Struct consalign::IndexedReader

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

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

Fields

index: Index

Implementations

impl IndexedReader<File>

pub fn from_file<P>(path: &P) -> Result<IndexedReader<File>, Error>where
    P: AsRef<Path>,

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

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

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

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

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

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

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

Fetch an interval from the sequence with the given name for reading. (stop position is exclusive).

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

Fetch an interval from the sequence with the given record index for reading. (stop position is exclusive).

pub fn fetch_all(&mut self, seq_name: &str) -> Result<(), Error>

Fetch the whole sequence with the given name for reading.

pub fn fetch_all_by_rid(&mut self, rid: usize) -> Result<(), Error>

Fetch the whole sequence with the given record index for reading.

pub fn read(&mut self, seq: &mut Vec<u8, Global>) -> Result<(), Error>

Read the fetched sequence into the given vector.

pub fn read_iter(&mut self) -> Result<IndexedReaderIterator<'_, R>, Error>

Return an iterator yielding the fetched sequence.

Trait Implementations

impl<R> Debug for IndexedReader<R>where
    R: Debug + Read + Seek,

fn fmt(&self, f: &mut Formatter<'_>) -> Result<(), Error>

Formats the value using the given formatter.