v0.7.7

New features

• Implementation of unsorted (index-free) loading
  • cooler.io.create_from_unsorted takes an iterable of pixel dataframe chunks that need not be properly sorted.
  • Use input sanitization procedures for pairs sanitize_records and binned data sanitize_pixels to feed data to create_from_unsorted. #87 #108 #109
  • The cooler load command is now index-free: unsorted COO and BG2 input data can be streamed in. #90. This will soon be implemented as an option for loading pairs as well.
• Prevent cooler balance command from exiting with non-zero status upon failed convergence using convergence error policies. #93
• Improve the create API to support pandas read_csv-style columns and dtype kwargs to add extra value columns or override default dtypes. #108
• Experimental implementation of trans-only balancing. #56

Bug fixes

• Fix argmax deprecation. #99

v0.7.6

New features

• Cooler zoomify with explicit resolutions
• Towards standardization of multicooler structure
• Support for loading 1-based COO triplet input files

Bug fixes

• Fixed issue of exceeding header limit with too many scaffolds. If header size is exceeded, chrom IDs are stored as raw integers instead of HDF5 enums. There should be no effect at the API level.
• Fixed issue of single-column chromosomes files not working in cload.
• Fixed edge case in performing joins when using both as_pixels and join options in the matrix selector.

Happy Halloween!

v0.7.5

• Fix pandas issue affecting cases when loading single chromosomes
• Add transform options to higlass API

v0.7.4

• Fix regression in automatic --balance option in cooler zoomify
• Fix special cases where cooler.io.create and append would not work with certain inputs

v0.7.3

• Added function to print higlass zoom resolutions for a given genome and base resolution.

v0.7.2

• Improve chunking and fix pickling issue with aggregating very large text datasets
• Restore zoom binsize metadata to higlass files

v0.7.1

• cooler load command can now accept supplemental pixel fields and custom field numbers
• Fix parsing errors with unused pixel fields
• Eliminate hard dependence on dask to make pip installs simpler. Conda package will retain dask as a run time requirement.

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