Releases: deeptools/HiCMatrix
March release bug fix 1
This release fixes a bug with metadata and hic2cool version 0.5 handling.
March release
Release 8 of HiCMatrix adds the feature to write metadata to a cool file and can handle the issue of multiplication vs division of hic2cool < 0.4 vs > 0.5.
This version drops the support for Python 2.
February release
This release fixes a slowdown in the writing of a cooler file and sets the default write location back to the user defined location.
- Changing the the default parameter
orderedtoTrue - Setting the temp_dir explicitly to the directory of the cooler file instead of default /tmp
January release
- Update to cooler version 0.8.2
- Improved way to load cooler matrix
November release update
-
Fixing how cooler data is load, dtype is now read dynamically
-
Changing way how cooler file is written:
- Less memory for cooler to cooler files, nan_factors are not applied anymore
- Fixed a bug writing wrong values to cooler file
-
Adding test cases:
- h5 to cool
- cool to cool
- option check for enforce integer
- check for if file was h5 in cooler write
- Make load of h5 file more stable, adding removal of zero values and set nan and inf values to 0.
November release
- Adding function to mask the bins of a chromosome
- More efficient way to write cool matrices. For really big matrices this is now possible with < 100 GB, before 120 GB was not enough. Using more panda data frames and less numpy functions, and splitting the output of the pixel table in chunks.
- Adding test cases for these
- Cleaned up and removed old, out commented source code.
- A few bug fixes for cooler datatype.
October release
This release adds:
- write support for Homer matrices
- Cooler:
- improved loading functions for cooler. Larger matrices can be loaded with less memory
- Enforce integer option for cooler
- Added to revert of correction factors function the different options how correction factors are applied
- Higher test case coverage, thanks @Rungetf
September release
This release is the first release of HiCMatrix, a library to manage Hi-C matrices for HiCExplorer and pyGenomeTracks.
It is identical to the development version of HiCExplorer 2.2 and therefore its version starts with 2.2.