Struct rust_htslib::bcf::IndexedReader

pub struct IndexedReader { /* fields omitted */ }

An indexed VCF/BCF reader.

Methods

impl IndexedReader

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

Create a new IndexedReader from path.

Arguments

• path - the path to open.

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

Create a new IndexedReader from an URL.

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

Jump to the given region.

Arguments

• rid - numeric ID of the reference to jump to; use HeaderView::name2rid for resolving contig name to ID.
• start - 0-based start coordinate of region on reference.
• end - 0-based end coordinate of region on reference.

Trait Implementations

impl Read for IndexedReader

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

Read the next record.

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>

Return an iterator over all records of the VCF/BCF file.

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

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

fn header(&self) -> &HeaderView

Return the header.

fn empty_record(&self) -> Record

Return empty record. Can be reused multiple times.

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.