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v0.8.0
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@nvictus nvictus released this 31 Dec 17:21
· 397 commits to master since this release
v0.8.0
e12cea3

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.
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