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 repeated Tree 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 and yhaplo_manual.pdf
• Speed up sample-major file processing
• Use Pysam to process VCF/BCF input

Removed

• Support for Python 2 and Python 3.8