Struct Scanner 

pub struct Scanner { /* private fields */ }

A GFF scanner.

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

Examples

use oxbow::gxf::scanner::gff::Scanner;
use std::fs::File;
use std::io::BufReader;

let inner = File::open("sample.gff").map(BufReader::new).unwrap();
let mut fmt_reader = noodles::gff::io::Reader::new(inner);

let attr_defs = Scanner::attribute_defs(&mut fmt_reader, Some(1000)).unwrap();
let scanner = Scanner::new(None, None, Some(attr_defs)).unwrap();
let batches = scanner.scan(fmt_reader, None, None, Some(1000));

Implementations

impl Scanner

pub fn new( header: Option<Header>, fields: Option<Vec<String>>, attr_defs: Option<Vec<(String, String)>>, ) -> Result<Self>

Creates a GFF scanner from schema parameters.

The schema is validated and cached at construction time.

pub fn header(&self) -> Option<&Header>

Returns the index header if one was provided.

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

Returns the reference sequence names if an index header was provided.

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

Returns the fixed field names.

pub fn schema(&self) -> &Schema

Returns the Arrow schema.

impl Scanner

pub fn attribute_defs<R: BufRead>( fmt_reader: &mut Reader<R>, scan_rows: Option<usize>, ) -> Result<Vec<(String, String)>>

Discovers attribute definitions by scanning over records.

The scan will begin at the current position of the reader and will move the cursor to the end of the last record scanned.

pub fn scan<R: BufRead>( &self, fmt_reader: Reader<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: BufRead + Seek>( &self, fmt_reader: Reader<R>, region: Region, index: impl BinningIndex, 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.

pub fn scan_byte_ranges<R: BufRead + Seek>( &self, fmt_reader: Reader<R>, byte_ranges: Vec<(u64, u64)>, columns: Option<Vec<String>>, batch_size: Option<usize>, limit: Option<usize>, ) -> Result<impl RecordBatchReader>

Returns an iterator yielding record batches from specified byte ranges.

pub fn scan_virtual_ranges<R: BufRead + Seek>( &self, fmt_reader: Reader<R>, vpos_ranges: Vec<(VirtualPosition, VirtualPosition)>, columns: Option<Vec<String>>, batch_size: Option<usize>, limit: Option<usize>, ) -> Result<impl RecordBatchReader>

Returns an iterator yielding record batches from specified virtual position ranges.