Crate noodles_bgzf

noodles-bgzf handles the reading and writing of the blocked gzip format (BGZF).

While the gzip format is typically a single stream, a BGZF is the concatenation of many gzip streams. Each stream is called a block, with its uncompressed data size being constrained to less than 64 KiB. This multistream gzip allows random access using virtual positions.

noodles-bgzf abstracts away the concept of blocks, implementing std::io::Read for the reader and std::io::Write for the writer.

Examples

Read an entire BGZF file

use noodles_bgzf as bgzf;
let mut reader = File::open("data.gz").map(bgzf::Reader::new)?;
let mut data = Vec::new();
reader.read_to_end(&mut data)?;

Write a BGZF file

use noodles_bgzf as bgzf;
let mut writer = File::create("data.gz").map(bgzf::Writer::new)?;
writer.write_all(b"noodles-bgzf")?;

Re-exports

pub use self::indexed_reader::IndexedReader;

pub use self::multithreaded_writer::MultithreadedWriter;

pub use self::reader::Reader;

pub use self::virtual_position::VirtualPosition;

pub use self::writer::Writer;

pub use self::async::Reader as AsyncReader;

pub use self::async::Writer as AsyncWriter;

Modules

async

Async BGZF I/O.

gzi

gzip index.

indexed_reader

Indexed BGZF reader.

io

BGZF I/O.

multithreaded_writer

Multithreaded BGZF writer.

reader

BGZF reader.

virtual_position

BGZF virtual position.

writer

BGZF writer.

Structs

MultithreadedReader

A multithreaded BGZF reader.