Struct noodles_bcf::record::Record

pub struct Record { /* private fields */ }

A BCF record.

Implementations

impl Record

pub fn try_into_vcf_record(
    &self,
    header: &Header,
    string_maps: &StringMaps
) -> 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_maps = raw_header.parse()?;

let record = bcf::Record::default();

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

impl Record

pub fn chromosome_id(&self) -> ChromosomeId

Returns the chromosome ID of the record.

The chromosome ID represents an index in the contig string map, which associates an ID (by position) with a contig record in the VCF header (by name). That is, to get the associated contig record in the VCF header, the contig string map must first be queried by position to find the chromosome name, and then the contigs in the VCF header can be queried by name.

Examples

use noodles_bcf as bcf;
let record = bcf::Record::default();
assert_eq!(record.chromosome_id(), 0);

pub fn position(&self) -> 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;
let record = bcf::Record::default();
assert_eq!(i32::from(record.position()), 1);

pub fn position_mut(&mut self) -> &mut Position

Returns a mutable reference to the start position.

Examples

use noodles_bcf as bcf;
use noodles_vcf::record::Position;

let mut record = bcf::Record::default();
*record.position_mut() = Position::try_from(8)?;

assert_eq!(i32::from(record.position()), 8);

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

Returns the end position of this record.

This value is 1-based.

Examples

use noodles_bcf as bcf;
let record = bcf::Record::default();
assert_eq!(record.end().map(i32::from)?, 1);

pub fn quality_score(&self) -> Option<QualityScore>

Returns the quality score.

Examples

use noodles_bcf as bcf;
let record = bcf::Record::default();
assert!(record.quality_score().is_none());

pub fn quality_score_mut(&mut self) -> &mut Option<QualityScore>

Return a mutable reference to the quality score.

Examples

use noodles_bcf as bcf;
use noodles_vcf::record::QualityScore;

let mut record = bcf::Record::default();
*record.quality_score_mut() = QualityScore::try_from(13.0).map(Some)?;

assert_eq!(record.quality_score().map(f32::from), Some(13.0));

pub fn ids(&self) -> &Ids

Returns the IDs.

Examples

use noodles_bcf as bcf;
let record = bcf::Record::default();
assert!(record.ids().is_empty());

pub fn ids_mut(&mut self) -> &mut Ids

Returns a mutable reference to the IDs.

Examples

use noodles_bcf as bcf;
use noodles_vcf::record::Ids;

let mut record = bcf::Record::default();
let ids: Ids = "nd0".parse()?;
*record.ids_mut() = ids.clone();

assert_eq!(record.ids(), &ids);

pub fn filters(&self) -> &Filters

Returns the filters.

Examples

use noodles_bcf as bcf;
let record = bcf::Record::default();
assert!(record.filters().is_empty());

pub fn info(&self) -> &Info

Returns the info.

Examples

use noodles_bcf as bcf;
let record = bcf::Record::default();
assert!(record.info().is_empty());

pub fn genotypes(&self) -> &Genotypes

Returns the genotypes.

Examples

use noodles_bcf as bcf;
let record = bcf::Record::default();
assert!(record.genotypes().is_empty());

Trait Implementations

impl Clone for Record

fn clone(&self) -> Record

Returns a copy of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for Record

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl Default for Record

fn default() -> Self

Returns the “default value” for a type.

impl PartialEq<Record> for Record

fn eq(&self, other: &Record) -> bool

This method tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Record) -> bool

This method tests for !=.

impl StructuralPartialEq for Record