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, info: Map<Info>) -> Self

Adds an information record (INFO).

Examples

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

let info = Map::<Info>::from(Key::SamplesWithDataCount);

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

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

pub fn add_filter(self, filter: Map<Filter>) -> Self

Adds a filter record (FILTER).

Examples

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

let filter = Map::<Filter>::new("q10", "Quality below 10");

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

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

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

Adds a genotype format record (FORMAT).

Examples

use noodles_vcf::{
    self as vcf,
    header::{format::Key, record::value::{map::Format, Map}},
};

let format = Map::<Format>::from(Key::Genotype);

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

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

pub fn add_alternative_allele(
    self,
    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 alt = Map::<AlternativeAllele>::new(
    Symbol::StructuralVariant(StructuralVariant::from(Type::Deletion)),
    "Deletion",
);

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

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

pub fn set_assembly<I>(self, assembly: I) -> Selfwhere
    I: Into<String>,

Sets an breakpoint assemblies record (assembly).

Examples

use noodles_vcf as vcf;

let header = vcf::Header::builder()
    .set_assembly("file:///assemblies.fasta")
    .build();

assert_eq!(header.assembly(), Some("file:///assemblies.fasta"));

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

Adds a contig record (contig).

Examples

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

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

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

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

pub fn add_meta(self, meta: Map<Meta>) -> Self

Adds a meta record (META).

Examples

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

let meta = Map::<Meta>::new(
    "Assay",
    vec![String::from("WholeGenome"), String::from("Exome")],
);

let header = vcf::Header::builder()
    .add_meta(meta.clone())
    .build();

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

pub fn set_pedigree_db<I>(self, pedigree_db: I) -> Selfwhere
    I: Into<String>,

Sets a pedigree database record (pedigreeDB).

Examples

use noodles_vcf as vcf;

let header = vcf::Header::builder()
    .set_pedigree_db("file:///pedigree.db")
    .build();

assert_eq!(header.pedigree_db(), Some("file:///pedigree.db"));

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: Key, value: Other) -> Self

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

Examples

use noodles_vcf::{self as vcf, header::{record::{self, Key}}};

let key = Key::from("fileDate");
let value = record::value::Other::from("20200709");

let header = vcf::Header::builder()
    .insert(key.clone(), value.clone())
    .build();

assert_eq!(header.get(&key), Some(&[value][..]));

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.