All notable changes to this project will be documented in this file.
-
CHANGELOG.md
for documenting changes -
DEVELOPER.md
developer notes -
environment.yml
conda environment specification -
Included versioneer for managing version strings through git tags
- Depends on python >= 3.7, ensure dict objects maintain insertion-order. See What’s New In Python 3.7
- Removed
bulk
andsc
subcommands since the single-cell stellarscope project has moved into its own repository.
- Error where numpy.int is deprecated
The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.
Prior to this CHANGELOG, changes were tracked in README.md. The previous version history is relocated here:
- Checks that GTF feature type is "exon"
- Skips GTF lines missing attribute (with warning)
- Added cimport statements to calignment.pyx (MacOS bug fix)
- Fixed warning about deprecated PyYAML yaml.load
- Compatibility with intervaltree v3.0.2
- Temporary files are written as BAM
- Changed default
theta_prior
to 200,000
- Removed dependency on
git
- Release version
- Support for sorted BAM files
- Parallel reading of sorted BAM files
- Improved performance of EM
- Improved memory-efficiency of spare matrix
- Fixed bug where random seed is out of range
- Added MIT license
- Changes to logging/reporting
- Improvements to
telescope resume
- Implemented checkpoint and
telescope resume
- Refactoring Telescope class with TelescopeLikelihood
- Improved memory usage
- Subcommand option parsing class
- Cython for alignment parsing
- HTSeq as alternate alignment parser
- Python3 compatibility
- Implemented IntervalTree for Annotation data structure
- Added support for annotation files where a locus may be non-contiguous.
- Overlapping annotations with the same key value (locus) are merged
- User can set minimum overlap criteria for assigning read to locus, default = 0.1
- Implemented checkpointing
- Output tables as pickled objects
- Changes to report format and output