Struct noodles_vcf::header::Builder

pub struct Builder { /* private fields */ }

A VCF header builder.

Implementations

impl Builder

pub fn set_file_format(self, file_format: FileFormat) -> Self

Sets the fileformat record (fileformat).

Examples

use noodles_vcf::{self as vcf, header::FileFormat};

let header = vcf::Header::builder()
    .set_file_format(FileFormat::default())
    .build();

assert_eq!(header.file_format(), FileFormat::default());

pub fn add_info(self, id: Key, info: Map<Info>) -> Self

Adds an information record (INFO).

Examples

use noodles_vcf::{
    self as vcf,
    header::record::value::{map::Info, Map},
    record::info::field::key,
};

let id = key::SAMPLES_WITH_DATA_COUNT;
let info = Map::<Info>::from(&id);

let header = vcf::Header::builder()
    .add_info(id, info.clone())
    .build();

let infos = header.infos();
assert_eq!(infos.len(), 1);
assert_eq!(&infos[0], &info);

pub fn add_filter<I>(self, id: I, filter: Map<Filter>) -> Selfwhere I: Into<String>,

Adds a filter record (FILTER).

Examples

use noodles_vcf::{self as vcf, header::record::value::{map::Filter, Map}};

let filter = Map::<Filter>::new("Quality below 10");

let header = vcf::Header::builder()
    .add_filter("q10", filter.clone())
    .build();

let filters = header.filters();
assert_eq!(filters.len(), 1);
assert_eq!(&filters[0], &filter);

pub fn add_format(self, id: Key, format: Map<Format>) -> Self

Adds a genotype format record (FORMAT).

Examples

use noodles_vcf::{
    self as vcf,
    header::record::value::{map::Format, Map},
    record::genotypes::keys::key,
};

let id = key::GENOTYPE;
let format = Map::<Format>::from(&id);

let header = vcf::Header::builder()
    .add_format(id, format.clone())
    .build();

let formats = header.formats();
assert_eq!(formats.len(), 1);
assert_eq!(&formats[0], &format);

pub fn add_alternative_allele( self, id: Symbol, alternative_allele: Map<AlternativeAllele> ) -> Self

Adds an alternative allele record (ALT).

Examples

use noodles_vcf::{
    self as vcf,
    header::record::value::{map::AlternativeAllele, Map},
    record::alternate_bases::allele::{
        symbol::{structural_variant::Type, StructuralVariant},
        Symbol,
    },
};

let id = Symbol::StructuralVariant(StructuralVariant::from(Type::Deletion));
let alt = Map::<AlternativeAllele>::new("Deletion");

let header = vcf::Header::builder()
    .add_alternative_allele(id, alt.clone())
    .build();

let alternative_alleles = header.alternative_alleles();
assert_eq!(alternative_alleles.len(), 1);
assert_eq!(&alternative_alleles[0], &alt);

pub fn add_contig(self, id: Name, contig: Map<Contig>) -> Self

Adds a contig record (contig).

Examples

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

let id = "sq0".parse()?;
let contig = Map::<Contig>::new();

let header = vcf::Header::builder()
    .add_contig(id, contig.clone())
    .build();

let contigs = header.contigs();
assert_eq!(contigs.len(), 1);
assert_eq!(&contigs[0], &contig);

pub fn set_sample_names(self, sample_names: SampleNames) -> Self

Sets sample names.

Examples

use indexmap::IndexSet;
use noodles_vcf as vcf;

let sample_names: IndexSet<_> = [String::from("sample0")]
    .into_iter()
    .collect();

let header = vcf::Header::builder()
    .set_sample_names(sample_names.clone())
    .build();

assert_eq!(header.sample_names(), &sample_names);

pub fn add_sample_name<I>(self, sample_name: I) -> Selfwhere I: Into<String>,

Adds a sample name.

Duplicate names are discarded.

Examples

use indexmap::IndexSet;
use noodles_vcf as vcf;

let header = vcf::Header::builder()
    .add_sample_name("sample0")
    .add_sample_name("sample1")
    .build();

let expected: IndexSet<_> = [String::from("sample0"), String::from("sample1")]
    .into_iter()
    .collect();

assert_eq!(header.sample_names(), &expected);

pub fn insert(self, key: Other, value: Value) -> Result<Self, AddError>

Inserts a key-value pair representing an unstructured record into the header.

Examples

use noodles_vcf::{
    self as vcf,
    header::record::{value::Collection, Value},
};

let header = vcf::Header::builder()
    .insert("fileDate".parse()?, Value::from("20200709"))?
    .build();

assert_eq!(
    header.get("fileDate"),
    Some(&Collection::Unstructured(vec![String::from("20200709")]))
);

pub fn build(self) -> Header

Builds a VCF header.

Examples

use noodles_vcf as vcf;
let header = vcf::Header::builder().build();

Trait Implementations

impl Debug for Builder

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

Formats the value using the given formatter.

impl Default for Builder

fn default() -> Builder

Returns the “default value” for a type.