Hifive

------------------
- Updated quasar to final version

.. _1_4:

------------------

- Added conversion scripts for butlr and cooler heatmp formats
- Added perliminary QuASAR scripts
- Added support for matrix output in text and npz formats
- Added hdf5 feature loading for fend files
- Added boundary index and comportment likelihood scoring

.. _1_3:

-------------------

- Added support for creating non-restriction enzyme-based HiC genome partitions
- Added ability to load RE HiC data into binned genome partition
- Added ability to directly load pre-binned matrix files
- Added support for normalization and plotting of binned HiC data
- Added matrix output option in hic-interval subcommand
- Fixed error in sub-binning cis heatmap arrays
- Compiled domain calling approaches into new hic_domain module
- Renamed _hic_tads to _hic_domains in libraries
- Removed ununsed functions in _hic_domains
- Added explicit variable casting for compatibility with cythoning in Windows

.. _1_2_2:

-------------------

- Added modified arrowhead transformation domain calling
- Re-implemented modified version of boundary-index domain finding
- Added cis sub-region binning function (no longer needs to extend to the diagonal)

.. _1_2:

-----------------

- Added detailed statistics for loaded HiC data
- Added testing of various data import functions
- Added option to skip PCR duplicate filtering
- Cleaned up HiC cis binning
- Various bug fixes

.. _1_1:

-----------------

- Added multi-resolution heatmaps (MRH).
- Added stand-alone script for plotting MRH data.
- Fixed requirements resolution for pip loading without requirements already installed.
- Re-implemented Poisson model for HiC probability algorithm.
- Lowered memory requirement for HiC data loading.
- Added dockerfile for building docker image.

.. _1_0_3: