Struct bio::io::fasta::IndexedReader

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

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

Fields

index: Index

Methods

impl IndexedReader<File>

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

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

impl<R: Read + Seek> IndexedReader<R>

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.

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.

fn read_all(&mut self, seqname: &str, seq: &mut Text) -> Result<()>

For a given seqname, read the whole sequence into the given vector.

fn read(&mut self, seqname: &str, start: u64, stop: u64, seq: &mut Text) -> Result<()>

Read the given interval of the given seqname into the given vector (stop position is exclusive).