Date : 2020-09-25
- Fixed the new header parsing in
cooler cload pairsto handle esoteric file stream implementations. SpecificallyGzipFilehad stopped working. By @golobor
Date : 2020-07-17
- Added single-cell cooler file flavor (.scool) (#201)
Date : 2020-06-23
- Improved code coverage
- Added missing autodoc for cooler balance
- Dropped pysam and biopython as hard dependencies
- Officially sunsetting Python 2.7 support
- Added zoom progressions (#203)
- Allow hashes in read IDs in cload pairs (#193)
Date: 2020-01-12
- Code styling with black
- Add coverage reporting
- Replace
jsonwithsimplejsonto deal with attrs stored as bytes
Date: 2019-08-12
- Added contributing guidelines
- Fixed a related regression that affected selection of the
chromcolumn.
Post-release v0.8.6.post0: requirements files added to MANIFEST.in
Date: 2019-04-08
- Fixed a regression that prevented selection of bins excluding the
chromcolumn.
Date: 2019-04-04
- 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 lsandlist_coolers()now output paths in natural order. #153- New option in
cooler.matrix()to handle divisive balancing weight vectors.
- Restore function of
--count-as-floatoption tocooler load - Fixed partitioning issue sometimes causing some bins to get split during coarsen
rename_chroms()will refresh cached chromosome names #147Cooler.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 requestingconvert_enum=True.
Date: 2019-02-11
- Fixed import bug in
rename_chroms create_coolerno longer requires a "count" column when specifying custom value columns
Date: 2019-01-20
New options for cooler dump pixel output:
--matrixoption: 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 dumpwill only return the data explicity stored in the pixel table (i.e. upper triangle).-one-based-idsand--one-based-startsconvenience options.
- 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.
Date: 2019-01-02
cooler zoomifycommand can take additional base resolutions as input.
- Fixed regression that slowed down pre-processing during coarsen.
- Fixed missing import on handling bad URIs.
- Restore but deprecate
cooler.io.lsfor backwards compatibility.
Date: 2018-12-31
This is a major release from 0.7 and includes an updated format version, and several API changes and deprecations.
- New schema version: v3
- Adds required
storage-modemetadata 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).
- Support for non-symmetric matrices, e.g. RNA-DNA maps.
- Create function accepts a boolean
symmetric_upperoption to set the storage mode. Default isTrue. - Creation commands also use
symmetric_upperby default, which can be overridden with a flag.
- Create function accepts a boolean
- All main functionality exposed through top-level functions (create, merge, coarsen, zoomify, balance)
- New commands for generic file operations and file inspection.
-
cooler.annotate()optionreplacenow defaults toFalse. -
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 ofcooler.io.createandcooler.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.
- Various output options added to
cooler info,cooler dump,cooler makebinsandcooler digest. - Generic data and attribute hierarchy viewers
cooler treeandcooler attrs. - Generic
cp,mvandlnconvenience commands. - New verbosity and process info options.
- Unit tests refactored and re-written for pytest.
Date: 2018-08-17
- 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-floatregression in load/cload.
Date: 2018-05-07
- Fix a shallow copy bug in validate pixels causing records to sometimes flip twice.
- Add ignore distance (bp) filter to cooler balance
- Start using shuffle filter by default
Date: 2018-03-30
- Indexed pairs loading commands now provide option for 0- or 1-based positions (1-based by default). #115
- Fixed error introduced into cload pairix in last release.
Date: 2018-03-18
- New
cooler cload pairscommand provides index-free loading of pairs. - Changed name of
create_from_unsortedto more correctcreate_from_unordered.
- Fixed broken use of single-file temporary store in
create_from_unordered. - Added heuristic in pairix cload to prevent excessively large chunks. #92
- Added extra checks in
cload pairixandcload tabix. #62, #75
Date: 2018-03-16
- Implementation of unsorted (index-free) loading
cooler.io.create_from_unsortedtakes an iterable of pixel dataframe chunks that need not be properly sorted.- Use input sanitization procedures for pairs
sanitize_recordsand binned datasanitize_pixelsto feed data tocreate_from_unsorted. #87 #108 #109 - The
cooler loadcommand is now index-free: unsortedCOOandBG2input data can be streamed in. #90. This will soon be implemented as an option for loading pairs as well.
- Prevent
cooler balancecommand from exiting with non-zero status upon failed convergence using convergence error policies. #93 - Improve the
createAPI to support pandas read_csv-stylecolumnsanddtypekwargs to add extra value columns or override default dtypes. #108 - Experimental implementation of trans-only balancing. #56
- Fix argmax deprecation. #99
Date: 2017-10-31
- Cooler zoomify with explicit resolutions
- Towards standardization of multicooler structure
- Support for loading 1-based COO triplet input files
- 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_pixelsandjoinoptions in the matrix selector.
Happy Halloween!
Date: 2017-07-13
- Fix pandas issue affecting cases when loading single chromosomes
- Add transform options to higlass API
Date: 2017-05-25
- Fix regression in automatic --balance option in cooler zoomify
- Fix special cases where cooler.io.create and append would not work with certain inputs
Date: 2017-05-22
- Added function to print higlass zoom resolutions for a given genome and base resolution.
Date: 2017-05-09
- Improve chunking and fix pickling issue with aggregating very large text datasets
- Restore zoom binsize metadata to higlass files
Date: 2017-04-29
cooler loadcommand 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.
Date: 2017-04-27
- 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 listcooler copycooler merge
cooler csortnow produces Pairix files by defaultcooler loadnow 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 coarsegrainrenamedcooler coarsen- Multi-resolution HiGlass input files can now be generated with the
cooler zoomifycommand - More flexible API functions to create and append columns to Coolers in
cooler.io
cooler.io.createsignature changed;chromsizesargument is deprecated.cooler csortargument order changed
- Chromosome name length restriction removed
Cooler.openfunction now correctly opens the specific root group of the Cooler and behaves like a proper context manager in all cases
Date: 2017-03-21
- Chromosome names longer than 32 chars are forbidden for now
- Improved pairix and tabix iterators, dropped need for slow first pass over contacts
Date: 2017-03-18
- Fixed pairix aggregator to properly deal with autoflipping of pairs
Date: 2017-03-17
- Migrated higlass multires aggregator to
cooler coarsegraincommand - Fixed pairix aggregator to properly deal with autoflipping of pairs
Date: 2017-02-22
- Merge PairixAggregator patch from Soo.
- Update repr string
- Return matrix scale factor in balance stats rather than the bias scale factor: #35.
Date: 2017-02-12
Fixed regressions in
- cooler cload tabix/pairix failed on non-fixed sized bins
- cooler show
Date: 2017-02-06
- This fixes stale build used in bdist_wheel packaging that broke 0.6.0. #29
Date: 2017-02-03
- Dropped Python 3.3 support. Added 3.6 support.
- Added
contribsubpackage containing utilities for higlass, including multires aggregation. - Fixed various issues with synchronizing read/write multiprocessing with HDF5.
- Replacing prints with logging.
- Added sandboxed
toolsmodule to develop utilities for out-of-core algorithms using Coolers.
- Cooler objects have additional convenience properties
chromsizes,chromnames. - New file introspection functions
lsandis_coolerto support nested Cooler groups. - Cooler initializer can accept a file path and path to Cooler group.
cloadaccepts contact lists in hiclib-style HDF5 format, the legacy tabix-indexed format, and new pairix-indexed format.
createonly accepts a file path and optional group path instead of an open file object.Cooler.matrixselector now returns a balanced dense 2D NumPy array by default. Explicitly setbalanceto False to get raw counts and setsparseto True to get acoo_matrixas per old behavior.- Command line parameters of
cloadchanged significantly
- Fixed bug in
csortthat led to incorrect triangularity of trans read pairs.
Date: 2016-09-10
- Check for existence of required external tools in CLI
- Fixed
cooler showincompatibility with older versions of matplotlib - Fixed
cooler.annotateto work on empty dataframe input - Fixed broken pipe signals not getting suppressed on Python 2
cooler cloadraises a warning when bin file lists a contig missing from the contact list
Date: 2016-08-26
- Fix bug in
cooler csortparsing 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.
Date: 2016-08-24
- Bug fix in input parser to
cooler csort - Update triu reording awk template in
cooler csort - Rename
cooler binnifytocooler makebins. Binnify sounds like "aggregate" which is whatcloaddoes.
Date: 2016-08-24
- Most scripts ported over to a new command line interface using the Click framework with many updates.
- New
showandinfoscripts. - Updated Readme.
- Minor bug fixes.
Date: 2016-08-18
- Updated file schema: v2
/bins/chromsis now an enum instead of string column
- 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.annotatefor doing joins
- Support for nested Cooler "trees" at any depth in an HDF5 hierarchy
- Refactored
cooler.ioto provide "contact readers" that process different kinds of input (aggregate from a contact list, load from an existing matrix, etc.) - Added new scripts for contact aggregation, loading, dumping and balancing
Date: 2016-02-18
- 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).
- 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.
Date: 2016-02-07
- Fixed bintable region fetcher
Date: 2016-01-17
- First beta release
Date: 2015-11-22
- Working initial prototype.