v0.8.8

Date : 2020-06-23

Maintenance

• Improved code coverage
• Added missing autodoc for cooler balance
• Dropped pysam and biopython as hard dependencies
• Officially sunsetting Python 2.7 support

Enhancements

• Added zoom progressions (#203)

Bug fixes

• Allow hashes in read IDs in cload pairs (#193)

v0.8.7

Maintenance

• Code styling with black
• Add coverage reporting

Bug fixes

• Replace json with simplejson to deal with attrs stored as bytes

v0.8.6

Maintenance

• Added contributing guidelines

Bug fixes

• Fixed a related regression to the one fixed in v0.8.5 that affected selection of the chrom column in the bin selector.

v0.8.5

Bug fixes

• Fixes a regression that prevented selection of bins excluding the chrom column.

v0.8.4

Enhancements

• When creating coolers from unordered input, change the default temporary dir to be the same as the output file instead of the system tmp (pass '-' to use the system one). #150
• cooler ls and list_coolers() now output paths in natural order. #153
• New option in cooler.matrix() to handle divisive balancing weight vectors.

Bug fixes

• Restore function of --count-as-float option to cooler load
• Fixed partitioning issue sometimes causing some bins to get split during coarsen
• rename_chroms() will refresh cached chromosome names #147
• Cooler.bins() selector will always properly convert bins/chrom integer IDs to categorical chromosome names when the number of contigs is very large and therefore the HDF5 ENUM header is missing. Before this would only happen when explicitly requesting convert_enum=True.

v0.8.3

Bug fixes

• Fixed import bug in rename_chroms
• create_cooler no longer requires a "count" column when specifying custom value columns

v0.8.2

Bug fixes

• A bug was introduced into the matrix-as-pixels selector in 0.8.0 that also affected cooler dump. The behavior has been restored to that in 0.7.

CLI changes

New options for cooler dump pixel output:

• --matrix option: Applies to symmetric-upper coolers; no-op for square coolers. Generates all lower triangular pixels necessary to fill the requested genomic query window. Without this option, cooler dump will only return the data explicity stored in the pixel table (i.e. upper triangle).
• -one-based-ids and --one-based-starts convenience options.

v0.8.1

New features

• cooler zoomify command can take additional base resolutions as input.
• Restore but deprecate cooler.io.ls for backwards compatibility.

Bug fixes

• Fixed regression that slowed down pre-processing during coarsen.
• Fixed missing import error on handling bad URIs.

Later update: fixed invalid .zenodo.json

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.

v0.7.11

• Genomic range parser supports humanized units (k/K(b), m/M(b), g/G(b))
• Experimental support for arbitrary aggregation operations in cooler csort (e.g. mean, median, max, min)
• Documentation updates

Bug fixes

• Fix newline handling for csort when p1 or p2 is last column.
• Fix --count-as-float regression in load/cload.