Struct noodles_bcf::Record[−][src]

pub struct Record(_);

Expand description

A BCF record.

A bcf::Record wraps a raw byte buffer, and the fields should be considered immutable.

Implementations

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impl Record

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pub fn try_into_vcf_record(
 &self,
 header: &Header,
 string_map: &StringMap
) -> Result<Record>

Converts a VCF record to a BCF record.

Examples

use noodles_bcf as bcf;
use noodles_vcf::{self as vcf, record::Position};

let raw_header = "##fileformat=VCFv4.3\n##contig=<ID=sq0>\n#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n";
let header: vcf::Header = raw_header.parse()?;
let string_map = raw_header.parse()?;

let record = bcf::Record::from(vec![
    0x00, 0x00, 0x00, 0x00, // chrom = sq0
    0x00, 0x00, 0x00, 0x00, // pos = 0 (base 0)
    0x01, 0x00, 0x00, 0x00, // rlen = 1
    0x01, 0x00, 0x80, 0x7f, // qual = Float::Missing
    0x00, 0x00, // n_info = 0
    0x01, 0x00, // n_allele = 1
    0x00, // n_sample = 0
    0x00, 0x00, 0x00, // n_fmt = 0
    0x07, // id = [missing]
    0x17, 0x41, // ref = A
    0x00, // filter = []
]);

let actual = record.try_into_vcf_record(&header, &string_map)?;

let expected = vcf::Record::builder()
    .set_chromosome("sq0".parse()?)
    .set_position(Position::try_from(1)?)
    .set_reference_bases("A".parse()?)
    .build()?;

assert_eq!(actual, expected);

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impl Record

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pub fn chromosome_id(&self) -> Result<i32>

Returns the chromosome ID of the record.

The chromosome ID is the index of the associated contig in the VCF header.

Examples

use noodles_bcf as bcf;

let record = bcf::Record::from(vec![
    0x08, 0x00, 0x00, 0x00, // CHROM
    // ...
]);

assert_eq!(record.chromosome_id()?, 8);

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pub fn position(&self) -> Result<Position>

Returns the start position of this record.

Despite the BCF format using 0-based positions, this normalizes the value as a 1-based position.

Examples

use noodles_bcf as bcf;
use noodles_vcf as vcf;

let record = bcf::Record::from(vec![
    0x08, 0x00, 0x00, 0x00, // CHROM
    0x0c, 0x00, 0x00, 0x00, // POS
    // ...
]);

assert_eq!(record.position().map(i32::from)?, 13);

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pub fn end(&self) -> Result<Position>

Returns the end position of this record.

This value is 1-based.

Examples

use noodles_bcf as bcf;
use noodles_vcf as vcf;

let record = bcf::Record::from(vec![
    0x08, 0x00, 0x00, 0x00, // CHROM
    0x0c, 0x00, 0x00, 0x00, // POS
    0x05, 0x00, 0x00, 0x00, // rlen
    // ...
]);

assert_eq!(record.end().map(i32::from)?, 17);