Struct noodles::vcf::header::Builder

pub struct Builder { /* fields omitted */ }

A VCF header builder.

Implementations

impl Builder

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

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: Info) -> Builder

Adds an information record (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 add_filter(self, filter: Filter) -> Builder

Adds a filter record (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 add_format(self, format: Format) -> Builder

Adds a genotype format record (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 add_alternative_allele(
    self,
    alternative_allele: AlternativeAllele
) -> Builder

Adds an alternative allele record (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 set_assembly<I>(self, assembly: I) -> Builder where
    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: Contig) -> Builder

Adds a contig record (contig).

Examples

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

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

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

pub fn add_meta(self, meta: Meta) -> Builder

Adds a meta record (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 add_sample(self, sample: Sample) -> Builder

Adds a sample record (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 add_pedigree(self, pedigree: Pedigree) -> Builder

Adds a pedigree record (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 set_pedigree_db<I>(self, pedigree_db: I) -> Builder where
    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: IndexSet<String, RandomState>
) -> Builder

Sets sample names.

Examples

use indexmap::IndexSet;
use noodles_vcf as vcf;

let sample_names: IndexSet<_> = vec![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) -> Builder where
    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<_> = vec![String::from("sample0"), String::from("sample1")]
    .into_iter()
    .collect();

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

pub fn insert(self, record: Record) -> Builder

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

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

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

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

Formats the value using the given formatter.

impl Default for Builder

pub fn default() -> Builder

Returns the “default value” for a type.