Struct Reader

pub struct Reader { /* private fields */ }

A Tabix file reader.

This struct and its associated functions are meant for reading plain-text tabix indexed by tabix.

Note that the tabix command from htslib can actually several more things, including building indices and converting BCF to VCF text output. Both is out of scope here.

Implementations

impl Reader

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

Create a new Reader from path.

Arguments

• path - the path to open.

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

pub fn tid(&self, name: &str) -> Result<u64>

Get sequence/target ID from sequence name.

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

Fetch region given by numeric sequence number and 0-based begin and end position.

pub fn seqnames(&self) -> Vec<String>

Return the sequence contig names.

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

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

Arguments

• n_threads - number of extra background reader threads to use

pub fn hts_format(&self) -> htsExactFormat

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 read(&mut self, record: &mut Vec<u8>) -> Result<bool>

Read next line into the given Vec<u8> (i.e., ASCII string).

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

Iterator over the lines/records of the seeked region.

fn header(&self) -> &Vec<String>

Return the text headers, split by line.

impl Send for Reader