Struct Contig

Source

pub struct Contig { /* private fields */ }

Expand description

The contig data, such as identifiers and its length.

Implementations§

Source §

impl Contig

Source

pub fn name(&self) -> &str

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

Source

pub fn builder() -> ContigBuilder<Uninit>

Get a builder to build the Contig.

§Example

Build a contig from the minimal required attributes.

use dabuild::Contig;

let contig = Contig::builder().name("Y").length(57_227_415u32).build();

assert_eq!(contig.name(), "Y");
assert_eq!(contig.length(), 57_227_415)

Build a contig with optional attributes, including GenBank, RefSeq, and UCSC accession identifiers.

use dabuild::Contig;

let contig = Contig::builder()
                .length(57_227_415u32)
                .name("Y")
                .genbank_name("CM000686.2")
                .refseq_name("NC_000024.10")
                .ucsc_name("chrY")
                .build();

 assert_eq!(contig.name(), "Y");
 assert_eq!(contig.length(), 57_227_415);
 assert_eq!(contig.genbank_name().unwrap(), "CM000686.2");
 assert_eq!(contig.refseq_name().unwrap(), "NC_000024.10");
 assert_eq!(contig.ucsc_name().unwrap(), "chrY");

Source

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::builder()
                .length(57_227_415u32)
                .name("Y")
                .genbank_name("CM000686.2")
                .refseq_name("NC_000024.10")
                .ucsc_name("chrY")
                .build();

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

Source

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::builder()
                .name("Y")
                .length(57_227_415u32)
                .genbank_name("CM000686.2")
                .build();

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

Source

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::builder()
                .name("Y")
                .length(57_227_415u32)
                .refseq_name("NC_000024.10")
                .build();

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

Source

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::builder()
                .name("Y")
                .length(57_227_415u32)
                .ucsc_name("chrY")
                .build();

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

Source

pub fn length(&self) -> u32

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

Source

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.

Source

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

👎Deprecated since 0.3.1: use Contig::builder() instead

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"));