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v0.7.0
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@nvictus nvictus released this 27 Apr 05:52
· 600 commits to master since this release
v0.7.0
9553303

New features

  • New Cooler URIs: Full support for Cooler objects anywhere in the data hierarchy of a .cool file
  • Experimental dask support via cooler.contrib.dask
  • New explicit bin blacklist option for cooler balance
  • Various new CLI tools:
    • cooler list
    • cooler copy
    • cooler merge
  • cooler csort now produces Pairix files by default
  • cooler load now accepts two types of matrix text input formats
    • 3-column sparse matrix
    • 7-column bg2.gz (2D bedGraph) indexed with Pairix (e.g. using csort)
  • cooler coarsegrain renamed cooler coarsen
  • Multi-resolution HiGlass input files can now be generated with the cooler zoomify command
  • More flexible API functions to create and append columns to Coolers in cooler.io

Backwards-incompatible changes

  • cooler.io.create signature changed; chromsizes argument is deprecated.
  • cooler csort argument order changed

Bug fixes

  • Chromosome name length restriction removed
  • Cooler.open function now correctly opens the specific root group of the Cooler and behaves like a proper context manager in all cases
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