Struct IndexedReader

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

An indexed BAM reader.

Implementations

impl<R> IndexedReader<R>

pub fn get_ref(&self) -> &R

Returns a reference to the underlying reader.

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

Returns a mutable reference to the underlying reader.

pub fn into_inner(self) -> R

Returns the underlying reader.

impl<R> IndexedReader<R>

where R: Read,

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

Reads the SAM header.

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

Reads a record into an alignment record buffer.

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

Reads a record.

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

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

pub fn records(&mut self) -> Records<'_, R>

Returns an iterator over records.

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

Returns the associated index.

impl<R> IndexedReader<Reader<R>>

where R: Read,

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

where I: BinningIndex + 'static,

Creates an indexed BAM reader.

impl<R> IndexedReader<R>

where R: BufRead + Seek,

pub fn query<'a>( &'a mut self, header: &'a Header, region: &Region, ) -> Result<Query<'_, R>>

Returns an iterator over records that intersect the given region.

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

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