Struct noodles_vcf::header::Header

pub struct Header { /* private fields */ }

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 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());

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);

pub fn infos(&self) -> &Infos

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 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::Info, record::info::field::Key};

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

let info = Info::from(Key::SamplesWithDataCount);
header.infos_mut().insert(info.id().clone(), info);

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

pub fn filters(&self) -> &Filters

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 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::Filter};

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

let filter = Filter::new("q10", "Quality below 10");
header.filters_mut().insert(filter.id().into(), filter);

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

pub fn formats(&self) -> &Formats

Returns a list of genotype format records (FORMAT).

Examples

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

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

let format = Format::from(Key::Genotype);
header.formats_mut().insert(format.id().clone(), format);

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

pub fn alternative_alleles(&self) -> &AlternativeAlleles

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 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::AlternativeAllele,
    record::alternate_bases::allele::{
        symbol::{structural_variant::Type, StructuralVariant},
        Symbol,
    },
};

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

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

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

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 assembly_mut(&mut self) -> &mut Option<String>

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

Examples

use noodles_vcf as vcf;
let mut header = vcf::Header::default();
*header.assembly_mut() = Some(String::from("file:///assemblies.fasta"));
assert_eq!(header.assembly(), Some("file:///assemblies.fasta"));

pub fn contigs(&self) -> &Contigs

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 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::Contig};

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

let contig = Contig::new("sq0");
header.contigs_mut().insert(contig.id().into(), contig.clone());

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

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

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 meta_mut(&mut self) -> &mut IndexMap<String, Meta>

Returns a mutable reference to a map of meta records (META).

Examples

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

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

let meta = Meta::new(
    String::from("Assay"),
    vec![String::from("WholeGenome"), String::from("Exome")],
);
header.meta_mut().insert(meta.id().into(), meta.clone());

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

pub fn samples(&self) -> &Samples

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 samples_mut(&mut self) -> &mut Samples

Returns a mutable reference to a map of sample records (SAMPLE).

Examples

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

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

let sample = Sample::new(String::from("sample0"), Default::default());
header.samples_mut().insert(sample.id().into(), sample.clone());

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

pub fn pedigrees(&self) -> &Pedigrees

Returns a map of pedigree records (PEDIGREE).

Examples

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

let pedigree = Pedigree::new(
    String::from("cid"),
    [
        (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 pedigrees_mut(&mut self) -> &mut Pedigrees

Returns a mutable reference to a map of pedigree records (PEDIGREE).

Examples

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

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

let pedigree = Pedigree::new(
    String::from("cid"),
    [
        (String::from("Father"), String::from("fid")),
        (String::from("Mother"), String::from("mid")),
    ]
    .into_iter()
    .collect(),
);
header.pedigrees_mut().insert(pedigree.id().into(), pedigree.clone());

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 pedigree_db_mut(&mut self) -> &mut Option<String>

Returns a mutable reference to a URI to the relationships between genomes (pedigreeDB).

Examples

use noodles_vcf as vcf;
let mut header = vcf::Header::default();
*header.pedigree_db_mut() = Some(String::from("file:///pedigree.db"));
assert_eq!(header.pedigree_db(), Some("file:///pedigree.db"));

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);

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);

pub fn records(&self) -> &Records

Returns a map of the unstructured header records.

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.records().first(),
    Some((&String::from("fileDate"), &vec![record])),
);

pub fn records_mut(&mut self) -> &mut Records

Returns a mutable reference to a map of the unstructured header records.

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

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

Examples

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

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

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

header.records_mut().insert(String::from("fileDate"), vec![record.clone()]);

assert_eq!(
    header.records().first(),
    Some((&String::from("fileDate"), &vec![record])),
);

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

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

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

Formats the value using the given formatter.

impl Default for Header

fn default() -> Self

Returns the “default value” for a type.

impl Display for Header

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

Formats the value using the given formatter.

impl FromStr for Header

type Err = ParseError

The associated error which can be returned from parsing.

fn from_str(s: &str) -> Result<Self, Self::Err>

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

impl PartialEq<Header> for Header

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

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

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

This method tests for !=.

impl Eq for Header

impl StructuralEq for Header

impl StructuralPartialEq for Header