Releases: 23andMe/yhaplo
2.1.10
The --haplogroup_query
option introduced in 2.1.9
now lists SNPs associated with the queried haplogroup.
For details, see CHANGELOG.md, 2.1.9...2.1.10.
2.1.9
This release:
- Adds a
--haplogroup_query
option - Fixes
Node.hg_snp
drift of SNP-less intermediate branches upon repeatedTree
instantiation
For details, see CHANGELOG.md or the full diff: 2.1.7...2.1.9.
2.1.7
This release adds a SNP.info
property and calls it from Tree.query_snp_path
.
For details, see CHANGELOG.md
or the full diff: 2.1.6...2.1.7.
2.1.6
This release adds Python 3.12 support, adds __repr__
methods, and unrotates Newick representation, among other minor changes.
For details, see CHANGELOG.md
or the full diff: 2.1.4...2.1.6.
2.1.4
This release adds various tree utilities.
For details see CHANGELOG.md
or the full diff: 2.1.0...2.1.4.
2.1.0
This release improves haplogroup calling by identifying and correcting various errors in the ISOGG variant metadata.
Full Changelog: 2.0.2...2.1.0
2.0.2
This is a major clean-up and refactoring release. Core logic has not changed, and output should be equivalent to prior versions. The key changes from an end-user perspective are BCF support, a cleaner API, and faster processing of most input types. See below for a fuller listing of public-facing updates.
The next release will correct ISOGG polarization errors for a few dozen SNPs.
Added
- BCF support
- Automated tests
- Optional dependencies
Sample
subclasses:TextSample
,VCFSample
CHANGELOG.md
Changed
- Lint code
- Update pre-commit hooks
- Update
Makefile
and configuration files - Refactor for PEP-8 compliance (snake case, etc.)
- Update directory structure
- Modernize packaging and infer version dynamically
- Namespace command-line entry points:
yhaplo
,yhaplo_convert_to_genos
,yhaplo_plot_tree
- Replace static methods
- Clean up logging and use file handlers
- Use f-strings
- Reformat docstrings
- Add type annotations
- Use
importlib.resources
to load metadata files - Move example input from package to
tests/fixtures/
- Update
README.md
andyhaplo_manual.pdf
- Speed up sample-major file processing
- Use Pysam to process VCF/BCF input
Removed
- Support for Python 2 and Python 3.8