Struct noodles::vcf::Header

pub struct Header { /* fields omitted */ }

A VCF header.

Implementations

impl Header

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();

pub fn file_format(&self) -> FileFormat

Returns the file format (fileformat) of the VCF.

fileformat is a reqiured 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());

pub fn infos(&self) -> &IndexMap<Key, Info, RandomState>

Returns a map of information records (INFO).

Examples

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

let header = vcf::Header::builder()
    .add_info(Info::from(Key::SamplesWithDataCount))
    .build();

let infos = header.infos();
assert_eq!(infos.len(), 1);
assert_eq!(infos[0].id(), &Key::SamplesWithDataCount);

pub fn filters(&self) -> &IndexMap<String, Filter, RandomState>

Returns a map of filter records (FILTER).

Examples

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

let header = vcf::Header::builder()
    .add_filter(Filter::new("q10", "Quality below 10"))
    .build();

let filters = header.filters();
assert_eq!(filters.len(), 1);
assert_eq!(filters[0].id(), "q10");

pub fn formats(&self) -> &IndexMap<Key, Format, RandomState>

Returns a list of genotype format records (FORMAT).

Examples

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

let header = vcf::Header::builder()
    .add_format(Format::from(Key::Genotype))
    .build();

let formats = header.formats();
assert_eq!(formats.len(), 1);
assert_eq!(formats[0].id(), &Key::Genotype);

pub fn alternative_alleles(
    &self
) -> &IndexMap<Symbol, AlternativeAllele, RandomState>

Returns a map of symbolic alternate alleles (ALT).

Examples

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

let header = vcf::Header::builder()
    .add_alternative_allele(AlternativeAllele::new(
        Symbol::StructuralVariant(StructuralVariant::from(Type::Deletion)),
        "Deletion",
    ))
    .build();

let alternative_alleles = header.alternative_alleles();
assert_eq!(alternative_alleles.len(), 1);
assert_eq!(
    alternative_alleles[0].id(),
    &Symbol::StructuralVariant(StructuralVariant::from(Type::Deletion))
);

pub fn assembly(&self) -> Option<&str>

Returns a URI to the breakpoint assemblies (assembly) referenced in records.

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 contigs(&self) -> &IndexMap<String, Contig, RandomState>

Returns a map of contig records (contig).

Examples

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

let header = vcf::Header::builder()
    .add_contig(Contig::new("sq0"))
    .build();

let contigs = header.contigs();
assert_eq!(contigs.len(), 1);
assert_eq!(contigs[0], Contig::new("sq0"));

pub fn meta(&self) -> &IndexMap<String, Meta, RandomState>

Returns a map of meta records (META).

Examples

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

let meta = Meta::new(
    String::from("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 samples(&self) -> &IndexMap<String, Sample, RandomState>

Returns a map of sample records (SAMPLE).

Examples

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

let sample = Sample::new(String::from("sample0"), Default::default());

let header = vcf::Header::builder()
    .add_sample(sample.clone())
    .build();

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

pub fn pedigrees(&self) -> &IndexMap<String, Pedigree, RandomState>

Returns a map of pedigree records (PEDIGREE).

Examples

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

let pedigree = Pedigree::new(
    String::from("cid"),
    vec![
        (String::from("Father"), String::from("fid")),
        (String::from("Mother"), String::from("mid")),
    ]
    .into_iter()
    .collect(),
);

let header = vcf::Header::builder()
    .add_pedigree(pedigree.clone())
    .build();

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

pub fn pedigree_db(&self) -> Option<&str>

Returns a URI to the relationships between genomes (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 sample_names(&self) -> &IndexSet<String, RandomState>

Returns a list 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<_> = vec![String::from("sample0"), String::from("sample1")]
    .into_iter()
    .collect();

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

pub fn get(&self, key: &str) -> Option<&[Record]>

Returns a header record with the given key.

This includes all records other than fileformat, INFO, FILTER, FORMAT, ALT, assembly, contig, META, SAMPLE, and pedigreeDB.

Examples

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

let record = Record::new(
    Key::Other(String::from("fileDate")),
    Value::String(String::from("20200709")),
);

let header = vcf::Header::builder().insert(record.clone()).build();

assert_eq!(header.get("fileDate"), Some(&[record][..]));
assert_eq!(header.get("reference"), None);

pub fn insert(&mut self, record: Record)

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

Examples

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

let record = Record::new(
    Key::Other(String::from("fileDate")),
    Value::String(String::from("20200709")),
);

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

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

header.insert(record.clone());

assert_eq!(header.get("fileDate"), Some(&[record][..]));

Trait Implementations

impl Clone for Header

pub fn clone(&self) -> Header

Returns a copy of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for Header

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

Formats the value using the given formatter.

impl Default for Header

pub fn default() -> Header

Returns the “default value” for a type.

impl Display for Header

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

Formats the value using the given formatter.

impl<'_> From<&'_ Header> for StringMap

pub fn from(header: &Header) -> StringMap

Performs the conversion.

impl FromStr for Header

type Err = ParseError

The associated error which can be returned from parsing.

pub fn from_str(s: &str) -> Result<Header, <Header as FromStr>::Err>

Parses a string s to return a value of this type.

impl PartialEq<Header> for Header

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

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

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

This method tests for !=.

impl Eq for Header

impl StructuralEq for Header

impl StructuralPartialEq for Header