• 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

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

Fix min/max distance setting, wasn't working in the recent versions!

Forgot to bump version!

Allow interactions between 2 bed files! Some bugfixes, and added testing.

Allow separate colorbars for each row or each subplot

• Fix import of plotpup.py
• Can add enrichment values when plotting

• Bugfixes
• Added a simple plotting script (plotpup.py)
• Allow different weight name used to get balanced data