Releases: open2c/cooler
Releases · open2c/cooler
v0.7.1
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 defaultcooler 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
renamedcooler 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
v0.6.5
v0.6.4
v0.6.3
v0.6.2
v0.6.1
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
andis_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 setbalance
to False to get raw counts and setsparse
to True to get acoo_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