Struct bam::bam_reader::IndexedReaderBuilder

pub struct IndexedReaderBuilder { /* fields omitted */ }

IndexedReader builder. Allows to specify paths to BAM and BAI files, as well as the number of threads and an option to ignore or warn BAI modification time check.

Implementations

impl IndexedReaderBuilder

pub fn new() -> Self

Creates a new IndexedReader 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 modification_time(
    &mut self,
    modification_time: ModificationTime
) -> &mut Self

By default, IndexedReader::from_path and IndexedReaderBuilder::from_path returns an io::Error if the last modification of the BAI index was earlier than the last modification of the BAM file.

Enum ModificationTime contains options to skip this check or raise a warning instead of returning an error.

pub fn additional_threads(&mut self, additional_threads: u16) -> &mut Self

Sets the number of additional threads.

Additional threads are used to decompress bgzip blocks, while the main thread reads the blocks from a file/stream. If additional_threads is 0 (default), the main thread will decompress blocks itself.

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: Read + Seek, 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.