Struct bio::io::fasta::IndexedReader

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pub struct IndexedReader<R: Read + Seek> {
    pub index: Index,
    /* private fields */
}

Expand description

A FASTA reader with an index as created by SAMtools (.fai).

Fields

index: Index

Implementations

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impl IndexedReader<File>

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pub fn from_file<P: AsRef<Path> + Debug>(path: &P) -> Result<Self>

Read from a given file path. This assumes the index ref.fasta.fai to be present for FASTA ref.fasta.

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impl<R: Read + Seek> IndexedReader<R>

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pub fn new<I: Read>(fasta: R, fai: I) -> Result<Self>

Read from a FASTA and its index, both given as io::Read. FASTA has to be io::Seek in addition.

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pub fn with_index(fasta: R, index: Index) -> Self

Read from a FASTA and its index, the first given as io::Read, the second given as index object.

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pub fn fetch(&mut self, seq_name: &str, start: u64, stop: u64) -> Result<()>

Fetch an interval from the sequence with the given name for reading.

start and stop are 0-based and stop is exclusive - i.e. [start, stop)

Example

use bio::io::fasta::IndexedReader;
// create dummy files
const FASTA_FILE: &[u8] = b">chr1\nGTAGGCTGAAAA\nCCCC";
const FAI_FILE: &[u8] = b"chr1\t16\t6\t12\t13";

let seq_name = "chr1";
let start: u64 = 0; // start is 0-based, inclusive
let stop: u64 = 10; // stop is 0-based, exclusive
                    // load the index
let mut faidx = IndexedReader::new(std::io::Cursor::new(FASTA_FILE), FAI_FILE).unwrap();
// move the pointer in the index to the desired sequence and interval
faidx
    .fetch(seq_name, start, stop)
    .expect("Couldn't fetch interval");
// read the subsequence defined by the interval into a vector
let mut seq = Vec::new();
faidx.read(&mut seq).expect("Couldn't read the interval");
assert_eq!(seq, b"GTAGGCTGAA");

Errors

If the seq_name does not exist within the index.

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pub fn fetch_by_rid(&mut self, rid: usize, start: u64, stop: u64) -> Result<()>

Fetch an interval from the sequence with the given record index for reading.

start and stop are 0-based and stop is exclusive - i.e. [start, stop)

Example

use bio::io::fasta::IndexedReader;
// create dummy files
const FASTA_FILE: &[u8] = b">chr1\nGTAGGCTGAAAA\nCCCC";
const FAI_FILE: &[u8] = b"chr1\t16\t6\t12\t13";

let rid: usize = 0;
let start: u64 = 0; // start is 0-based, inclusive
let stop: u64 = 10; // stop is 0-based, exclusive
                    // load the index
let mut faidx = IndexedReader::new(std::io::Cursor::new(FASTA_FILE), FAI_FILE).unwrap();
// move the pointer in the index to the desired sequence and interval
faidx
    .fetch_by_rid(rid, start, stop)
    .expect("Couldn't fetch interval");
// read the subsequence defined by the interval into a vector
let mut seq = Vec::new();
faidx.read(&mut seq).expect("Couldn't read the interval");
assert_eq!(seq, b"GTAGGCTGAA");