Enum noodles_core::region::Region

pub enum Region {
    Mapped(Mapped),
    Unmapped,
    All,
}

A genomic region.

Genomic regions can either be mapped to a reference sequence, unmapped (*), or an inclusion of all reads (.).

Variants

Mapped(Mapped)

A mapped region.

Tuple Fields of Mapped

0: Mapped

Unmapped

An unmapped region.

All

All reads.

Implementations

impl Region

pub fn from_str_reference_sequences(
    s: &str,
    reference_sequences: &ReferenceSequences
) -> Result<Self, ParseError>

Parses a string to a region.

A region string is specified as <reference-sequence-name>[:<start-position>[-<end-position>]].

The reference sequence name can be “*” to represent unmapped records; or “.”, all records. Otherwise, the reference sequence name must exist in the reference sequence dictionary.

pub fn mapped<I, B>(name: I, interval: B) -> Self where
    I: Into<String>,
    B: RangeBounds<i32>, 

Creates a new mapped region.

Positions are assumed to be 1-based.

Examples

use noodles_core::Region;
let region = Region::mapped("sq0", 1..=5);
assert!(matches!(region, Region::Mapped(_)));

pub fn name(&self) -> &str

Returns the reference name of the region.

If the region is unmapped, this returns “*”. If the region represents all records, this returns “.”.

Examples

use noodles_core::Region;

let region = Region::mapped("sq0", 1..=5);
assert_eq!(region.name(), "sq0");

assert_eq!(Region::Unmapped.name(), "*");
assert_eq!(Region::All.name(), ".");

pub fn is_mapped(&self) -> bool

Returns whether the region is mapped.

Examples

use noodles_core::Region;
assert!(Region::mapped("sq0", 5..=8).is_mapped());
assert!(!Region::Unmapped.is_mapped());

pub fn as_mapped(&self) -> Option<&Mapped>

Returns the region as a mapped region if it is mapped.

Examples

use noodles_core::Region;
assert!(Region::mapped("sq0", 5..=8).as_mapped().is_some());
assert!(Region::Unmapped.as_mapped().is_none());

Trait Implementations

impl Clone for Region

fn clone(&self) -> Region

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Debug for Region

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

Formats the value using the given formatter.

impl Display for Region

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

Formats the value using the given formatter.

impl FromStr for Region

type Err = ParseError

The associated error which can be returned from parsing.

fn from_str(s: &str) -> Result<Self, Self::Err>

Parses a string s to return a value of this type.

impl PartialEq<Region> for Region

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

This method tests for self and other values to be equal, and is used by ==.

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

This method tests for !=.

impl Eq for Region

impl StructuralEq for Region

impl StructuralPartialEq for Region