Struct RecordBuf

pub struct RecordBuf { /* private fields */ }

A variant record buffer.

Implementations

impl RecordBuf

pub fn try_from_variant_record<R>(header: &Header, record: &R) -> Result<Self>

where R: Record,

Converts a variant record to a buffer.

impl RecordBuf

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::variant::RecordBuf::builder();

pub fn reference_sequence_name(&self) -> &str

Returns the reference sequence name.

Examples

use noodles_vcf as vcf;

let record = vcf::variant::RecordBuf::builder()
    .set_reference_sequence_name("sq0")
    .build();

assert_eq!(record.reference_sequence_name(), "sq0");

pub fn reference_sequence_name_mut(&mut self) -> &mut String

Returns a mutable reference to the reference sequence name.

Examples

use noodles_vcf as vcf;

let mut record = vcf::variant::RecordBuf::builder()
    .set_reference_sequence_name("sq0")
    .build();

*record.reference_sequence_name_mut() = String::from("sq1");

assert_eq!(record.reference_sequence_name(), "sq1");

pub fn variant_start(&self) -> Option<Position>

Returns the variant start position.

This position is 1-based, inclusive. If the record represents the start of a telomeric breakend, this returns None.

Examples

use noodles_core::Position;
use noodles_vcf as vcf;

let record = vcf::variant::RecordBuf::builder()
    .set_variant_start(Position::MIN)
    .build();

assert_eq!(record.variant_start(), Some(Position::MIN));

pub fn variant_start_mut(&mut self) -> &mut Option<Position>

Returns a mutable reference to the variant start position.

This position is 1-based, inclusive. If the record represents the start of a telomeric breakend, this returns None.

Examples

use noodles_core::Position;
use noodles_vcf as vcf;

let mut record = vcf::variant::RecordBuf::default();
*record.variant_start_mut() = Some(Position::MIN);
assert_eq!(record.variant_start(), Some(Position::MIN));

pub fn ids(&self) -> &Ids

Returns a list of IDs of the record.

Examples

use noodles_vcf::{self as vcf, variant::record_buf::Ids};

let ids: Ids = [String::from("nd0")].into_iter().collect();

let record = vcf::variant::RecordBuf::builder()
    .set_ids(ids.clone())
    .build();

assert_eq!(record.ids(), &ids);

pub fn ids_mut(&mut self) -> &mut Ids

Returns a mutable reference to the IDs.

Examples

use noodles_vcf::{self as vcf, variant::record_buf::Ids};

let mut record = vcf::variant::RecordBuf::default();

let ids: Ids = [String::from("nd0")].into_iter().collect();
*record.ids_mut() = ids.clone();

assert_eq!(record.ids(), &ids);

pub fn reference_bases(&self) -> &str

Returns the reference bases of the record.

Examples

use noodles_vcf as vcf;

let record = vcf::variant::RecordBuf::builder()
    .set_reference_bases("A")
    .build();

assert_eq!(record.reference_bases(), "A");

pub fn reference_bases_mut(&mut self) -> &mut String

Returns a mutable reference to the reference bases of the record.

Examples

use noodles_vcf as vcf;

let mut record = vcf::variant::RecordBuf::builder()
    .set_reference_bases("A")
    .build();

*record.reference_bases_mut() = String::from("T");

assert_eq!(record.reference_bases(), "T");

pub fn alternate_bases(&self) -> &AlternateBases

Returns the alternate bases of the record.

Examples

use noodles_vcf::{self as vcf, variant::record_buf::AlternateBases};

let alternate_bases = AlternateBases::from(vec![String::from("C")]);

let record = vcf::variant::RecordBuf::builder()
    .set_alternate_bases(alternate_bases.clone())
    .build();

assert_eq!(record.alternate_bases(), &alternate_bases);

pub fn alternate_bases_mut(&mut self) -> &mut AlternateBases

Returns a mutable reference to the alternate bases of the record.

Examples

use noodles_vcf::{self as vcf, variant::record_buf::AlternateBases};

let mut record = vcf::variant::RecordBuf::builder()
    .set_reference_bases("A")
    .build();

let alternate_bases = AlternateBases::from(vec![String::from("C")]);
*record.alternate_bases_mut() = alternate_bases.clone();

assert_eq!(record.alternate_bases(), &alternate_bases);

pub fn quality_score(&self) -> Option<f32>

Returns the quality score of the record.

Examples

use noodles_vcf as vcf;

let record = vcf::variant::RecordBuf::builder()
    .set_quality_score(13.0)
    .build();

assert_eq!(record.quality_score(), Some(13.0));

pub fn quality_score_mut(&mut self) -> &mut Option<f32>

Returns a mutable reference to the quality score.

Examples

use noodles_vcf as vcf;

let mut record = vcf::variant::RecordBuf::default();
*record.quality_score_mut() = Some(13.0);
assert_eq!(record.quality_score(), Some(13.0));

pub fn filters(&self) -> &Filters

Returns the filters of the record.

The filters can either be pass (PASS), a list of filter names that caused the record to fail, (e.g., q10), or missing (.).

Examples

use noodles_vcf::{self as vcf, variant::record_buf::Filters};

let record = vcf::variant::RecordBuf::builder()
    .set_filters(Filters::pass())
    .build();

assert!(record.filters().is_pass());

pub fn filters_mut(&mut self) -> &mut Filters

Returns a mutable reference to the filters.

Examples

use noodles_vcf::{self as vcf, variant::record_buf::Filters};

let mut record = vcf::variant::RecordBuf::default();
*record.filters_mut() = Filters::pass();
assert!(record.filters().is_pass());

pub fn info(&self) -> &Info

Returns the addition information of the record.

Examples

use noodles_vcf::{
    self as vcf,
    variant::{
        record::info::field::key,
        record_buf::{info::field::Value, Info},
    },
};

let info: Info = [
    (String::from(key::SAMPLES_WITH_DATA_COUNT), Some(Value::from(3))),
    (String::from(key::ALLELE_FREQUENCIES), Some(Value::from(vec![Some(0.5)]))),
]
.into_iter()
.collect();

let record = vcf::variant::RecordBuf::builder()
    .set_info(info.clone())
    .build();

assert_eq!(record.info(), &info);

pub fn info_mut(&mut self) -> &mut Info

Returns a mutable reference to the additional info fields.

Examples

use noodles_vcf::{
    self as vcf,
    variant::{
        record::info::field::key,
        record_buf::{info::field::Value, Info},
    }
};

let info: Info = [
    (String::from(key::SAMPLES_WITH_DATA_COUNT), Some(Value::from(3))),
    (String::from(key::ALLELE_FREQUENCIES), Some(Value::from(vec![Some(0.5)]))),
]
.into_iter()
.collect();

let mut record = vcf::variant::RecordBuf::builder()
    .set_info(info)
    .build();

record.info_mut().insert(String::from(key::TOTAL_DEPTH), Some(Value::Integer(13)));

let expected = [
    (String::from(key::SAMPLES_WITH_DATA_COUNT), Some(Value::Integer(3))),
    (String::from(key::ALLELE_FREQUENCIES), Some(Value::from(vec![Some(0.5)]))),
    (String::from(key::TOTAL_DEPTH), Some(Value::Integer(13))),
]
.into_iter()
.collect();

assert_eq!(record.info(), &expected);

pub fn format(&self) -> &Keys

Returns the format of the genotypes of the record.

Examples

use noodles_vcf::{
    self as vcf,
    variant::{
        record::samples::keys::key,
        record_buf::{samples::{sample::Value, Keys}, Samples},
    },
};

let keys: Keys = [
    String::from(key::GENOTYPE),
    String::from(key::CONDITIONAL_GENOTYPE_QUALITY),
].into_iter().collect();
let samples = Samples::new(
    keys.clone(),
    vec![vec![Some(Value::from("0|0")), Some(Value::from(13))]],
);

let record = vcf::variant::RecordBuf::builder()
    .set_samples(samples)
    .build();

assert_eq!(record.format(), &keys);

pub fn samples(&self) -> &Samples

Returns the genotypes of the record.

Examples

use noodles_vcf::{
    self as vcf,
    variant::{
        record::samples::keys::key,
        record_buf::{samples::sample::Value, Samples},
    },
};

let keys = [
    String::from(key::GENOTYPE),
    String::from(key::CONDITIONAL_GENOTYPE_QUALITY),
].into_iter().collect();
let samples = Samples::new(
    keys,
    vec![vec![Some(Value::from("0|0")), Some(Value::from(13))]],
);

let record = vcf::variant::RecordBuf::builder()
    .set_samples(samples.clone())
    .build();

assert_eq!(record.samples(), &samples);

pub fn samples_mut(&mut self) -> &mut Samples

Returns a mutable reference to the genotypes of the record.

Examples

use noodles_vcf::{
    self as vcf,
    variant::{
        record::samples::keys::key,
        record_buf::{samples::sample::Value, Samples},
    },
};

let mut record = vcf::variant::RecordBuf::default();

let keys = [
    String::from(key::GENOTYPE),
    String::from(key::CONDITIONAL_GENOTYPE_QUALITY),
].into_iter().collect();
let samples = Samples::new(
    keys,
    vec![vec![Some(Value::from("0|0")), Some(Value::from(13))]],
);

*record.samples_mut() = samples.clone();

assert_eq!(record.samples(), &samples);

Trait Implementations

impl Clone for RecordBuf

fn clone(&self) -> RecordBuf

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Debug for RecordBuf

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

Formats the value using the given formatter.

impl Default for RecordBuf

fn default() -> Self

Returns the “default value” for a type.

impl PartialEq for RecordBuf

fn eq(&self, other: &RecordBuf) -> 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 Record for RecordBuf

fn reference_sequence_name<'a, 'h: 'a>( &'a self, _: &'h Header, ) -> Result<&'a str>

Returns the reference sequence name.

fn variant_start(&self) -> Option<Result<Position>>

Returns the variant start position.

fn ids(&self) -> Box<dyn Ids + '_>

Returns the IDs.

fn reference_bases(&self) -> Box<dyn ReferenceBases + '_>

Returns the reference bases.

fn alternate_bases(&self) -> Box<dyn AlternateBases + '_>

Returns the alternate bases.

fn quality_score(&self) -> Option<Result<f32>>

Returns the quality scores.

fn filters(&self) -> Box<dyn Filters + '_>

Returns the filters.

fn info(&self) -> Box<dyn Info + '_>

Return the info fields.

fn samples(&self) -> Result<Box<dyn Samples + '_>>

Returns the samples.

fn variant_span(&self, header: &Header) -> Result<usize>

Returns the variant span.

fn variant_end(&self, header: &Header) -> Result<Position>

Returns or calculates the variant end position.

impl StructuralPartialEq for RecordBuf