Struct Contig 

pub struct Contig { /* private fields */ }

The contig data, such as identifiers and its length.

Implementations

impl Contig

pub fn name(&self) -> &str

Get the main name of the contig (e.g. 10, X, MT).

pub fn alt_names(&self) -> impl Iterator<Item = &str>

Get the alternative contig identifiers.

For instance, CM000686.2, NC_000024.10, and chrY for chromosome Y.

Example

use dabuild::Contig;

let contig = Contig::new("Y", &["CM000686.2", "NC_000024.10", "chrY"], 57_227_415).expect("The contig data are valid");

let alt_names: Vec<_> = contig.alt_names().collect();
assert_eq!(&alt_names, &["CM000686.2", "NC_000024.10", "chrY"]);

pub fn genbank_name(&self) -> Option<&str>

Get the GenBank contig identifier, if available.

For instance, CM000686.2 for chromosome Y of the GRCh38.p13 assembly.

Example

use dabuild::Contig;

let contig = Contig::new("Y", &["CM000686.2", "NC_000024.10", "chrY"], 57_227_415).expect("The contig data are valid");

assert_eq!(contig.genbank_name(), Some("CM000686.2"));

pub fn refseq_name(&self) -> Option<&str>

Get the RefSeq contig identifier, if available.

For instance, NC_000024.10 for chromosome Y of the GRCh38.p13 assembly.

Example

use dabuild::Contig;

let contig = Contig::new("Y", &["CM000686.2", "NC_000024.10", "chrY"], 57_227_415).expect("The contig data are valid");

assert_eq!(contig.refseq_name(), Some("NC_000024.10"));

pub fn ucsc_name(&self) -> Option<&str>

Get the UCSC contig identifier, if available.

For instance, chrY for chromosome Y of the GRCh38.p13 assembly.

Example

use dabuild::Contig;

let contig = Contig::new("Y", &["CM000686.2", "NC_000024.10", "chrY"], 57_227_415).expect("The contig data are valid");

assert_eq!(contig.ucsc_name(), Some("chrY"));

pub fn length(&self) -> u32

Get the number of bases of the contig, a.k.a. its length.

pub fn transpose_coordinate(&self, other: u32) -> Option<u32>

Transpose coordinate on a double-stranded sequence to the opposite strand.

Returns None if the operation would lead to an overflow.

pub fn new( name: impl ToString, alt_names: &[impl ToString], length: u32, ) -> Option<Self>

Create a Contig from name, the alternative names, and its length.

Example

Create a Contig with fields from the GRC assembly report:

use dabuild::Contig;

let contig = Contig::new("Y", &["CM000686.2", "NC_000024.10", "chrY"], 57_227_415);

assert!(contig.is_some());
let contig = contig.unwrap();
assert_eq!(contig.name(), "Y");
assert_eq!(contig.genbank_name(), Some("CM000686.2"));

Create a Contig with sequence name and UCSC accession:

use dabuild::Contig;

let contig = Contig::new("Y", &["na", "", "chrY"], 57_227_415);

assert!(contig.is_some());

let contig = contig.unwrap();
assert_eq!(contig.name(), "Y");
assert!(contig.genbank_name().is_none());
assert!(contig.refseq_name().is_none());
assert_eq!(contig.ucsc_name(), Some("chrY"));

The new expects alt_names with three items that correspond to:

• GenBank accession
• RefSeq accession
• UCSC accession

An accession equaling to an empty string or "na" is filtered out.

Trait Implementations

impl Clone for Contig

fn clone(&self) -> Contig

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for Contig

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

Formats the value using the given formatter.

impl Hash for Contig

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 Contig

fn cmp(&self, other: &Contig) -> 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 Contig

fn eq(&self, other: &Contig) -> 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 Contig

fn partial_cmp(&self, other: &Contig) -> 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 Eq for Contig

impl StructuralPartialEq for Contig