Enum Compression 

#[non_exhaustive]
pub enum Compression {
    None,
    Gzip,
    Bgzf,
    Zstd,
}

Compression applied to a sequence file.

Marked #[non_exhaustive]: match with a _ arm. New containers keep appearing — this list has already grown twice — and each one should be a minor release rather than a breaking one.

Variants (Non-exhaustive)

Non-exhaustive enums could have additional variants added in future. Therefore, when matching against variants of non-exhaustive enums, an extra wildcard arm must be added to account for any future variants.

None

Plain, uncompressed bytes.

Gzip

One deflate stream, as gzip produces. Readable start to finish only.

Bgzf

Block-compressed gzip, as bgzip produces.

Valid gzip that any tool can decompress, but split into independent members so that a reader with a .gzi index can seek into it. Costs a percent or two of compression ratio and is what the samtools ecosystem expects, so it is the default for compressed output.

Zstd

Zstandard (requires the zstd feature).

Compresses faster and smaller than gzip, which makes it attractive for intermediate files, but the wider bioinformatics toolchain does not read it and a plain zstd frame cannot be randomly accessed — so a reference genome still wants Compression::Bgzf.

Implementations

impl Compression

pub const GZIP_MAGIC: [u8; 2]

The first two bytes of a gzip member.

pub const ZSTD_MAGIC: [u8; 4]

The four-byte magic number of a Zstandard frame.

pub fn from_path<P: AsRef<Path>>(path: P) -> Compression

Infer compression from a file extension.

Note that .gz maps to Compression::Gzip rather than Compression::Bgzf: an extension cannot tell the two apart, and only the bytes can. Writers pick BGZF for .gz deliberately; readers sniff.

pub fn from_magic(bytes: &[u8]) -> Compression

Infer compression from the leading bytes of a stream.

Does not distinguish plain gzip from BGZF — both report Compression::Gzip, since telling them apart means parsing the extra field. Use crate::bgzf::is_bgzf for that.

Trait Implementations

impl Clone for Compression

fn clone(&self) -> Compression

Returns a duplicate of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Copy for Compression

impl Debug for Compression

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl Default for Compression

fn default() -> Compression

Returns the “default value” for a type.

impl Eq for Compression

impl Hash for Compression

fn hash<__H: Hasher>(&self, state: &mut __H)

Feeds this value into the given Hasher.

fn hash_slice<H>(data: &[Self], state: &mut H)

where H: Hasher, Self: Sized,

Feeds a slice of this type into the given Hasher.

impl PartialEq for Compression

fn eq(&self, other: &Compression) -> bool

Equality operator ==.

fn ne(&self, other: &Rhs) -> bool

Inequality operator !=.

impl StructuralPartialEq for Compression