rustbam 0.1.0

A Rust-based BAM depth calculator for Python.

🦀 rustbam - Fast BAM Depth Calculator in Rust & Python

🚀 rustbam is a high-performance BAM depth calculator written in Rust, with Python bindings for fast and efficient genomic data analysis. It offers a pysam-like API but is significantly faster due to Rust’s performance advantages.

📦 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:

python

CopyEdit

import rustbam
depths = rustbam.get_depth("example.bam", "chr1", 1000000, 1000100, 
    step=10,     # As in range(start, end, step)
    min_mapq=0,  # Minimum mapping quality (samtools -q)
    min_bq=13,   # Minimum base quality (samtools -Q)
    max_depth=8000  # Max per-file depth (samtools -d)
)
print(depths)

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.