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.)
You can install rustbam directly with pip:
pip install rustbam
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.
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]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 formatAn example usage of the CLI:
$ rustbam tests/example.bam chr1 1000000 1000005
1000000 51
1000001 52
1000002 44
1000003 52
1000004 53
1000005 47You 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 0m2.060sDon't even get me started about pysam (rustbam is about 12x fater with -n 2). 😠
✅ 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.
rustbam is released under the MIT License. See LICENSE for details.
- Fork the repo on GitHub.
- Create a new branch:
git checkout -b feature-new - Commit your changes:
git commit -m "Add new feature" - Push to your branch:
git push origin feature-new - Open a Pull Request 🎉
Built using rust-htslib and pyo3.