rustbam 0.1.5

A Rust-based BAM depth calculator for Python.

🦀 rustbam - Rust-powered fast BAM depth extraction with Python bindings

rustbam is a high-performance BAM depth calculator written in Rust, with Python bindings for fast and efficient genomic data analysis.

📦 Installation

Install from PyPI (No Conda Required)

You can install rustbam directly with pip:

pip install rustbam

🛠️ Usage

Python API

After installation, you can use rustbam in Python:

import rustbam

positions, depths = rustbam.get_depths(
    bam_path,         # path to bam file
    chromosome,       # chromosome/contig name
    start,            # 1-based inclusive start coordinate
    end,              # 1-based inclusive end coordinate
    step=1,           # step as in range(start, end, step) - default: 1
    min_mapq=0,       # minimum mapping quality - default 0
    min_bq=13,        # minimum base quality - default 13 (as in samtools mpileup)
    max_depth=8000,   # maximum depth to return per base position
    num_threads=12,   # number of threads for parallelization
)

print(positions[:5])  # e.g. [100000, 100010, 100020, 100030, 100040]
print(depths[:5])     # e.g. [12, 15, 10, 8, 20]

CLI (Command Line Interface)

Coming soon! 🚀

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🔥 Features

✅ Fast: Uses Rust’s efficient rust-htslib for BAM processing.
✅ Python bindings: Seamless integration with Python via pyo3.
✅ Custom filtering: Supports read quality (-q), base quality (-Q), and max depth (-d).
✅ Supports large BAM files: Uses IndexedReader for efficient region querying.

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📜 License

rustbam is released under the MIT License. See LICENSE for details.

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🤝 Contributing

1. Fork the repo on GitHub.
2. Create a new branch: git checkout -b feature-new
3. Commit your changes: git commit -m "Add new feature"
4. Push to your branch: git push origin feature-new
5. Open a Pull Request 🎉

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🌍 Acknowledgments

Built using rust-htslib and pyo3.