April 2024 Release

Simply put back the compatibility with python 3.7. As python 3.7 is already EOL, it will be drop in the next release.

December 2023 Release

No change in code but a lot of linting and compatibility with pypi.

Edit: This version is incompatible with python version 3.7

January 2023 Release

Fix compatibility with numpy 1.24

July 2021 release

• Adding write support for hicPro files
• Fixing a bug in for cool files to adopt the reference genome information (deeptools/HiCExplorer#657)
• Moving CI testing from Travis to Microsoft Azure
• Adding a skip triu option to compute z-scores
• Fixing a potential bug computing cut_intervals positions: #39 Thanks @lldelisle

October 2020 release

• Fixing a major bug concerning the application of the correction factors for cooler files. In version 14 it was not applied, version 15 fixes this.
• A test case for this was added and another test case was corrected.
• New function get_chromosome_sizes_real to get the size of a chromosome as it is stored in the matrix i.e. it considers if the start or the end of the chromosome is pruned.

Summer 2020

• Adding scool support
• Add support for cool files to load only the csr_matrix with instances, features and data, bypassing all 'expensive' operation like to create the cut_intervals.

May 2020 release

Bug fix:

• load and store cool file created via hic2cool and additional correction factor application.
• str vs bytes bug. Thanks @dmalzl
• remove internal scaling in cool load/store which was more a workaround for the bug fixed in 1
• Fix #23 , #25

New:

• If one chromosome or region is given cool files can now load interactions only within a distance. This is reducing the amount memory.
• Homer files can now be gzipped too. #9

March 2020 release

• Make getBinSize working with only one bin
• Remove last indices from nan_bins list
• change all exit to exception
• fix the behaviour if a non-existing region is called.

August 2019

• Fix a bug in cooler if a csr-matrix contains no data
• Remove python2 compatibility layers (six, past, future, builtins)
• Add python 3.7 to travis testing
• Change np.matrix to np.array due to deprecation warnings

Mid 2019 release

• Automatic scaling if corrected value range is not matching original value range (happens usually with cooler balanced matrices)
• Optimized cooler load to use less memory
• Added option to save a cool file with uncorrected raw data and correction factors. Before the data needed to be corrected and then the correction needed to be reversed.