https://github.com/weinstockj/parquet2bcf

https://github.com/weinstockj/parquet2bcf

Last synced: 5 days ago
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• Host: GitHub
• URL: https://github.com/weinstockj/parquet2bcf
• Owner: weinstockj
• Created: 2024-12-17T22:17:26.000Z (5 days ago)
• Default Branch: master
• Last Pushed: 2024-12-18T16:37:33.000Z (5 days ago)
• Last Synced: 2024-12-18T17:27:08.572Z (5 days ago)
• Language: Rust
• Size: 25.4 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# parquet2bcf

This project reads variant data from a Parquet file and writes the results to a BCF (Binary Call Format) file. 

The input Parquet file should contain variant data in the following format:

    Columns: 

        - `chrom`: Chromosome name.

        - `pos`: Position on the chromosome.

        - `ref`: Reference allele.

        - `alt`: Alternate allele.

        - `eid`: Numeric sample ID.

There should be one row per non-reference genotype, i.e., this is a sparse representation of the genotypes since homozygous reference genotypes are not included.

## Installation

To build and run this project, you need to have Rust installed. You can install Rust using [rustup](https://rustup.rs/).

Clone the repository and navigate to the project directory, then build the project:

```sh

cargo build --release

```

## Usage

### Command-line Arguments

- `--parquet-path`: Path to the input Parquet file containing variant data (default: `test_variants.parquet`).

- `--samples-path`: Path to the file containing sample names (default: `samples.txt`).

- `--output-path`: Path to the output BCF file (default: `output.bcf`).

- `--n-threads`: Number of threads to use for writing the BCF file (default: `2`).

## Example

```sh

target/release/parquet2bcf --parquet-path variants.parquet \

    --samples-path samples.txt \

    --output-path output.bcf \

    --n-threads 4 # output threads

```

## Logging

The project uses the `log` crate for logging. By default, it logs informational messages. You can adjust the logging level by setting the `RUST_LOG` environment variable:

```sh

RUST_LOG=info cargo run --release

```

## Testing

The project includes unit tests for the BCF writing functionality. To run the tests, use the following command:

```sh

cargo test

```

## Contact

Email Josh Weinstock  .