Struct noodles_vcf::header::format::Format

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pub struct Format { /* private fields */ }

Expand description

A VCF header genotype format record (FORMAT).

Implementations

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impl Format

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pub fn try_from_record_file_format(
record: Record,
file_format: FileFormat
) -> Result<Self, TryFromRecordError>

Converts a generic VCF header record to a VCF header format record.

Examples

use noodles_vcf::{
    header::{format::Type, record::{Key, Value}, FileFormat, Format, Number, Record},
    record::genotypes::genotype,
};

let record = Record::new(
    Key::Format,
    Value::Struct(vec![
        (String::from("ID"), String::from("GT")),
        (String::from("Number"), String::from("1")),
        (String::from("Type"), String::from("String")),
        (String::from("Description"), String::from("Genotype")),
    ]),
);

assert_eq!(
    Format::try_from_record_file_format(record, FileFormat::new(4, 3)),
    Ok(Format::new(
        genotype::field::Key::Genotype,
        Number::Count(1),
        Type::String,
        String::from("Genotype"),
    ))
);

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pub fn new(id: Key, number: Number, ty: Type, description: String) -> Self

Creates a VCF header genotype format record.

Examples

use noodles_vcf::{
    header::{format::Type, Format, Number},
    record::genotypes::genotype::field::Key,
};

let format = Format::new(
    Key::Genotype,
    Number::Count(1),
    Type::String,
    String::from("Genotype"),
);

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pub fn id(&self) -> &Key

Returns the genotype field key.

Examples

use noodles_vcf::{header::Format, record::genotypes::genotype::field::Key};
let format = Format::from(Key::Genotype);
assert_eq!(format.id(), &Key::Genotype);

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pub fn number(&self) -> Number

Returns the cardinality of the genotype field value.

Examples

use noodles_vcf::{header::{Format, Number}, record::genotypes::genotype::field::Key};
let format = Format::from(Key::Genotype);
assert_eq!(format.number(), Number::Count(1));

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pub fn ty(&self) -> Type

Returns the type of the genotype field value.

Examples

use noodles_vcf::{header::{format::Type, Format}, record::genotypes::genotype::field::Key};
let format = Format::from(Key::Genotype);
assert_eq!(format.ty(), Type::String);

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pub fn description(&self) -> &str

Returns the description of the genotype field.

Examples

use noodles_vcf::{header::Format, record::genotypes::genotype::field::Key};
let format = Format::from(Key::Genotype);
assert_eq!(format.description(), "Genotype");

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pub fn idx(&self) -> Option<usize>

Returns the index of the ID in the dictionary of strings.

This is typically used in BCF.

Examples

use noodles_vcf::{header::Format, record::genotypes::genotype::field::Key};
let format = Format::from(Key::Genotype);
assert!(format.idx().is_none());

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

Returns the extra fields in the record.

This includes fields other than ID, Number, Type, Description, and IDX.

Examples

use noodles_vcf::{header::Format, record::genotypes::genotype::field::Key};
let format = Format::from(Key::Genotype);
assert!(format.fields().is_empty());