All notable changes to this project will be documented in this file.
The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.
- Move to pyproject.toml packaging for compatibility with newer PIP versions
- Fixed incorrect parameter name in gamtools call_windows
- Allow the doit dependencies database to be reset
- Calculate coverage on individual bamfiles instead of all at once
- Calculate intrinsic bias of a contact matrix
- Added functions for calculating normalized pointwise mutual information (NPMI)
- Added functions for checking the quality of a segregation table
- Added a CONTRIBUTORS file
- Changed default matrix type from Dprime to NPMI
- Use base-pair instead of read-count coverage for window calling
- Use Orphan windows algorithm to call positive windows
1.1.1 - 2019-02-08
- Added a CHANGELOG
- Fix problem processing uncompressed fastas
- Fix bug where pandas converts sample names to numeric types
- Removed command line option for MACS window calling
- Removed support for Python3.4
1.1.0 - 2017-05-06
- Added fixed threshold option to process_nps
- Added functions for extracting sub-regions of a matrix
- Enable coveralls
- Enable codeclimate
1.0.0 - 2017-03-04
- First release of GAMtools package
- Created a master command line script
- Added support for gzipped input/output
- Added a command to calculate enrichments
- Added a command to convert different matrix formats
- Added a command for circular permutation
- Added a command for getting compaction
- Added a command for getting radial position
- Added QC scripts and automatic exclusion of bad samples
- Added documentation
- Added unit tests
- Added tutorial
- Added continuous integration through tox and Travis
- Made code PEP8 compliant
- Made code python3 compatible
- Old command line scripts