Struct StringMaps

pub struct StringMaps { /* private fields */ }

An indexed map of VCF strings.

This includes both the dictionary of strings and dictionary of contigs.

Implementations

impl StringMaps

pub fn strings(&self) -> &StringStringMap

Returns an indexed map of VCF strings (FILTER, FORMAT, and INFO).

The filter ID “PASS” is always the first entry in the string string map.

Examples

use noodles_vcf::{
    self as vcf,
    header::{
        record::value::{map::{Contig, Filter, Format, Info}, Map},
        StringMaps,
    },
    variant::record::{info, samples},
};

let header = vcf::Header::builder()
    .add_info(info::field::key::TOTAL_DEPTH, Map::<Info>::from(info::field::key::TOTAL_DEPTH))
    .add_filter("q10", Map::<Filter>::new("Quality below 10"))
    .add_format(samples::keys::key::READ_DEPTH, Map::<Format>::from(samples::keys::key::READ_DEPTH))
    .add_contig("sq0", Map::<Contig>::new())
    .build();

let string_maps = StringMaps::try_from(&header)?;
let string_string_map = string_maps.strings();

assert_eq!(string_string_map.get_index(0), Some("PASS"));
assert_eq!(string_string_map.get_index(1), Some("DP"));
assert_eq!(string_string_map.get_index(2), Some("q10"));
assert!(string_string_map.get_index(3).is_none());

pub fn contigs(&self) -> &ContigStringMap

Returns an indexed map of contig names.

Examples

use noodles_vcf::{
    self as vcf,
    header::{
        record::value::{map::{Contig, Filter, Format, Info}, Map},
        StringMaps,
    },
    variant::record::{info, samples},
};

let header = vcf::Header::builder()
    .add_info(info::field::key::TOTAL_DEPTH, Map::<Info>::from(info::field::key::TOTAL_DEPTH))
    .add_filter("q10", Map::<Filter>::new("Quality below 10"))
    .add_format(samples::keys::key::READ_DEPTH, Map::<Format>::from(samples::keys::key::READ_DEPTH))
    .add_contig("sq0", Map::<Contig>::new())
    .build();

let string_maps = StringMaps::try_from(&header)?;
let contig_string_map = string_maps.contigs();

assert_eq!(contig_string_map.get_index(0), Some("sq0"));
assert!(contig_string_map.get_index(1).is_none());

Trait Implementations

impl Clone for StringMaps

fn clone(&self) -> StringMaps

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Debug for StringMaps

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

Formats the value using the given formatter.

impl Default for StringMaps

fn default() -> Self

Returns the “default value” for a type.

impl FromStr for StringMaps

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 for StringMaps

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

Tests for self and other values to be equal, and is used by ==.

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

Tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl TryFrom<&Header> for StringMaps

type Error = ParseError

The type returned in the event of a conversion error.

fn try_from(header: &Header) -> Result<Self, Self::Error>

Performs the conversion.

impl Eq for StringMaps

impl StructuralPartialEq for StringMaps