Struct bam::index::Index

pub struct Index { /* fields omitted */ }

BAI Index. Allows to get chunks in a bgzip file, that contain records from a specific genomic region.

Implementations

impl Index

pub fn from_stream<R: Read>(stream: R) -> Result<Index>

Loads index from stream.

pub fn from_path<P: AsRef<Path>>(path: P) -> Result<Index>

Loads index from path.

pub fn fetch_chunks(&self, ref_id: u32, start: i32, end: i32) -> Vec<Chunk>

Fetches chunks of the BAM file that contain all records for a given region.

pub fn start_offset(&self) -> Option<VirtualOffset>

Returns the offset to the start of the data, if the index is not empty.

pub fn end_offset(&self) -> Option<VirtualOffset>

Returns the offset of the end of all mapped records, if the index is not empty. Takes at most 37448 bins lookups.

pub fn references(&self) -> &[Reference]

Returns all references present in the BAI index.

pub fn n_unmapped(&self) -> Option<u64>

Returns the number of unmapped records, if present in the index.

Trait Implementations

impl Clone for Index

fn clone(&self) -> Index

Returns a copy of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Display for Index

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

Formats the value using the given formatter.