v0.10.7

Added

• Snakemake workflow included in FinaleToolkit documentation. (@Kudostoy0u)

Fixed

• Issue with filter-file where the lack of output_file.flush() would
  create incorrect outputs. (@ravibandaru-lab)

v0.10.6

Fixed

• More descriptive error message in multi_wps when an invalid interval
  with start > stop is encountered. Now the chromosome name is mentioned
  to assist users.

v0.10.5

Changed

• added intersect_policy to filter_file

Fixed

• blacklist functionality of filter_file

v0.10.4

Changed

• Changed filter-bam function into filter-file; Now accepts BED and CRAM in addition to BAM (#138)
• filter-file command can now accept a blacklist file (#138)

Thanks to @Kudostoy0u

v0.10.3

Fixed

• Update various docstrings and help statements to no longer mention SAM
  files as an accepted format

v0.10.2

Fixed

• changed default args for wps would lead to errors. Now wps defaults to
  LWPS fragment lengths (120-180nt).

Changed

• made finaeltoolkit.utils.typing public. This is a module containing some
  useful type aliases
• minor formatting and typing changes
• renamed fraction_low and fraction_high to min_length and max_length
  for .utils.frag_array and .frag.wps. wps retains the deprecated arg names
  but issues a warning.

v0.10.1

Fixed

• Added missing -n arg to end-motifs.
• Fixed incorrect ValueError regarding the negative_strand arg.
• Incorrect function name for wps leading to errors when called from CLI.

Added

• Additional tests for the CLI lazy loading implementation

v0.10.0

Changed

• several modules containing implementations of fragmentomic features or
  utility functions have been made internal. This means there is now only one
  obvious import for each function. For example, multi_wps is imported from
  finaletoolkit.frag, and no longer can be imported from
  finaletoolkit.frag.multi_wps
• The CLI now uses lazy importing, drastically speeding up finaletoolkit when
  called from a command line.
• Added negative_strand option for end-motifs related functions. When
  used in conjunction with both_strands, only end motifs on the negative
  (Crick) strand are considered in calculations.
• Renamed fraction_high and fraction_low in utils.utils.frag_generator
  to min_length and max_length.

Fixed

• deprecated arguments for end-motifs had default values which could
  lead to an error. This is fixed.

v0.9.1

Fixed

• CLI no longer prints an error message if finaletoolkit is called without args.
  Instead, a help statement is printed.
• frag-length-bins, when writing a file, now writes the interval between
  min and max as inclusive. That is, previously when min=1 and max=2,
  only fragments of length 1 are reported. Now when such a result is calculated,
  the interval given is min=1 and max=1.
• Updated some descriptions and docstrings.

Added

• adjust-wps now has an option -S or --exclude-savgol to not perform
  Savitsky-Golay filtering.

Changed

• Several CLI options were renamed so that underscores become hyphens. This is
  for consistency and to simplify writing commands.

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.