Struct KnownReference 

pub struct KnownReference {

    pub id: ReferenceId,
    pub display_name: String,
    pub assembly: Assembly,
    pub source: ReferenceSource,
    pub naming_convention: NamingConvention,
    pub download_url: Option<String>,
    pub assembly_report_url: Option<String>,
    pub contigs: Vec<Contig>,
    pub description: Option<String>,
    pub tags: Vec<String>,
    pub contigs_missing_from_fasta: Vec<String>,
    pub md5_set: HashSet<String>,
    pub name_length_set: HashSet<(String, u64)>,
    pub signature: Option<String>,
}

A known reference genome in the catalog

Fields

id: ReferenceId

Unique identifier

display_name: String

Human-readable display name

assembly: Assembly

Assembly version

source: ReferenceSource

Source organization

naming_convention: NamingConvention

Naming convention used

download_url: Option<String>

Download URL for the reference FASTA

assembly_report_url: Option<String>

Path to NCBI assembly report (if applicable)

contigs: Vec<Contig>

All contigs in this reference

description: Option<String>

Description/notes about this reference

tags: Vec<String>

Tags for filtering (e.g., “with_decoy”, “no_alt”, “analysis_set”)

contigs_missing_from_fasta: Vec<String>

Contigs that appear in the assembly report but not in the FASTA/dict (e.g., MT in CHM13 which uses standard rCRS mitochondria)

md5_set: HashSet<String>

Set of all MD5 checksums in this reference

name_length_set: HashSet<(String, u64)>

Set of all (exact_name, length) pairs for matching

signature: Option<String>

Signature for exact matching (hash of sorted MD5s)

Implementations

impl KnownReference

pub fn new( id: impl Into<String>, display_name: impl Into<String>, assembly: Assembly, source: ReferenceSource, ) -> Self

pub fn with_contigs(self, contigs: Vec<Contig>) -> Self

pub fn rebuild_indexes(&mut self)

Rebuild the internal indexes after modifying contigs

pub fn has_decoy(&self) -> bool

Check if this reference has decoy sequences

pub fn has_alt(&self) -> bool

Check if this reference has ALT contigs

pub fn role_counts(&self) -> RoleCounts

Count contigs by sequence role

Trait Implementations

impl Clone for KnownReference

fn clone(&self) -> KnownReference

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for KnownReference

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

Formats the value using the given formatter.

impl<'de> Deserialize<'de> for KnownReference

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

where __D: Deserializer<'de>,

Deserialize this value from the given Serde deserializer.

impl Serialize for KnownReference

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

where __S: Serializer,

Serialize this value into the given Serde serializer.