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.