Enum Format 

pub enum Format {
    Fasta,
    Fastq,
}

A sequence file format.

Deliberately not #[non_exhaustive]: FASTA and FASTQ are the whole domain of this crate, so matching on both arms exhaustively is meant to be pleasant and is a promise we intend to keep.

Variants

Fasta

FASTA: >id description followed by one or more sequence lines.

Fastq

FASTQ: @id description, sequence, +, quality.

Implementations

impl Format

pub const FASTA_EXTENSIONS: &'static [&'static str]

Recognised FASTA extensions (without the leading dot).

pub const FASTQ_EXTENSIONS: &'static [&'static str]

Recognised FASTQ extensions (without the leading dot).

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

Infer the format from a file extension, ignoring a trailing .gz/.bgz/.z.

use fastx::Format;
assert_eq!(Format::from_path("reads.fq.gz"), Some(Format::Fastq));
assert_eq!(Format::from_path("genome.fna"), Some(Format::Fasta));
assert_eq!(Format::from_path("notes.txt"), None);

pub fn from_extension(ext: &str) -> Option<Format>

Infer the format from a bare extension such as "fasta".

pub fn from_first_byte(byte: u8) -> Option<Format>

Infer the format from the first meaningful byte of a stream.

use fastx::Format;
assert_eq!(Format::from_first_byte(b'>'), Some(Format::Fasta));
assert_eq!(Format::from_first_byte(b'@'), Some(Format::Fastq));

pub const fn header_byte(self) -> u8

The byte that starts a record header in this format.

pub const fn extension(self) -> &'static str

The canonical extension used when creating files.

pub const fn has_quality(self) -> bool

Whether records in this format carry per-base quality scores.

Trait Implementations

impl Clone for Format

fn clone(&self) -> Format

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Copy for Format

impl Debug for Format

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

Formats the value using the given formatter.

impl Display for Format

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

Formats the value using the given formatter.

impl Eq for Format

impl Hash for Format

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 Format

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

Equality operator ==.

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

Inequality operator !=.

impl StructuralPartialEq for Format