https://github.com/informationsea/vcf-rs

Rust implmentation of VCF parser
https://github.com/informationsea/vcf-rs

bioinformatics parser rust

Last synced: 3 months ago
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Rust implmentation of VCF parser

• Host: GitHub
• URL: https://github.com/informationsea/vcf-rs
• Owner: informationsea
• License: apache-2.0
• Created: 2020-03-17T15:18:26.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2022-10-02T11:08:22.000Z (over 3 years ago)
• Last Synced: 2025-12-13T23:43:36.807Z (6 months ago)
• Topics: bioinformatics, parser, rust
• Language: Rust
• Size: 37.2 MB
• Stars: 25
• Watchers: 2
• Forks: 2
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
vcf-rs

======

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[![Crates.io](https://img.shields.io/crates/v/vcf)](https://crates.io/crates/vcf)

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Rust implementation of VCF parser.

License

-------

Apache 2.0

Example

-------

```rust

use vcf::*;

use flate2::read::MultiGzDecoder;

use std::fs::File;

fn usage_test() -> Result<(), VCFError> {

    let mut reader = VCFReader::new(BufReader::new(MultiGzDecoder::new(File::open(

        "./testfiles/NA12878-subset.vcf.gz",

    )?)))?;

    // access FILTER contents

    assert_eq!(

        Some(VCFHeaderFilterAlt {

            id: b"PASS",

            description: b"All filters passed"

        }),

        reader.header().filter(b"PASS")

    );

    // access INFO contents

    assert_eq!(

        b"Stop position of the interval",

        reader.header().info(b"END").unwrap().description

    );

    // prepare VCFRecord object

    let mut vcf_record = VCFRecord::new(reader.header());

    // read one record

    reader.next_record(&mut vcf_record)?;

    // get record attributes

    assert_eq!(vcf_record.chromosome, b"13");

    assert_eq!(vcf_record.position, 32889968);

    assert_eq!(vcf_record.id, Vec::::new());

    assert_eq!(vcf_record.reference, b"G");

    assert_eq!(vcf_record.alternative, vec![b"A"]);

    assert_eq!(vcf_record.qual, Some(25743.5));

    assert_eq!(vcf_record.info(b"AC"), Some(&vec![b"54".to_vec()]));

    assert_eq!(

        vcf_record.genotype(b"ERP001775_HiSeq2000_SAMEA1531955-1", b"GT"),

        Some(&vec![b"1/1".to_vec()])

    );

    assert_eq!(

        vcf_record.genotype(b"ERP001775_HiSeq2000_SAMEA1531955-1", b"AD"),

        Some(&vec![b"0".to_vec(), b"14".to_vec()])

    );

    Ok(())

}

```