motifs to True to match
  behavior of original scripts
• rename fraction_high and fraction_low to min_length and max_length
  for all features, deprecating old args as aliases if needed.
• numpy 2 compatible
• fragmentomics functions assume Tabix indexed files all follow the
  FinaleDB Frag.gz file format. That is, columns are chrom, start, stop,
  score, and strand. If more columns are detected, a warning is issued, and
  FinaleToolkit will attempt to parse the file in a BED6 format.
• renamed genome_file to chrom_sizes for most functions.
• multi_wps and multi_cleavage_profile no longer return a value due to memory issues when attempting to calculate these genomewide. Instead, users should refer to the file specified with output_file.

Added

• internal utils._typing and utils._deprecation modules.
• test for delfi

Deprecated

• delfi-gc-correct command. GC-correction is performed automatically by delfi
  already.