Struct IndexedReader

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

An indexed VCF 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: BufRead,

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

Reads the VCF header.

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

Reads a single raw VCF record.

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

Returns an iterator over records starting from the current stream position.

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

Reads a single record without eagerly parsing its fields.

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

Returns an iterator over records.

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

Returns the associated index.

impl<R> IndexedReader<R>

where R: BufRead + Seek,

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

Returns an iterator over records that intersects the given region.

impl<R> IndexedReader<Reader<R>>

where R: Read,

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

where I: BinningIndex + 'static,

Creates an indexed VCF reader.