Trait rust_htslib::bcf::Read

pub trait Read: Sized {
    fn read(&mut self, record: &mut Record) -> Result<(), ReadError>;
    fn records(&mut self) -> Records<Self>;
    fn header(&self) -> &HeaderView;
    fn empty_record(&self) -> Record;
    fn set_threads(&mut self, n_threads: usize) -> Result<(), ThreadingError>;
}

A trait for a BCF reader with a read method.

Required Methods

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

Read the next record.

Arguments

• record - an empty record, that can be created with bcf::Reader::empty_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 header(&self) -> &HeaderView

Return the header.

fn empty_record(&self) -> Record

Return empty record. Can be reused multiple times.

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.

Setting nthreads to 0 does not change the current state. Note that it is not possible to set the number of background threads below 1 once it has been set.

Arguments

• n_threads - number of extra background writer threads to use, must be > 0.

Implementors

• impl Read for Reader
• impl Read for IndexedReader