v0.8.0

New features

• Support for non-symmetric matrices, e.g. RNA-DNA maps.
• Create function accepts a boolean symmetric_upper option to set the storage mode. Default is True.
• Creation commands also use symmetric_upper by default, which can be overridden with a flag.

New schema version: 3

• Adds required storage-mode metadata attribute. Two possible values: "symmetric-upper" indicates a symmetric matrix encoded as upper triangle (previously the only storage mode); "square" indicates no special encoding (e.g. for non-symmetric matrices).

API changes

• cooler.annotate() option replace now defaults to False.

• Submodule renaming. Old names are preserved as aliases but are deprecated.

  • cooler.io -> cooler.create.
  • cooler.ice -> cooler.balance.

• New top level public functions:

  • cooler.create_cooler(). Use instead of cooler.io.create and cooler.io.create_from_unordered.
  • cooler.merge_coolers()
  • cooler.coarsen_cooler()
  • cooler.zoomify_cooler()
  • cooler.balance_cooler(). Alias: cooler.balance.iterative_correction().

• Refactored file operations available in cooler.fileops. See the API reference.

CLI changes

• Various output options added to cooler info, cooler dump, cooler makebins and cooler digest.
• Generic data and attribute hierarchy viewers cooler tree and cooler attrs.
• Generic cp, mv and ln convenience commands.
• New verbosity and process info options.