vcf-rs

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::<U8Vec>::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(())

} ```