Struct rust_htslib::bam::Reader

pub struct Reader { /* private fields */ }

A BAM reader.

Implementations

impl Reader

pub fn from_path<P: AsRef<Path>>(path: P) -> Result<Self, ReaderPathError>

Create a new Reader from path.

Arguments

• path - the path to open.

pub fn from_stdin() -> Result<Self, BGZFError>

Create a new Reader from STDIN.

pub fn from_url(url: &Url) -> Result<Self, BGZFError>

Create a new Reader from URL.

pub fn iter_chunk(
    &mut self,
    start: Option<i64>,
    end: Option<i64>
) -> ChunkIterator<'_, Self>

Iterator over the records between the (optional) virtual offsets start and end

Arguments

• start - Optional starting virtual offset to seek to. Throws an error if it is not a valid virtual offset.

• end - Read until the virtual offset is less than end

Trait Implementations

impl Debug for Reader

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

Formats the value using the given formatter.

impl Drop for Reader

fn drop(&mut self)

Executes the destructor for this type.

impl Read for Reader

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

Iterator over the records of the fetched region. Note that, while being convenient, this is less efficient than pre-allocating a Record and reading into it with the read method, since every iteration involves the allocation of a new Record.

fn read(&mut self, record: &mut Record) -> Result<(), ReadError>

Read next BAM record into given record. Use this method in combination with a single allocated record to avoid the reallocations occurring with the iterator.

fn pileup(&mut self) -> Pileups<'_, Self>

Iterator over pileups.

fn bgzf(&self) -> *mut BGZF

Return the BGZF struct

fn header(&self) -> &HeaderView

Return the header.

fn seek(&mut self, offset: i64) -> Result<(), SeekError>

Seek to the given virtual offset in the file

fn tell(&self) -> i64

Report the current virtual offset

fn set_threads(&mut self, n_threads: usize) -> Result<(), ThreadingError>

Activate multi-threaded BAM read support in htslib. This should permit faster reading of large BAM files.

impl Send for Reader