Skip to content

Latest commit

 

History

History
71 lines (40 loc) · 3.38 KB

CHANGELOG.md

File metadata and controls

71 lines (40 loc) · 3.38 KB
Raw

Release notes

Upcoming release

[v1.1.0] (https://github.com/open2c/coolpuppy/compare/v1.0.0...v1.1.0)

  • Added ignore_group_order and --ignore_group_order argument to flip and combine groups when using groupby, i.e. combining e.g. group1-group2 and group2-group1

  • Changed how flipping and group reassignment is implemented

  • Fixed zooming near diagonal

  • divide_pups now allows dividing even if columns are different, gives warning instead

  • Added additional tests

  • Bug fixes and logs/warnings added

  • Changes to walkthroughs

v1.0.0

This is a major release with a lot of changes. The main ones are included below, but probably there are a lot of smaller ones too.

API changes

  • New HDF5-based storage format, with functions to write and read the files in coolpuppy.lib.io

  • New “user-facing” pileup function in python API for convenient single-step pileups, and with interface similar to cooltools.pileup

  • Pileups can be restricted using a genomic view (--view in CLI and view_df in API) in line with cooltools/bioframe (note that the expected has to be calculated for the same view, if used)

  • If using expected, by default each snippet is now normalized to expected and only averaged afterwards; this is controlled by ooe argument in API and --not-ooe argument in CLI)

  • Added options to split snippets based on strands, genomic distance, or both

  • Added option flip_negative_strand (API) and --flip-negative-strand (CLI) to flip features located on the negative strand

  • Added option to groupby snippets by their properties and generate multiple pileups in one run (groupby in API and --groupby in CLI)

  • Added option trans=True (API) and --trans (CLI) to generate inter-chromosomal (trans) pileups

  • Added option store_stripes=True (API) and --store_stripes (CLI) to store individual vertical and horizontal stripe pairs

  • Added advanced option (modify_2Dintervals_func of PileUpper.pileupsWithControls) to apply an arbitrary function to pairs of intervals before they are used for generating pileups (i.e. bedpe-style intervals generated internally from either bedpe- or bed-style input features)

  • Added advanced option to apply an arbitrary function to each snippet before averaging in API (postprocess_func of PileUpper.pileupsWithControls)

  • Added function divide_pups() (API) and dividepups.py (CLI) to divide two pileups

  • CLI detects headers of bed and bedpe files

  • Overall API and CLI argument names are aligned with cooltools wherever possible

Plotting changes

  • Changed names of plotpup.make_heatmap_grid() to plotpup.plot()
  • Added option plotpup.plot_stripes() (API) and --stripe (CLI) for plotting stripes
  • Added option --divide_pups (CLI) to plot the ratio of two pileups

Documentation

  • Extensive tutorials for both python API and CLI

Maintenance

  • Code restructured, so all CLI tools are in one package, and created .lib with shared internal functions in lib/io.py, lib/numutils.py, lib/puputils.py and lib/util.py

  • Tests migrated to github actions, and also running nbsmoke on the CLI notebook to ensure it runs without errors

  • Only support python >=3.8, cooltools >=0.5.2

Miscellaneous

  • Logging has been fixed so the --logLevel properly works
  • Removed the launch_pileups.sh script