Struct GenomicRange 

pub struct GenomicRange(/* private fields */);

A minimal BED record with only 3 fields.

Implementations

impl GenomicRange

pub fn new<C>(chrom: C, start: u64, end: u64) -> Self

where C: Into<String>,

pub fn pretty_show(&self) -> String

Convert the record to a string representation: chr:start-end

Trait Implementations

impl Archive for GenomicRange

where String: Archive, u64: Archive,

const COPY_OPTIMIZATION: CopyOptimization<Self>

An optimization flag that allows the bytes of this type to be copied directly to a writer instead of calling serialize.

type Archived = ArchivedGenomicRange

The archived representation of this type.

type Resolver = GenomicRangeResolver

The resolver for this type. It must contain all the additional information from serializing needed to make the archived type from the normal type.

fn resolve(&self, resolver: Self::Resolver, out: Place<Self::Archived>)

Creates the archived version of this value at the given position and writes it to the given output.

impl BEDLike for GenomicRange

fn chrom(&self) -> &str

Return the chromosome name of the record

fn set_chrom(&mut self, chrom: &str) -> &mut Self

Change the chromosome name of the record

fn start(&self) -> u64

Return the 0-based start position of the record

fn set_start(&mut self, start: u64) -> &mut Self

Change the 0-based start position of the record

fn end(&self) -> u64

Return the end position (non-inclusive) of the record

fn set_end(&mut self, end: u64) -> &mut Self

Change the end position (non-inclusive) of the record

fn name(&self) -> Option<&str>

Return the name of the record

fn score(&self) -> Option<Score>

Return the score of the record

fn strand(&self) -> Option<Strand>

Return the strand of the record

fn len(&self) -> u64

Return the length of the record. Return 0 if the end position is smaller than the start position.

fn compare(&self, other: &Self) -> Ordering

fn overlap<B: BEDLike>(&self, other: &B) -> Option<GenomicRange>

Return the overlap

fn n_overlap<B: BEDLike>(&self, other: &B) -> u64

Return the size of overlap between two records

fn to_genomic_range(&self) -> GenomicRange

Convert the record to a GenomicRange

fn split_by_len(&self, bin_size: u64) -> impl Iterator<Item = GenomicRange>

Split into consecutive records with the specified length. The length of the last record may be shorter.

fn rsplit_by_len(&self, bin_size: u64) -> impl Iterator<Item = GenomicRange>

Split into consecutive records with the specified length starting from the end. The result is in reverse order compared to split_by_len. The length of the last record may be shorter.

impl Clone for GenomicRange

fn clone(&self) -> GenomicRange

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for GenomicRange

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

Formats the value using the given formatter.

impl<__D: Fallible + ?Sized> Deserialize<GenomicRange, __D> for Archived<GenomicRange>

where String: Archive, <String as Archive>::Archived: Deserialize<String, __D>, u64: Archive, <u64 as Archive>::Archived: Deserialize<u64, __D>,

fn deserialize( &self, deserializer: &mut __D, ) -> Result<GenomicRange, <__D as Fallible>::Error>

Deserializes using the given deserializer

impl Display for GenomicRange

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

Formats the value using the given formatter.

impl FromStr for GenomicRange

Convert string to GenomicRange. ‘\t’, ‘:’, and ‘-’ are all considered as valid delimiters. So any of the following formats is valid:

• chr1\t100\t200
• chr1:100-200

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 Hash for GenomicRange

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 Ord for GenomicRange

fn cmp(&self, other: &GenomicRange) -> Ordering

This method returns an Ordering between self and other.

fn max(self, other: Self) -> Self

where Self: Sized,

Compares and returns the maximum of two values.

fn min(self, other: Self) -> Self

where Self: Sized,

Compares and returns the minimum of two values.

fn clamp(self, min: Self, max: Self) -> Self

where Self: Sized,

Restrict a value to a certain interval.

impl PartialEq for GenomicRange

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

Tests for self and other values to be equal, and is used by ==.

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

Tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl PartialOrd for GenomicRange

fn partial_cmp(&self, other: &GenomicRange) -> Option<Ordering>

This method returns an ordering between self and other values if one exists.

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

Tests less than (for self and other) and is used by the < operator.

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

Tests less than or equal to (for self and other) and is used by the <= operator.

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

Tests greater than (for self and other) and is used by the > operator.

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

Tests greater than or equal to (for self and other) and is used by the >= operator.

impl<__S: Fallible + ?Sized> Serialize<__S> for GenomicRange

where String: Serialize<__S>, u64: Serialize<__S>,

fn serialize( &self, serializer: &mut __S, ) -> Result<<Self as Archive>::Resolver, <__S as Fallible>::Error>

Writes the dependencies for the object and returns a resolver that can create the archived type.

impl Eq for GenomicRange

impl StructuralPartialEq for GenomicRange