Struct RegionSet 

pub struct RegionSet {
    pub regions: Vec<Region>,
    pub header: Option<String>,
    pub path: Option<PathBuf>,
}

RegionSet struct, the representation of the interval region set file, such as bed file.

Fields

regions: Vec<Region>

header: Option<String>

path: Option<PathBuf>

Implementations

impl RegionSet

pub fn to_bed<T: AsRef<Path>>(&self, path: T) -> Result<()>

Save a regionset to disk as bed file

Arguments

• path: the path to the file to dump to

pub fn to_bed_gz<T: AsRef<Path>>(&self, path: T) -> Result<()>

Save a regionset to disk as bed.gz file

Arguments

• path: the path to the file to dump to

pub fn identifier(&self) -> String

Calculate identifier for RegionSet

This function doesn’t sort file, and identifer is based on unsorted first 3 columns.

Returns

String containing RegionSet identifier

pub fn file_digest(&self) -> String

pub fn iter_chroms(&self) -> impl Iterator<Item = &String>

Iterate unique chromosomes located in RegionSet

pub fn iter_chr_regions<'a>( &'a self, chr: &'a str, ) -> impl Iterator<Item = &'a Region>

Iterate through regions located on specific Chromosome in RegionSet

Arguments

• chr: chromosome name

pub fn sort(&mut self)

Sort bed file based on first 3 columns. Sorting is happening inside the object, where original order will be overwritten

pub fn is_empty(&self) -> bool

Is regionSet empty?

pub fn region_widths(&self) -> Result<Vec<u32>>

Calculate all regions width

pub fn mean_region_width(&self) -> f64

Calculate mean region width for whole RegionSet

pub fn calc_mid_points(&self) -> HashMap<String, Vec<u32>>

Calculate middle point for each region, and return hashmap with midpoints for each chromosome

pub fn len(&self) -> usize

Get number of regions in RegionSet

Returns: number of regions

pub fn get_max_end_per_chr(&self) -> HashMap<String, u32>

Get the furthest region location for each region

pub fn nucleotides_length(&self) -> u32

Get total nucleotide count

Trait Implementations

impl Clone for RegionSet

fn clone(&self) -> RegionSet

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for RegionSet

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

Formats the value using the given formatter.

impl Display for RegionSet

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

Formats the value using the given formatter.

impl From<&[u8]> for RegionSet

fn from(value: &[u8]) -> Self

Converts to this type from the input type.

impl From<Vec<Region>> for RegionSet

fn from(regions: Vec<Region>) -> Self

Converts to this type from the input type.

impl<'a> IntoIterator for &'a RegionSet

type Item = &'a Region

The type of the elements being iterated over.

type IntoIter = RegionSetIterator<'a>

Which kind of iterator are we turning this into?

fn into_iter(self) -> Self::IntoIter

Creates an iterator from a value.

impl TryFrom<&Path> for RegionSet

fn try_from(value: &Path) -> Result<Self>

Create a new RegionSet from a bed file.

Arguments:

• value: path to bed file on disk.

type Error = Error

The type returned in the event of a conversion error.

impl TryFrom<&str> for RegionSet

type Error = Error

The type returned in the event of a conversion error.

fn try_from(value: &str) -> Result<Self>

Performs the conversion.

impl TryFrom<PathBuf> for RegionSet

type Error = Error

The type returned in the event of a conversion error.

fn try_from(value: PathBuf) -> Result<Self>

Performs the conversion.

impl TryFrom<String> for RegionSet

type Error = Error

The type returned in the event of a conversion error.

fn try_from(value: String) -> Result<Self>

Performs the conversion.