🦀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.
(It's only a coincidence that "bam" means "snake" in Korean.)

📦 Installation

Install from PyPI

You can install rustbam directly with pip:

pip install rustbam

Requirements

rustbam requires Python ≥3.8 and a compatible Linux environment. Prebuilt wheels are available for most systems, but if you encounter installation issues, ensure your system has glibc ≥2.17 (manylinux2014 compatibility). To check your version, run ldd --version.

If you need to compile from source, install Rust (cargo), Python development headers (python3-dev or python3-devel), and GCC (build-essential or Development Tools). For the best experience, we recommend using pip install rustbam, but if necessary, you can force a source installation with pip install --no-binary rustbam 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=10,          # 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)

After installation, you can use rustbam in your shell (note that coordinates are 1-based and inclusive, as in samtools mpileup):

$ rustbam --help
usage: rustbam [-h] [-t STEP] [-Q MIN_MAPQ] [-q MIN_BQ] [-d MAX_DEPTH] [-n NUM_THREADS] [-j] bam chromosome start end

Compute sequencing depth from a BAM file.

positional arguments:
  bam                   Path to the indexed BAM file
  chromosome            Chromosome name (e.g., 'chr1')
  start                 Start position (1-based)
  end                   End position (1-based)

options:
  -h, --help            show this help message and exit
  -t STEP, --step STEP  Step size for sampling positions (default: 1)
  -Q MIN_MAPQ, --min_mapq MIN_MAPQ
                        Minimum mapping quality (default: 0)
  -q MIN_BQ, --min_bq MIN_BQ
                        Minimum base quality (default: 13)
  -d MAX_DEPTH, --max_depth MAX_DEPTH
                        Maximum depth allowed (default: 8000)
  -n NUM_THREADS, --num_threads NUM_THREADS
                        Number of threads (default: 12)
  -j, --json            Output results in JSON format

An example usage of the CLI:

$ rustbam tests/example.bam chr1 1000000 1000005
1000000 51
1000001 52
1000002 44
1000003 52
1000004 53
1000005 47

You can get much faster depths result compared to samtools mpileup (as long as you use the multithreading option, -n):

$ time samtools mpileup /path/to/a/large/bam -r chr1:1-30000000 > /dev/null
[mpileup] 1 samples in 1 input files

real    2m9.018s
user    2m8.100s
sys     0m0.685s

$ time rustbam /path/to/a/large/bam chr1 1 30000000 -n 12 > /dev/null

real    0m22.038s
user    1m40.802s
sys     0m2.060s

Don't even get me started about pysam (rustbam is about 12x fater with -n 2). 😠

🔥 Features

✅ Fast: Uses Rust’s efficient rust-htslib for BAM processing, and supports parallelism.
✅ 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.

📜 License

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

🤝 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 🎉

🌍 Acknowledgments

Built using rust-htslib and pyo3.