Struct noodles_bcf::record::Info

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pub struct Info { /* private fields */ }

Expand description

BCF record info.

Implementations

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impl Info

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pub fn try_into_vcf_record_info(
 &self,
 header: &Header,
 string_string_map: &StringStringMap
) -> Result<Info>

Converts BCF record info to VCF record info.

Examples

use noodles_bcf as bcf;
use noodles_vcf as vcf;

let bcf_info = bcf::record::Info::default();
let header = vcf::Header::default();
let string_maps = bcf::header::StringMaps::default();

let vcf_info = bcf_info.try_into_vcf_record_info(&header, string_maps.strings())?;
assert!(vcf_info.is_empty());

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pub fn new(buf: Vec<u8>, field_count: usize) -> Self

Creates an info map by wrapping the given buffer.

Examples

use noodles_bcf::record::Info;

let data = vec![
    0x11, 0x01, 0x11, 0x05, // AC=5
    0x11, 0x02, 0x11, 0x08, // DP=8
];

let info = Info::new(data, 2);

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pub fn len(&self) -> usize

Returns the number of info fields.

Examples

use noodles_bcf::record::Info;
let info = Info::default();
assert_eq!(info.len(), 0);

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pub fn is_empty(&self) -> bool

Returns whether there are any info fields.

Examples

use noodles_bcf::record::Info;
let info = Info::default();
assert!(info.is_empty());

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pub fn clear(&mut self)

Removes all fields from the info map.

This does not affect the capacity of the map.

Examples

use noodles_bcf::record::Info;
let mut info = Info::default();
info.clear();
assert!(info.is_empty());

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pub fn get(
 &self,
 header: &Header,
 string_string_map: &StringStringMap,
 key: &Key
) -> Option<Result<Field>>

Returns the field with the given key.

Examples

use noodles_bcf::{header::StringMaps, record::Info};
use noodles_vcf::{self as vcf, record::info::{field::{Key, Value}, Field}, Header};

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

let string_maps = StringMaps::from(&header);

let data = vec![
    0x11, 0x01, 0x11, 0x05, // AC=5
    0x11, 0x02, 0x11, 0x08, // DP=8
];

let info = Info::new(data, 2);

assert_eq!(
    info.get(&header, string_maps.strings(), &Key::AlleleCount).transpose()?,
    Some(Field::new(Key::AlleleCount, Some(Value::Integer(5))))
);

assert!(info.get(&header, string_maps.strings(), &Key::AncestralAllele).is_none());

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pub fn values<'a>(
 &'a self,
 header: &'a Header,
 string_string_map: &'a StringStringMap
) -> impl Iterator<Item = Result<Field>> + 'a

Returns an iterator over all info fields.

Examples

use noodles_bcf::{header::StringMaps, record::Info};
use noodles_vcf::{self as vcf, record::info::{field::{Key, Value}, Field}, Header};

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

let string_maps = StringMaps::from(&header);

let data = vec![
    0x11, 0x01, 0x11, 0x05, // AC=5
    0x11, 0x02, 0x11, 0x08, // DP=8
];

let info = Info::new(data, 2);
let mut fields = info.values(&header, string_maps.strings());

assert_eq!(
    fields.next().transpose()?,
    Some(Field::new(Key::AlleleCount, Some(Value::Integer(5))))
);

assert_eq!(
    fields.next().transpose()?,
    Some(Field::new(Key::TotalDepth, Some(Value::Integer(8))))
);

assert!(fields.next().is_none());