Struct noodles_vcf::header::Header

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pub struct Header { /* private fields */ }

Expand description

A VCF header.

Implementations§

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impl Header

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pub fn builder() -> Builder

Returns a builder to create a record from each of its fields.

Examples

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

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pub fn file_format(&self) -> FileFormat

Returns the file format (fileformat) of the VCF.

fileformat is a required meta record and is guaranteed to be set.

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());

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pub fn file_format_mut(&mut self) -> &mut FileFormat

Returns a mutable reference to the file format (fileformat) of the VCF.

fileformat is a required meta record and is guaranteed to be set.

Examples

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

let mut header = vcf::Header::default();

let file_format = FileFormat::new(4, 2);
*header.file_format_mut() = file_format;

assert_eq!(header.file_format(), file_format);

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pub fn infos(&self) -> &Infos

Returns a map of information records (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);

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pub fn infos_mut(&mut self) -> &mut Infos

Returns a mutable reference to a map of information records (INFO).

Examples

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

let mut header = vcf::Header::default();

let id = key::SAMPLES_WITH_DATA_COUNT;
let info = Map::<Info>::from(&id);
header.infos_mut().insert(id, info.clone());

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

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pub fn filters(&self) -> &Filters

Returns a map of filter records (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);

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pub fn filters_mut(&mut self) -> &mut Filters

Returns a mutable reference to a map of filter records (FILTER).

Examples

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

let mut header = vcf::Header::default();

let filter = Map::<Filter>::new("Quality below 10");
header.filters_mut().insert(String::from("q10"), filter.clone());

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

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pub fn formats(&self) -> &Formats

Returns a list of genotype format records (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);

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pub fn formats_mut(&mut self) -> &mut Formats

Returns a mutable reference to a list of genotype format records (FORMAT).

Examples

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

let mut header = vcf::Header::default();

let id = key::GENOTYPE;
let format = Map::<Format>::from(&id);
header.formats_mut().insert(id, format.clone());

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

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pub fn alternative_alleles(&self) -> &AlternativeAlleles

Returns a map of symbolic alternate alleles (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);

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pub fn alternative_alleles_mut(&mut self) -> &mut AlternativeAlleles

Returns a mutable reference to a map of symbolic alternate alleles (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 mut header = vcf::Header::default();

let id = Symbol::StructuralVariant(StructuralVariant::from(Type::Deletion));
let alt = Map::<AlternativeAllele>::new("Deletion");
header.alternative_alleles_mut().insert(id, alt.clone());

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

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pub fn contigs(&self) -> &Contigs

Returns a map of contig records (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);

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pub fn contigs_mut(&mut self) -> &mut Contigs

Returns a mutable reference to a map of contig records (contig).

Examples

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

let mut header = vcf::Header::default();

let id = "sq0".parse()?;
let contig = Map::<Contig>::new();
header.contigs_mut().insert(id, contig.clone());

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

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pub fn sample_names(&self) -> &SampleNames

Returns a list of sample names that come after the FORMAT column in the header record.

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);

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pub fn sample_names_mut(&mut self) -> &mut SampleNames

Returns a mutable reference to a list of sample names that come after the FORMAT column in the header record.

Examples

use indexmap::IndexSet;
use noodles_vcf as vcf;

let mut header = vcf::Header::builder().add_sample_name("sample0").build();
header.sample_names_mut().insert(String::from("sample1"));

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

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

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pub fn other_records(&self) -> &OtherRecords

Returns a map of records with nonstandard keys.

This includes all records other than fileformat, INFO, FILTER, FORMAT, ALT, and contig.

Examples

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

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

assert_eq!(header.other_records().len(), 1);

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pub fn other_records_mut(&mut self) -> &mut OtherRecords

Returns a mutable reference to a map of collections of records with nonstandard keys.

This includes all records other than fileformat, INFO, FILTER, FORMAT, ALT, and contig.

To simply add an nonstandard record, consider using Self::insert instead.

Examples

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

let mut header = vcf::Header::default();

let collection = Collection::Unstructured(vec![String::from("20200709")]);
header.other_records_mut().insert("fileDate".parse()?, collection.clone());

assert_eq!(header.other_records().get("fileDate"), Some(&collection));

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pub fn get<Q>(&self, key: &Q) -> Option<&Collection>where Q: ?Sized + Hash + Equivalent<Other>,

Returns a collection of header values with the given key.

This includes all records other than fileformat, INFO, FILTER, FORMAT, ALT, and contig.

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")]))
);

assert!(header.get("reference").is_none());

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

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

Examples

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

let mut header = vcf::Header::default();
assert!(header.get("fileDate").is_none());

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