Struct IndexedReader

pub struct IndexedReader { /* private fields */ }

An indexed VCF/BCF reader.

Implementations

impl IndexedReader

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

Create a new IndexedReader from path.

Arguments

• path - the path to open.

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

Create a new IndexedReader from an URL.

pub fn fetch(&mut self, rid: u32, start: u64, end: Option<u64>) -> Result<()>

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 inclusive start coordinate of region on reference.
• end - Optional 0-based inclusive end coordinate of region on reference. If None is given, records are fetched from start until the end of the contig.

Note

The entire contig can be fetched by setting start to 0 and end to None.

Trait Implementations

impl Debug for IndexedReader

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

Formats the value using the given formatter.

impl Drop for IndexedReader

fn drop(&mut self)

Executes the destructor for this type.

impl Read for IndexedReader

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

Read the next record.

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<()>

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 Send for IndexedReader