Trait rust_htslib::bam::Read

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pub trait Read: Sized {
    fn read(&mut self, record: &mut Record) -> Result<(), ReadError>;
    fn records(&mut self) -> Records<'_, Self> ⓘ;
    fn pileup(&mut self) -> Pileups<'_, Self> ⓘ;
    fn bgzf(&self) -> *mut BGZF;
    fn header(&self) -> &HeaderView;

    fn seek(&mut self, offset: i64) -> Result<(), SeekError> { ... }
    fn tell(&self) -> i64 { ... }
    fn set_threads(&mut self, n_threads: usize) -> Result<(), ThreadingError> { ... }
}

Expand description

A trait for a BAM reader with a read method.

Required Methods§

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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.

Arguments

record - the record to be filled

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

Iterator over the records of the seeked 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.

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fn pileup(&mut self) -> Pileups<'_, Self> ⓘ

Iterator over pileups.

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fn bgzf(&self) -> *mut BGZF

Return the BGZF struct

Return the header.

Provided Methods§

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fn seek(&mut self, offset: i64) -> Result<(), SeekError>

Seek to the given virtual offset in the file

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fn tell(&self) -> i64

Report the current virtual offset

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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.

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.