Struct rust_htslib::bam::IndexedReader

pub struct IndexedReader { /* fields omitted */ }

Methods

impl IndexedReader

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

Create a new Reader from path.

Arguments

• path - the path to open.

pub fn from_path_and_index<P: AsRef<Path>>(
    path: P,
    index_path: P
) -> Result<Self, IndexedReaderPathError>

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

pub fn fetch(&mut self, tid: u32, beg: u32, end: u32) -> Result<(), FetchError>

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 IndexedReader

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 IndexedReader

fn drop(&mut self)

Executes the destructor for this type.

impl Send for IndexedReader

impl Debug for IndexedReader

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

Formats the value using the given formatter.