Struct noodles_tabix::index::Index

pub struct Index { /* fields omitted */ }

A tabix index.

Implementations

impl Index

pub fn builder() -> Builder

Returns a builder to create an index from each of its fields.

Examples

use noodles_tabix as tabix;
let builder = tabix::Index::builder();

pub fn indexer() -> Indexer

Returns an indexer to create an index from records.

pub fn header(&self) -> &Header

Returns the header.

Examples

use noodles_tabix as tabix;
let header = tabix::index::Header::default();
let index = tabix::Index::builder().set_header(header.clone()).build();
assert_eq!(index.header(), &header);

pub fn reference_sequence_names(&self) -> &ReferenceSequenceNames

Returns the reference sequence names.

Examples

use noodles_tabix::{self as tabix, index::ReferenceSequenceNames};

let reference_sequence_names: ReferenceSequenceNames = vec![String::from("sq0")]
    .into_iter()
    .collect();

let index = tabix::Index::builder()
    .set_reference_sequence_names(reference_sequence_names.clone())
    .build();

assert_eq!(index.reference_sequence_names(), &reference_sequence_names);

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

👎 Deprecated since 0.2.0:

Use unplaced_unmapped_record_count instead.

Returns the number of unmapped records in the associated file.

Examples

use noodles_tabix as tabix;

let index = tabix::Index::builder()
    .set_unmapped_read_count(21)
    .build();

assert_eq!(index.unmapped_read_count(), Some(21));

Trait Implementations

impl BinningIndex<ReferenceSequence> for Index

fn reference_sequences(&self) -> &[ReferenceSequence]

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());

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());

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

Returns the chunks that overlap with the given region.

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.

impl Debug for Index

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

Formats the value using the given formatter.

impl Default for Index

fn default() -> Self

Returns the “default value” for a type.