Struct Scanner 

pub struct Scanner { /* private fields */ }

A BigWig scanner.

Schema parameters (fields) are declared at construction time. Scan methods accept only column projection, batch size, and limit.

Examples

use oxbow::bbi::scanner::bigwig::Scanner;
let mut fmt_reader = bigtools::BigWigRead::open_file("sample.bigWig").unwrap();
let info = fmt_reader.info();

let scanner = Scanner::new(info.clone(), None).unwrap();
let batches = scanner.scan(fmt_reader, None, None, Some(1000));

Implementations

impl Scanner

pub fn new(info: BBIFileInfo, fields: Option<Vec<String>>) -> Result<Self>

Creates a BigWig scanner from BBI file info and optional field names.

The schema is validated and cached at construction time.

pub fn field_names(&self) -> Vec<String>

Returns the field names.

pub fn schema(&self) -> &ArrowSchema

Returns the Arrow schema.

impl Scanner

pub fn info(&self) -> &BBIFileInfo

Returns the BBI file info.

pub fn chrom_names(&self) -> Vec<String>

Returns the reference sequence names.

pub fn chrom_sizes(&self) -> Vec<(String, u32)>

Returns the reference sequence names and lengths.

pub fn zoom_levels(&self) -> Vec<u32>

Returns the zoom/reduction level resolutions in the BigWig file.

pub fn scan<R: Read + Seek>( &self, fmt_reader: BigWigRead<R>, columns: Option<Vec<String>>, batch_size: Option<usize>, limit: Option<usize>, ) -> Result<impl RecordBatchReader>

Returns an iterator yielding record batches.

pub fn scan_query<R: Read + Seek + Send + 'static>( &self, fmt_reader: BigWigRead<R>, region: Region, columns: Option<Vec<String>>, batch_size: Option<usize>, limit: Option<usize>, ) -> Result<impl RecordBatchReader>

Returns an iterator yielding record batches satisfying a genomic range query.