Struct IndexedReader

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

An indexed CRAM reader.

Implementations

impl<R> IndexedReader<R>

where R: Read,

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

Creates an indexed CRAM reader.

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

Unwraps and returns the underlying reader.

pub fn reference_sequence_repository(&self) -> &Repository

Returns the reference sequence repository.

pub fn read_file_definition(&mut self) -> Result<FileDefinition>

Reads the CRAM file definition.

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

Reads the SAM header.

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

Reads the SAM header.

pub fn read_data_container(&mut self) -> Result<Option<DataContainer>>

Reads a data container.

pub fn records<'r>(&'r mut self, header: &'r Header) -> Records<'r, R>

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

pub fn index(&self) -> &Index

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<Query<'a, R>>

Returns an iterator over records that intersects the given region.