Struct noodles::bam::bai::index::Index

pub struct Index { /* fields omitted */ }

A BAM index.

Implementations

impl Index

pub fn builder() -> Builder

Creates a BAM index builder.

Examples

use noodles_bam::bai;
let builder = bai::Index::builder();

pub fn new(
    reference_sequences: Vec<ReferenceSequence, Global>,
    n_no_coor: Option<u64>
) -> Index

Creates a BAM index.

Examples

use noodles_bam::bai;
let index = bai::Index::new(Vec::new(), None);

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

👎 Deprecated since 0.2.0:

Use unplaced_unmapped_record_count instead.

Returns the number of unplaced unmapped reads in the associated BAM file.

An unplaced unmapped read is a read that is has neither a reference sequence ID nor position set.

Examples

use noodles_bam::bai;

let index = bai::Index::default();
assert_eq!(index.unplaced_unmapped_read_count(), None);

let index = bai::Index::new(Vec::new(), Some(13));
assert_eq!(index.unplaced_unmapped_read_count(), Some(13));

Trait Implementations

impl BinningIndex<ReferenceSequence> for Index

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

Returns a list of indexed reference sequences.

This list is parallel to the reference sequences defined in the associated BAM file.

Examples

use noodles_bam::bai;
use noodles_csi::BinningIndex;
let index = bai::Index::default();
assert!(index.reference_sequences().is_empty());

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

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

An unplaced, unmapped record is one that is has neither a reference sequence ID nor position set.

Examples

use noodles_bam::bai;
use noodles_csi::BinningIndex;
let index = bai::Index::default();
assert!(index.unplaced_unmapped_record_count().is_none());

pub fn query<B>(
    &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.

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 Clone for Index

pub fn clone(&self) -> Index

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Debug for Index

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

Formats the value using the given formatter.

impl Default for Index

pub fn default() -> Index

Returns the “default value” for a type.

impl PartialEq<Index> for Index

pub fn eq(&self, other: &Index) -> bool

This method tests for self and other values to be equal, and is used by ==.

pub fn ne(&self, other: &Index) -> bool

This method tests for !=.

impl Eq for Index

impl StructuralEq for Index

impl StructuralPartialEq for Index