Struct noodles::vcf::record::Builder

pub struct Builder { /* fields omitted */ }

A VCF record builder.

Implementations

impl Builder

pub fn set_chromosome(self, chromosome: Chromosome) -> Builder

Sets the chromosome.

Examples

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

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

assert_eq!(record.chromosome(), &Chromosome::Name(String::from("sq0")));

pub fn set_position(self, position: Position) -> Builder

Sets the start position.

Examples

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

let record = vcf::Record::builder()
    .set_chromosome("sq0".parse()?)
    .set_position(Position::try_from(8)?)
    .set_reference_bases("A".parse()?)
    .build()?;

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

pub fn set_ids(self, ids: Ids) -> Builder

Sets a list of IDs.

Examples

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

let record = vcf::Record::builder()
    .set_chromosome("sq0".parse()?)
    .set_position(Position::try_from(1)?)
    .set_ids("nd0".parse()?)
    .set_reference_bases("A".parse()?)
    .build()?;

assert_eq!(*record.ids(), "nd0".parse()?);

pub fn set_reference_bases(self, reference_bases: ReferenceBases) -> Builder

Sets the reference bases.

Examples

use noodles_vcf::{
    self as vcf,
    record::{reference_bases::Base, Position, ReferenceBases},
};

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

assert_eq!(
    record.reference_bases(),
    &ReferenceBases::try_from(vec![Base::A])?,
);

pub fn add_reference_base(self, reference_base: Base) -> Builder

Adds a base to reference bases.

Examples

use noodles_vcf::{
    self as vcf,
    record::{reference_bases::Base, Position, ReferenceBases},
};

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

assert_eq!(
    record.reference_bases(),
    &ReferenceBases::try_from(vec![Base::A])?,
);

pub fn set_alternate_bases(self, alternate_bases: AlternateBases) -> Builder

Sets the alternate bases.

Examples

use noodles_vcf::{
    self as vcf,
    record::{alternate_bases::Allele, reference_bases::Base, AlternateBases, Position},
};

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

assert_eq!(
    record.alternate_bases(),
    &AlternateBases::from(vec![Allele::Bases(vec![Base::C])]),
);

pub fn set_quality_score(self, quality_score: QualityScore) -> Builder

Sets the quality score.

Examples

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

let record = vcf::Record::builder()
    .set_chromosome("sq0".parse()?)
    .set_position(Position::try_from(1)?)
    .set_reference_bases("A".parse()?)
    .set_quality_score(QualityScore::try_from(13.0)?)
    .build()?;

assert_eq!(*record.quality_score(), Some(13.0));

pub fn set_filters(self, filters: Filters) -> Builder

Sets the filters.

Examples

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

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

assert_eq!(record.filters(), &Filters::Pass);

pub fn set_info(self, info: Info) -> Builder

Sets additional information.

Examples

use noodles_vcf::{
    self as vcf,
    record::{info::{field::{Key, Value}, Field}, Info, Position},
};

let record = vcf::Record::builder()
    .set_chromosome("sq0".parse()?)
    .set_position(Position::try_from(1)?)
    .set_reference_bases("A".parse()?)
    .set_alternate_bases("C".parse()?)
    .set_info("NS=3;AF=0.5".parse()?)
    .build()?;

let expected = Info::try_from(vec![
    Field::new(Key::SamplesWithDataCount, Value::Integer(3)),
    Field::new(Key::AlleleFrequencies, Value::FloatArray(vec![0.5])),
])?;

assert_eq!(record.info(), &expected);

pub fn set_format(self, format: Format) -> Builder

Sets the genotype format.

Examples

use noodles_vcf::{
    self as vcf,
    record::{genotype::field::Key, Format, Genotype, Position},
};

let format: Format = "GT:GQ".parse()?;

let record = vcf::Record::builder()
    .set_chromosome("sq0".parse()?)
    .set_position(Position::try_from(1)?)
    .set_reference_bases("A".parse()?)
    .set_format(format.clone())
    .add_genotype(Genotype::from_str_format("0|0:13", &format)?)
    .build()?;

assert_eq!(record.format(), Some(&Format::try_from(vec![
    Key::Genotype,
    Key::ConditionalGenotypeQuality,
])?));

pub fn set_genotypes(self, genotypes: Vec<Genotype, Global>) -> Builder

Sets the list of genotypes.

Examples

use noodles_vcf::{
    self as vcf,
    record::{genotype::{field::{Key, Value}, Field}, Format, Genotype, Position},
};

let format: Format = "GT:GQ".parse()?;

let record = vcf::Record::builder()
    .set_chromosome("sq0".parse()?)
    .set_position(Position::try_from(1)?)
    .set_reference_bases("A".parse()?)
    .set_format(format.clone())
    .set_genotypes(vec![Genotype::from_str_format("0|0:13", &format)?])
    .build()?;

assert_eq!(record.genotypes(), [
    Genotype::try_from(vec![
        Field::new(Key::Genotype, Some(Value::String(String::from("0|0")))),
        Field::new(Key::ConditionalGenotypeQuality, Some(Value::Integer(13))),
    ])?,
]);

pub fn add_genotype(self, genotype: Genotype) -> Builder

Adds a genotype.

Examples

use noodles_vcf::{
    self as vcf,
    record::{genotype::{field::{Key, Value}, Field}, Format, Genotype, Position},
};

let format: Format = "GT:GQ".parse()?;

let record = vcf::Record::builder()
    .set_chromosome("sq0".parse()?)
    .set_position(Position::try_from(1)?)
    .set_reference_bases("A".parse()?)
    .set_format(format.clone())
    .add_genotype(Genotype::from_str_format("0|0:13", &format)?)
    .build()?;

assert_eq!(record.genotypes(), [
    Genotype::try_from(vec![
        Field::new(Key::Genotype, Some(Value::String(String::from("0|0")))),
        Field::new(Key::ConditionalGenotypeQuality, Some(Value::Integer(13))),
    ])?,
]);

pub fn build(self) -> Result<Record, BuildError>

Builds a VCF record.

Examples

use noodles_vcf as vcf;
let record = vcf::Record::builder().build();

Trait Implementations

impl Debug for Builder

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

Formats the value using the given formatter.

impl Default for Builder

pub fn default() -> Builder

Returns the “default value” for a type.

impl PartialEq<Builder> for Builder

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

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

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

This method tests for !=.

impl StructuralPartialEq for Builder