Struct Scanner 

pub struct Scanner { /* private fields */ }

A CRAM scanner.

Examples

use oxbow::alignment::format::cram::Scanner;
use std::fs::File;
use noodles::fasta::io::indexed_reader::Builder as FastaIndexedReaderBuilder;
use noodles::fasta::repository::adapters::IndexedReader as FastaIndexedReaderAdapter;

let fa_reader = FastaIndexedReaderBuilder::default().build_from_path("reference.fa").unwrap();
let adapter = FastaIndexedReaderAdapter::new(fa_reader);
let repository = noodles::fasta::Repository::new(adapter);

let inner = File::open("sample.cram").unwrap();
let mut fmt_reader = noodles::cram::io::Reader::new(inner);
let header = fmt_reader.read_header().unwrap();

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

Implementations

impl Scanner

pub fn new(header: Header) -> Self

Creates a CRAM scanner from a SAM header.

pub fn header(&self) -> Header

Returns the SAM header.

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 field_names(&self) -> Vec<String>

Returns the fixed field names.

pub fn schema( &self, fields: Option<Vec<String>>, tag_defs: Option<Vec<(String, String)>>, ) -> Result<Schema>

Returns the Arrow schema.

impl Scanner

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

Discovers tag 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: Read>( &self, fmt_reader: Reader<R>, repo: Repository, fields: Option<Vec<String>>, tag_defs: Option<Vec<(String, String)>>, batch_size: Option<usize>, limit: Option<usize>, ) -> Result<impl RecordBatchReader>

Returns an iterator yielding record batches.

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_query<R: Read + Seek>( &self, fmt_reader: Reader<R>, repo: Repository, region: Region, index: Index, fields: Option<Vec<String>>, tag_defs: Option<Vec<(String, String)>>, batch_size: Option<usize>, limit: Option<usize>, ) -> Result<impl RecordBatchReader>

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

This operation requires a CRAI Index and the FASTA reference repository must be provided separately from the CRAM reader.

The scan will traverse one or more CRAM data containers and slices and filter for records that overlap the given region. The cursor will stop at the end of the last record scanned.