v0.5.1

Hotfixes:

• Bug fix in input parser to cooler csort
• Update triu reording awk template in cooler csort

CLI changes:

• Rename cooler binnify to cooler makebins. Binnify sounds like "aggregate" which is what cload does.

v0.5.0

• Cooler CLI: most scripts ported over to a new command line interface using the Click framework with many updates.
• New show and info commands.
• Updated Readme.
• Minor bug fixes.

v0.4.0

• Modifed file schema: v2
• Support for nested Cooler "trees" at any depth in an HDF5 hierarchy
• cooler.io: tools for cooler creation
  • cooler.io.write is a generic writer that takes input from a contact reader
  • Contact readers can take a variety of input (aggregate from a contact list, load from an existing matrix, etc.)
• Added new scripts for contact aggregation, loading, dumping and balancing
• API changes
  • Table views are a bit more intuitive: selecting field names on table view objects returns a new view on the subset of columns.
  • New API function: cooler.annotate for doing joins
• Documentation updated

v0.3.0

Added features:

• 2D range selector matrix() now provides either rectangular data as coo_matrix or triangular data as a pixel table dataframe.
• Added binning support for any genome segmentation (i.e., fixed or variable bin width).

Bug fixes:

• Fixed issues with binning data from mapped read files.
• Genomic locus string parser now accepts ENSEMBL-style number-only chromosome names and FASTA-style sequence names containing pipes. It will still reject a name that begins with a number followed by other characters.