Struct noodles::sam::io::IndexedReader

pub struct IndexedReader<R> { /* private fields */ }

An indexed SAM reader.

Implementations

impl<R> IndexedReader<R>

pub fn get_ref(&self) -> &Reader<R>

Returns a reference to the underlying reader.

pub fn get_mut(&mut self) -> &mut Reader<R>

Returns a mutable reference to the underlying reader.

pub fn into_inner(self) -> Reader<R>

Returns the underlying reader.

impl<R> IndexedReader<R>

where R: Read,

pub fn new<I>(inner: R, index: I) -> IndexedReader<R>

where I: BinningIndex + 'static,

Creates an indexed SAM reader.

pub fn read_header(&mut self) -> Result<Header, Error>

Reads the SAM header.

pub fn read_record_buf( &mut self, header: &Header, record: &mut RecordBuf ) -> Result<usize, Error>

Reads a record into an alignment record buffer.

pub fn record_bufs<'a>( &'a mut self, header: &'a Header ) -> RecordBufs<'a, Reader<R>>

Returns an iterator over alignment record buffers starting from the current stream position.

pub fn read_record(&mut self, record: &mut Record) -> Result<usize, Error>

Reads a record.

pub fn records(&mut self) -> impl Iterator<Item = Result<Record, Error>>

Returns an iterator over records.

pub fn index(&self) -> &dyn BinningIndex

Returns the associated index.

impl<R> IndexedReader<R>

where R: Read + Seek,

pub fn query<'a>( &'a mut self, header: &'a Header, region: &Region ) -> Result<impl Iterator<Item = Result<Record, Error>> + 'a, Error>

Returns an iterator over records that intersect the given region.

pub fn query_unmapped( &mut self ) -> Result<impl Iterator<Item = Result<Record, Error>>, Error>

Returns an iterator of unmapped records after querying for the unmapped region.