Struct Indexer

pub struct Indexer<I> { /* private fields */ }

A binning index indexer.

Implementations

impl<I> Indexer<I>

where I: Index + Default,

pub fn new(min_shift: u8, depth: u8) -> Self

Creates a binning index indexer.

Examples

use noodles_csi::binning_index::{index::reference_sequence::index::BinnedIndex, Indexer};
let indexer = Indexer::<BinnedIndex>::new(14, 5);

pub fn set_header(self, header: Header) -> Self

Sets a tabix header.

Examples

use noodles_csi::binning_index::{
    index::{reference_sequence::index::BinnedIndex, Header},
    Indexer,
};

let header = Header::default();
let indexer = Indexer::<BinnedIndex>::new(14, 5).set_header(header);

pub fn add_record( &mut self, alignment_context: Option<(usize, Position, Position, bool)>, chunk: Chunk, ) -> Result<()>

Adds a record.

Examples

use noodles_bgzf as bgzf;
use noodles_core::Position;
use noodles_csi::binning_index::{
    index::reference_sequence::{bin::Chunk, index::BinnedIndex},
    Indexer,
};

let mut indexer = Indexer::<BinnedIndex>::new(14, 5);

let reference_sequence_id = 0;
let start = Position::try_from(8)?;
let end = Position::try_from(13)?;
let is_mapped = true;
let chunk = Chunk::new(
    bgzf::VirtualPosition::from(144),
    bgzf::VirtualPosition::from(233),
);

indexer.add_record(Some((reference_sequence_id, start, end, is_mapped)), chunk)?;

pub fn build(self, reference_sequence_count: usize) -> Index<I>

Builds a binning index.

Examples

use noodles_csi::binning_index::{index::reference_sequence::index::BinnedIndex, Indexer};
let indexer = Indexer::<BinnedIndex>::new(14, 5);
let index = indexer.build(0);

Trait Implementations

impl<I: Debug> Debug for Indexer<I>

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

Formats the value using the given formatter.

impl<I> Default for Indexer<I>

where I: Index + Default,

fn default() -> Self

Returns the “default value” for a type.