3 unstable releases
0.2.1 | May 15, 2023 |
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0.2.0 | May 9, 2023 |
0.1.0 | May 4, 2023 |
#10 in #batching
365KB
277 lines
📑️ VCF Batcher
This is a Rust crate to cut VCF (variant call files) into smaller batches, intended to be used for multiprocessing or distributed computing.
🧰️ Installation
Depending on what your goals are, you can use this tool as a CLI or as a library in 🦀️ Rust or 🐍️ Python.
Installing the CLI
In order to install the program as a CLI, you will need to have cargo
installed.
Instructions to install cargo
Once you have it, you can run the following command in your terminal to install the VCF batcher.
cargo install vcf_batcher
Installing Rust Crate
In order to install the tool as a rust crate, you can add it to your Cargo.toml
dependencies or
run:
cargo add vcf_batcher
You can find the crate documentation on docs.rs.
Installing python bindings
We provide python bindings for the VCF batcher which can be installed via pip
.
pip install vcf-batcher
🪄️ Usage
CLI
Using the CLI after installing can be done through the vcf_batcher_cli
command.
vcf_batcher_cli path/to/your_file.vcf path/to/ouput/directory
By default, this will create batches with 25'000 samples each. If you'd like to override this
default, you can do so by providing a custom --batch-size
or -b
argument:
vcf_batcher_cli -b 1000 path/to/your_file.vcf path/to/ouput/directory
Library
After installing either the rust crate or python module, you can use the provided function.
🦀️ Rust
pub fn extract_variants_to_batches(
file_path: &str,
batch_size: usize,
output_path: &Path,
compression_level: Option<Compression>
)
🐍️ Python
vcf_batcher.py_extract_variants_to_batches(
input_file,
batches_folder,
batch_size,
)
License
The software is licensed under the MIT License.
Dependencies
~8–16MB
~207K SLoC