Initial commit

[jonperdomo]

No description provided.

[Copilot]

Pull request overview

Initial import of the ContextScore codebase, including the prediction CLI, feature extraction/annotation pipeline, training script, packaging metadata, and a pytest-based test suite to validate key helpers and I/O.

Changes:

• Added contextscore.predict CLI to score/filter SVs and emit per-variant prediction outputs.
• Added contextscore.extract_features to build feature matrices with bedtools + ANNOVAR/UCSC-based annotations.
• Added packaging/CI/test scaffolding (setup.py/conda recipe/GitHub Actions/pytest tests + fixtures).

Reviewed changes

Copilot reviewed 18 out of 23 changed files in this pull request and generated 15 comments.

Show a summary per file

File	Description
tests/test_predict_io.py	Adds end-to-end-ish tests around VCF reading and predict.score output generation.
tests/test_predict_helpers.py	Adds unit tests for model/ANNOVAR path resolution and optional plotting imports.
tests/test_extract_features_helpers.py	Adds unit tests for chromosome normalization and BED→ANNOVAR input conversion.
tests/conftest.py	Ensures repo root is importable during tests (sys.path injection).
tests/fixtures/example.vcf	Adds a placeholder VCF fixture referenced by tests.
tests/fixtures/output.vcf.gz	Adds a large gzipped VCF fixture used for I/O + scoring tests.
tests/fixtures/output.vcf.gz.tbi	Adds the tabix index for the gzipped VCF fixture.
contextscore/predict.py	Implements CLI and scoring/filtering pipeline including output artifacts.
contextscore/extract_features.py	Implements feature extraction + annotation integration (bedtools/ANNOVAR/UCSC).
contextscore/train_full_model.py	Adds a training/evaluation script for building models.
contextscore/download_tables.py	Adds a utility for downloading UCSC annotation tables via MySQL.
contextscore/__main__.py	Enables python -m contextscore execution.
contextscore/__init__.py	Initializes the package.
contextscore/TrainingAnnotationsSummary.tsv	Adds a TSV artifact related to training annotations.
setup.py	Adds setuptools packaging config and data file packaging attempt.
MANIFEST.in	Declares included files for source distributions.
pytest.ini	Configures pytest discovery.
environment.yml	Defines a conda environment for development/tests.
conda/meta.yaml	Adds a conda recipe for packaging/distribution.
.github/workflows/unit-tests.yml	Adds GitHub Actions workflow to run unit tests in a conda env.
.gitignore	Adds ignores for outputs, generated artifacts, and data directories.
.vscode/settings.json	Adds VS Code pytest configuration.
README.md	Adds installation + usage documentation and annotation source references.

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