Struct noodles_bcf::record::Record

pub struct Record(/* private fields */);

A BCF record.

Implementations

impl Record

pub fn reference_sequence_id(&self) -> Result<usize>

Returns the reference sequence ID of the record.

The reference sequence 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.reference_sequence_id()?, 0);

pub fn reference_sequence_name<'h>( &self, string_maps: &'h StringMaps, ) -> Result<&'h str>

Returns the reference sequence name.

Examples

use noodles_bcf as bcf;
use noodles_vcf::{
    self as vcf,
    header::{record::value::{map::Contig, Map}, StringMaps},
};

let header = vcf::Header::builder()
    .add_contig("sq0", Map::<Contig>::new())
    .build();
let string_maps = StringMaps::try_from(&header)?;

let record = bcf::Record::default();
assert_eq!(record.reference_sequence_name(&string_maps)?, "sq0");

pub fn variant_start(&self) -> Option<Result<Position>>

Returns the variant start position.

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_core::Position;
let record = bcf::Record::default();
assert_eq!(record.variant_start().transpose()?, Some(Position::MIN));

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_core::Position;
let record = bcf::Record::default();
assert_eq!(record.end()?, Position::MIN);

pub fn quality_score(&self) -> Result<Option<f32>>

Returns the quality score.

Examples

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

pub fn ids(&self) -> Ids<'_>

Returns the IDs.

Examples

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

pub fn reference_bases(&self) -> ReferenceBases<'_>

Returns the reference bases.

Examples

use noodles_bcf as bcf;
let record = bcf::Record::default();
assert_eq!(record.reference_bases().as_ref(), b"N");

pub fn alternate_bases(&self) -> AlternateBases<'_>

Returns the alternate bases.

Examples

use noodles_bcf as bcf;
use noodles_vcf::variant::record::AlternateBases;
let record = bcf::Record::default();
assert!(record.alternate_bases().is_empty());

pub fn filters(&self) -> Filters<'_>

Returns the filters.

Examples

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

pub fn info(&self) -> Info<'_>

Returns the info.

Examples

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

pub fn samples(&self) -> Result<Samples<'_>>

Returns the samples.

Examples

use noodles_bcf as bcf;
use noodles_vcf::variant::record::Samples;
let record = bcf::Record::default();
assert!(record.samples()?.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() -> Record

Returns the “default value” for a type.

impl PartialEq 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: &Rhs) -> bool

This method tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl Record for Record

fn reference_sequence_name<'a, 'h: 'a>( &'a self, header: &'h Header, ) -> Result<&'a str>

Returns the reference sequence name.

fn variant_start(&self) -> Option<Result<Position>>

Returns the variant start position.

fn ids(&self) -> Box<dyn Ids + '_>

Returns the IDs.

fn reference_bases(&self) -> Box<dyn ReferenceBases + '_>

Returns the reference bases.

fn alternate_bases(&self) -> Box<dyn AlternateBases + '_>

Returns the alternate bases.

fn quality_score(&self) -> Option<Result<f32>>

Returns the quality scores.

fn filters(&self) -> Box<dyn Filters + '_>

Returns the filters.

fn info(&self) -> Box<dyn Info + '_>

Return the info fields.

fn samples(&self) -> Result<Box<dyn Samples + '_>>

Returns the samples.

fn variant_span(&self, header: &Header) -> Result<usize, Error>

Returns the variant span.

fn variant_end(&self, header: &Header) -> Result<Position, Error>

Returns or calculates the variant end position.

impl StructuralPartialEq for Record