Struct noodles::csi::index::ReferenceSequence[−][src]

pub struct ReferenceSequence { /* fields omitted */ }

Expand description

A CSI reference sequence.

Implementations

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impl ReferenceSequence

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pub fn new(
bins: Vec<Bin, Global>,
metadata: Option<Metadata>
) -> ReferenceSequence

Creates a CSI reference sequence.

Examples

use noodles_csi::index::ReferenceSequence;
let reference_sequence = ReferenceSequence::new(Vec::new(), None);

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pub fn bins(&self) -> &[Bin ]ⓘ
Notable traits for &'_ [u8 ]
`impl<'_> Read for &'_ [u8]impl<'_> Write for &'_ mut [u8]`

Returns the list of bins in the reference sequence.

This list does not include the metadata pseudo-bin. Use Self::metadata instead.

Examples

use noodles_csi::index::ReferenceSequence;
let reference_sequence = ReferenceSequence::new(Vec::new(), None);
assert!(reference_sequence.bins().is_empty());

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pub fn query(
 &self,
 min_shift: i32,
 depth: i32,
 interval: B
) -> Result<Vec<&Bin, Global>, QueryError> where
 B: RangeBounds<i64>,

Returns a list of bins in this reference sequence that intersects the given range.

The interval values are 1-based.

Examples

use noodles_csi::index::ReferenceSequence;
let reference_sequence = ReferenceSequence::new(Vec::new(), None);
let query_bins = reference_sequence.query(14, 5, 8..=13)?;
assert!(query_bins.is_empty());

Trait Implementations

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impl BinningIndex<ReferenceSequence> for Index

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pub fn reference_sequences(&self) -> &[ReferenceSequence ]ⓘ
Notable traits for &'_ [u8 ]
`impl<'_> Read for &'_ [u8]impl<'_> Write for &'_ mut [u8]`

Returns a list of indexed reference sequences.

Examples

use noodles_csi::{self as csi, BinningIndex};
let index = csi::Index::default();
assert!(index.reference_sequences().is_empty());

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pub fn unplaced_unmapped_record_count(&self) -> Option<u64>

Returns the number of unplaced, unmapped records in the associated file.

Examples

use noodles_csi::{self as csi, BinningIndex};
let index = csi::Index::default();
assert!(index.unplaced_unmapped_record_count().is_none());

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pub fn query(
 &self,
 reference_sequence_id: usize,
 interval: B
) -> Result<Vec<Chunk, Global>, Error> where
 B: RangeBounds<i32> + Clone,

Returns the chunks that overlap with the given region.

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fn first_record_in_last_linear_bin_start_position(
&self
) -> Option<VirtualPosition>

Returns the start position of the first record in the last linear bin. Read more

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impl BinningIndexReferenceSequence for ReferenceSequence

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pub fn metadata(&self) -> Option<&Metadata>

Returns the optional metadata for the reference sequence.

Examples

use noodles_bgzf as bgzf;
use noodles_csi::{
    index::{reference_sequence::Metadata, ReferenceSequence},
    BinningIndexReferenceSequence,
};

let reference_sequence = ReferenceSequence::new(Vec::new(), Some(Metadata::new(
    bgzf::VirtualPosition::from(610),
    bgzf::VirtualPosition::from(1597),
    55,
    0,
)));

assert!(reference_sequence.metadata().is_some());

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pub fn first_record_in_last_linear_bin_start_position(
&self
) -> Option<VirtualPosition>

Returns the start position of the first record in the last linear bin.

Examples

use noodles_bgzf as bgzf;
use noodles_csi::{
    index::{reference_sequence::Bin, ReferenceSequence},
    BinningIndexReferenceSequence,
};

let reference_sequence = ReferenceSequence::new(Vec::new(), None);
assert!(reference_sequence.first_record_in_last_linear_bin_start_position().is_none());

let bins = vec![
    Bin::new(0, bgzf::VirtualPosition::from(8), Vec::new()),
    Bin::new(1, bgzf::VirtualPosition::from(13), Vec::new()),
];
let reference_sequence = ReferenceSequence::new(bins, None);
assert_eq!(
    reference_sequence.first_record_in_last_linear_bin_start_position(),
    Some(bgzf::VirtualPosition::from(13))
);