ncbi-vdb-sys

This crate provides FFIs for the ncbi-vdb C-library.

It provides a safe and structured way to interact with the SRA file format (Sequence Read Archive).

The library is designed to be used primarily with xsra, but is available as a standalone crate for other projects.

Usage

The library is designed around accessing Records and Segments from an SRA archive. A Record is a collection of Segments that represent a single read (or spot) from the archive. The library is designed around Record and Segment Iterators.

use ncbi_vdb_sys::{SraReader, Result};

fn main() -> Result<()> {
    let path = "path/to/sra/file.sra";
    let reader = SraReader::new(path)?;

    // Iterate over all records in the archive
    for record in reader.into_iter() {

        // Handle any errors that occur at the record level
        let record = record?;

        // Iterate over all segments in the record
        for segment in record {
            // Do something with the segment
        }
    }
    Ok(())
}

Each Segment contains the sequence data and quality scores for a single read segment. You can also access the SegmentType to determine if it is a biological read or a technical read.

For a simple example of how you can use the library, see the examples directory. I've implemented a basic fastq-dump style tool that will extract all records from an SRA archive and write them to stdout. This also supports specifying a range of records to extract.

git clone https://github.com/arcinstitute/ncbi-vdb-sys
cd ncbi-vdb-sys
cargo build --release --examples dump

# Run the example
target/release/examples/dump <path/to/sra/file.sra>

Limitations

This library is not meant to be a complete feature-for-feature replacement for the ncbi-vdb C-library. It was written for a specific use-case and may not support all possible SRA archive layouts.

Note that this will build the ncbi-vdb C-library as a static library and link against it. This may make your resulting binary system-specific and may not work on all systems (will be limited to what ncbi-vdb can be built on).

Note: Interfacing with the underlying C-library is unsafe. This library is not fully tested against all possible edge-cases so while it should be safe to use, there may be bugs.

Contributing

If you have a specific use-case that is not supported by this library, please open an issue or a pull request.