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

pub struct ReferenceSequence { /* fields omitted */ }

Expand description

A tabix index reference sequence.

Implementations

[src]

impl ReferenceSequence

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

Creates a tabix index reference sequence.

Examples

use noodles_tabix::index::ReferenceSequence;
let reference_sequence = ReferenceSequence::new(Vec::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 (bin 37450). Use Self::metadata instead.

Examples

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

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

Returns the list of 16 kbp intervals that make up the linear index.

Examples

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

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

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

The interval values are 1-based.

Examples

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

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pub fn min_offset(&self, start: i32) -> VirtualPosition

Finds in minimum start offset in the linear index for a given start position.

start is 1-based.

Examples

use noodles_bgzf as bgzf;
use noodles_tabix::index::ReferenceSequence;
let reference_sequence = ReferenceSequence::new(Vec::new(), Vec::new(), None);
assert_eq!(reference_sequence.min_offset(13), bgzf::VirtualPosition::from(0));

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::BinningIndex;
use noodles_tabix as tabix;
let index = tabix::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::BinningIndex;
use noodles_tabix as tabix;
let index = tabix::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.

Metadata is parsed from the optional pseudo-bin 37450.

Examples

use noodles_bgzf::VirtualPosition;
use noodles_csi::{index::reference_sequence::Metadata, BinningIndexReferenceSequence};
use noodles_tabix::index::ReferenceSequence;

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

let reference_sequence = ReferenceSequence::new(
    Vec::new(),
    Vec::new(),
    Some(Metadata::new(VirtualPosition::from(610), 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::BinningIndexReferenceSequence;
use noodles_tabix::index::ReferenceSequence;

let reference_sequence = ReferenceSequence::default();
assert!(reference_sequence.first_record_in_last_linear_bin_start_position().is_none());

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