Struct noodles::bed::Record

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pub struct Record<const N: u8> { /* private fields */ }

Expand description

A BED record.

Implementations§

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impl<const N: u8> Record<N>
where Record<N>: BedN<3>,

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pub fn builder() -> Builder<N>

Creates a BED record builder.

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pub fn reference_sequence_name(&self) -> &str

Returns the reference sequence name (chrom).

§Examples

use noodles_bed as bed;
use noodles_core::Position;

let record = bed::Record::<3>::builder()
    .set_reference_sequence_name("sq0")
    .set_start_position(Position::try_from(8)?)
    .set_end_position(Position::try_from(13)?)
    .build()?;

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

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pub fn start_position(&self) -> Position

Returns the feature start position (chromStart).

§Examples

use noodles_bed as bed;
use noodles_core::Position;

let start_position = Position::try_from(8)?;

let record = bed::Record::<3>::builder()
    .set_reference_sequence_name("sq0")
    .set_start_position(start_position)
    .set_end_position(Position::try_from(13)?)
    .build()?;

assert_eq!(record.start_position(), start_position);

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pub fn end_position(&self) -> Position

Returns the feature end position (chromEnd).

§Examples

use noodles_bed as bed;
use noodles_core::Position;

let end_position = Position::try_from(13)?;

let record = bed::Record::<3>::builder()
    .set_reference_sequence_name("sq0")
    .set_start_position(Position::try_from(8)?)
    .set_end_position(end_position)
    .build()?;

assert_eq!(record.end_position(), end_position);

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pub fn optional_fields(&self) -> &OptionalFields

Returns the list of raw optional fields.

§Examples

use noodles_bed as bed;
use noodles_core::Position;

let record = bed::Record::<3>::builder()
    .set_reference_sequence_name("sq0")
    .set_start_position(Position::try_from(8)?)
    .set_end_position(Position::try_from(13)?)
    .build()?;

assert!(record.optional_fields().is_empty());

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impl<const N: u8> Record<N>
where Record<N>: BedN<4>,

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pub fn name(&self) -> Option<&Name>

Returns the feature name (name).

§Examples

use noodles_bed::{self as bed, record::Name};
use noodles_core::Position;

let name: Name = "ndls1".parse()?;

let record = bed::Record::<4>::builder()
    .set_reference_sequence_name("sq0")
    .set_start_position(Position::try_from(8)?)
    .set_end_position(Position::try_from(13)?)
    .set_name(name.clone())
    .build()?;

assert_eq!(record.name(), Some(&name));

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impl<const N: u8> Record<N>
where Record<N>: BedN<5>,

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pub fn score(&self) -> Option<Score>

Returns the score (score).

§Examples

use noodles_bed::{self as bed, record::Score};
use noodles_core::Position;

let record = bed::Record::<5>::builder()
    .set_reference_sequence_name("sq0")
    .set_start_position(Position::try_from(8)?)
    .set_end_position(Position::try_from(13)?)
    .set_score(Score::try_from(21)?)
    .build()?;

assert_eq!(record.score().map(u16::from), Some(21));

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impl<const N: u8> Record<N>
where Record<N>: BedN<6>,

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pub fn strand(&self) -> Option<Strand>

Returns the feature strand (strand).

§Examples

use noodles_bed::{self as bed, record::Strand};
use noodles_core::Position;

let record = bed::Record::<6>::builder()
    .set_reference_sequence_name("sq0")
    .set_start_position(Position::try_from(8)?)
    .set_end_position(Position::try_from(13)?)
    .set_strand(Strand::Forward)
    .build()?;

assert_eq!(record.strand(), Some(Strand::Forward));

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impl<const N: u8> Record<N>
where Record<N>: BedN<7>,

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pub fn thick_start(&self) -> Position

Returns the thick start position (thickStart).

§Examples

use noodles_bed as bed;
use noodles_core::Position;

let thick_start = Position::try_from(8)?;

let record = bed::Record::<7>::builder()
    .set_reference_sequence_name("sq0")
    .set_start_position(Position::try_from(8)?)
    .set_end_position(Position::try_from(13)?)
    .set_thick_start(thick_start)
    .build()?;

assert_eq!(record.thick_start(), thick_start);

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impl<const N: u8> Record<N>
where Record<N>: BedN<8>,

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pub fn thick_end(&self) -> Position

Returns the thick end position (thickEnd).

§Examples

use noodles_bed as bed;
use noodles_core::Position;

let thick_end = Position::try_from(13)?;

let record = bed::Record::<8>::builder()
    .set_reference_sequence_name("sq0")
    .set_start_position(Position::try_from(8)?)
    .set_end_position(Position::try_from(13)?)
    .set_thick_end(thick_end)
    .build()?;

assert_eq!(record.thick_end(), thick_end);

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impl<const N: u8> Record<N>
where Record<N>: BedN<9>,

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pub fn color(&self) -> Option<Color>

Returns the color (itemRgb).

§Examples

use noodles_bed::{self as bed, record::Color};
use noodles_core::Position;

let thick_end = Position::try_from(13)?;

let record = bed::Record::<9>::builder()
    .set_reference_sequence_name("sq0")
    .set_start_position(Position::try_from(8)?)
    .set_end_position(Position::try_from(13)?)
    .set_color(Color::RED)
    .build()?;

assert_eq!(record.color(), Some(Color::RED));

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impl<const N: u8> Record<N>
where Record<N>: BedN<12>,

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pub fn blocks(&self) -> &[(usize, usize)]

Returns the blocks ([(blockStarts, blockSizes)]).

§Examples

use noodles_bed as bed;
use noodles_core::Position;

let blocks = vec![(0, 2)];

let record = bed::Record::<12>::builder()
    .set_reference_sequence_name("sq0")
    .set_start_position(Position::try_from(8)?)
    .set_end_position(Position::try_from(13)?)
    .set_blocks(blocks.clone())
    .build()?;

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