vrsix: Indexing VRS-Annotated VCFs

Proof of concept for sqlite-based indexing of ANViL-hosted VCFs annotated with VRS IDs and attributes.

From a VCF, ingest a VRS ID and the corresponding VCF-called location (i.e. sufficient inputs for a tabix lookup), and store them in a sqlite database.

% vrsix load chr1.vcf

Given a VRS ID, retrieve VCF-associated data (output format TBD)

% vrsix fetch-by-id --db-location=sqlite.db dwwiZdvVtfAmomu0OBsiHue1O-bw5SpG
ga4gh:VA.dwwiZdvVtfAmomu0OBsiHue1O-bw5SpG,1,783006

Or fetch all rows within a coordinate range:

% vrsix fetch-by-range --db-location=sqlite.db 1 783000 783200
ga4gh:VA.dwwiZdvVtfAmomu0OBsiHue1O-bw5SpG,1,783006
ga4gh:VA.MiasxyXMXtOpsZgGelL3c4QgtflCNLHD,1,783006
ga4gh:VA.5cY2k53xdW7WeHw2WG1HA7jl50iH-r9p,1,783175
ga4gh:VA.jHaXepIvlbnapfPtH_62y-Qm81hCrBYn,1,783175

Set up for development

Ensure that a recent version of the Rust toolchain is available.

Create a virtual environment and install developer dependencies:

python3 -m virtualenv venv
source venv/bin/activate
python3 -m pip install -e '.[dev,tests]'

This installs Python code as editable, but after any changes to Rust code, run maturin develop to rebuild the Rust binary:

maturin develop

Be sure to install pre-commit hooks:

pre-commit install

Check Python style with ruff:

python3 -m ruff format . && python3 -m ruff check --fix .

Use cargo fmt to check Rust style (must be run from within the rust/ subdirectory):

cd rust/
cargo fmt