Struct rust_htslib::bam::Reader

pub struct Reader { /* fields omitted */ }

A BAM reader.

Methods

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.

Important traits for ChunkIterator<'a, R>

impl<'a, R: Read> Iterator for ChunkIterator<'a, R> type Item = Result<Record, ReadError>;

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

pub fn set_reference<P: AsRef<Path>>(
    &mut self,
    path: P
) -> Result<(), ReferencePathError>

Set the reference path for reading CRAM files.

Arguments

• path - path to the FASTA reference

Trait Implementations

impl Read for Reader

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.

Important traits for Records<'a, R>

impl<'a, R: Read> Iterator for Records<'a, R> type Item = Result<Record, ReadError>;

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.

Important traits for Pileups<'a, R>

impl<'a, R: Read> Iterator for Pileups<'a, R> type Item = Result<Pileup, PileupError>;

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

Iterator over pileups.

fn htsfile(&self) -> *mut htsFile

Return the htsFile 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 Drop for Reader

fn drop(&mut self)

Executes the destructor for this type.

impl Send for Reader

impl Debug for Reader

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

Formats the value using the given formatter.