Storm

A high-performance data processing library with both Rust and Python interfaces.

SV + tandem-repeat (Hail)

For union SV call sets: generate site-only TR metadata with storm-tr-sidecar, then in Hail use storm.annotate_svs(mt, tr_sidecar_sites=...) so the TR sidecar joins on allele_id after multi-allelic split. See data/tr_loci_hg38/README.md and examples/hail_join_example.py. Hail is optional at install time (pip install 'storm[hail]' pins 0.2.134 to match Terra, or use conda); annotate_svs imports Hail only when called.

Requirements

• Rust 1.87.0 or later
• Python 3.7 or later
• Cargo (Rust package manager)
• pip (Python package manager)
• Docker (optional, for containerized builds)

Installation

Rust Binary

To install the Rust binary:

# Clone the repository
git clone https://github.com/broadinstitute/storm.git
cd storm

# Build the release binary
cargo build --release --features python

# The binary will be available at target/release/storm

Python Package

To install the Python package:

# Create and activate a virtual environment
python -m venv venv
source venv/bin/activate  # On Windows, use: venv\Scripts\activate

# Install development dependencies
pip install -r dev-requirements.txt

# Build and install the package
maturin build --release
pip install target/wheels/*.whl

Docker

To build and run using Docker:

# Build the Docker image
docker build -t storm ./docker

# Run the container
docker run storm

Development

Setting up the development environment

1. Install Rust toolchain:

   rustup install stable
   rustup default stable

2. Set up Python environment:

   # Create and activate a virtual environment
   python -m venv venv
   source venv/bin/activate  # On Windows, use: venv\Scripts\activate
   
   # Install development dependencies
   pip install -r dev-requirements.txt

Building from source

1. Build the Rust binary:

   cargo build --release --features python

2. Build the Python package:

   maturin build --release

Running tests

# Run Rust tests
cargo test --verbose --features python

# Run Python tests
cd python
pytest

Code formatting

# Format Rust code
cargo fmt

# Format Python code
cd python
black .
isort .

License

[Add your license information here]

Contributing

[Add contribution guidelines here]