Struct Contig 

pub struct Contig {
    pub name: String,
    pub length: u64,
    pub md5: Option<String>,
    pub assembly: Option<String>,
    pub uri: Option<String>,
    pub species: Option<String>,
    pub aliases: Vec<String>,
    pub sequence_role: SequenceRole,
}

A single contig/sequence in a reference genome

Fields

name: String

Sequence name (SN tag in SAM)

length: u64

Sequence length (LN tag in SAM)

md5: Option<String>

MD5 checksum of the sequence (M5 tag in SAM) Lowercase hex, 32 characters

assembly: Option<String>

Assembly identifier (AS tag in SAM)

uri: Option<String>

URI where sequence can be retrieved (UR tag in SAM)

species: Option<String>

Species (SP tag in SAM)

aliases: Vec<String>

Known alternative names for this contig

sequence_role: SequenceRole

Sequence role from NCBI assembly report

Implementations

impl Contig

pub fn new(name: impl Into<String>, length: u64) -> Self

pub fn is_primary_chromosome(&self) -> bool

Check if this contig is a primary chromosome (1-22, X, Y) Matches both UCSC (chr1) and NCBI (1) naming conventions exactly

pub fn is_mitochondrial(&self) -> bool

Check if this is a mitochondrial contig Matches common mitochondrial names from various reference builds

pub fn is_alt(&self) -> bool

Check if this is an ALT contig (GRCh38)

pub fn is_decoy(&self) -> bool

Check if this is a decoy contig

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<'de> Deserialize<'de> for Contig

fn deserialize<__D>(__deserializer: __D) -> Result<Self, __D::Error>

where __D: Deserializer<'de>,

Deserialize this value from the given Serde deserializer.

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 Serialize for Contig

fn serialize<__S>(&self, __serializer: __S) -> Result<__S::Ok, __S::Error>

where __S: Serializer,

Serialize this value into the given Serde serializer.

impl Eq for Contig

impl StructuralPartialEq for Contig