Struct bam::bam_reader::IndexedReaderBuilder

pub struct IndexedReaderBuilder { /* fields omitted */ }

IndexedReader builder. Allows to specify paths to BAM and BAI files, as well as LRU cache size and the option to skip BAI modification time check.

Methods

impl IndexedReaderBuilder

pub fn new() -> Self

Creates a new indexed reader builder.

pub fn bai_path<P: AsRef<Path>>(&mut self, path: P) -> &mut Self

Sets a path to a BAI index. By default, it is {bam_path}.bai. Overwrites the last value, if any.

pub fn check_time(&mut self, value: bool) -> &mut Self

Sets or unsets BAI modification time check (set by default).

If on, the build will fail if the BAI index is younger than the BAM file.

pub fn cache_capacity(&mut self, cache_capacity: usize) -> &mut Self

Sets new LRU cache capacity. See cache_capacity for more details.

pub fn from_path<P: AsRef<Path>>(
    &self,
    bam_path: P
) -> Result<IndexedReader<File>>

Creates a new IndexedReader from bam_path. If BAI path was not specified, the functions tries to open {bam_path}.bai.

pub fn from_streams<R: Seek + Read, T: Read>(
    &self,
    bam_stream: R,
    bai_stream: T
) -> Result<IndexedReader<R>>

Creates a new IndexedReader from two streams. BAM stream should support random access, while BAI stream does not need to. check_time and bai_path values are ignored.