v0.7.0

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

v0.6.6

• Chromosome names longer than 32 chars are forbidden for now
• Improved pairix and tabix iterators, dropped need for slow first pass over contacts

v0.6.5

• Fixed pairix aggregator to properly deal with autoflipping of pairs

v0.6.4

• Migrated higlass multires aggregator to cooler coarsegrain command
• Fixed pairix aggregator to properly deal with autoflipping of pairs

v0.6.3

• Patched PairixAggregator and added pypairix dependency
• Updated Cooler repr string
• Return matrix scale factor in balance stats rather than the bias scale factor: #35.

v0.6.2

Fixed regressions in

• cooler cload tabix/pairix failed on non-fixed sized bins
• cooler show

v0.6.1

This fixes stale build used in bdist_wheel packaging that broke 0.6.0. #29

v0.6.0

General

• Dropped Python 3.3 support. Added 3.6 support.
• Added contrib subpackage containing utilities for higlass, including multires aggregation.
• Fixed various issues with synchronizing read/write multiprocessing with HDF5.
• Replacing prints with logging.
• Added sandboxed tools module to develop utilities for out-of-core algorithms using Coolers.

New features

• Cooler objects have additional convenience properties chromsizes, chromnames.
• New file introspection functions ls and is_cooler to support nested Cooler groups.
• Cooler initializer can accept a file path and path to Cooler group.
• cload accepts contact lists in hiclib-style HDF5 format, the legacy tabix-indexed format, and new pairix-indexed format.

Backwards-incompatible changes

• create only accepts a file path and optional group path instead of an open file object.
• Cooler.matrix selector now returns a balanced dense 2D NumPy array by default. Explicitly set balance to False to get raw counts and set sparse to True to get a coo_matrix as per old behavior.
• Command line parameters of cload changed significantly

Bug fixes

• Fixed bug in csort that led to incorrect triangularity of trans read pairs.

v0.5.3

Bug fix release

• Check for existence of required external tools in cooler csort
• Fixed cooler show incompatibility of label setting with older versions of matplotlib
• Fixed cooler.annotate to work on empty dataframe input
• Fixed broken pipe signals not getting suppressed on Python 2
• cooler cload raises a warning when bin file lists a contig missing from the contact list

v0.5.2

• Fix bug in cooler csort parsing of chromsizes file.
• Workaround for two locale-related issues on Python 3. Only affects cases where a machine's locale is set to ASCII or Unices which use the ambiguous C or POSIX locales.
• Fix typo in setup.py and add pysam to dependencies.