Struct ReferenceGenome 

pub struct ReferenceGenome { /* private fields */ }

Wrapper structure for a reference genome

Implementations

impl ReferenceGenome

pub fn empty_reference() -> Self

Creates an empty reference genome, which we can be populated through add_contig(...)

pub fn from_fasta(fasta_fn: &Path) -> Result<ReferenceGenome, Box<dyn Error>>

Loads a reference genome from a given FASTA file

Arguments

• fasta_fn - the FASTA filename, gzip is allowed

Errors

This will pass through any error detected from loading the provided FASTA file. This includes file reading and/or record reading errors.

pub fn add_contig( &mut self, contig_key: String, contig_sequence: &str, ) -> Result<(), SimpleError>

Adds a new contig to the reference genome

Arguments

• contig_key - the name of the contig
• contig_sequence - the sequence to add; all sequence is automatically upper-cased

pub fn filename(&self) -> &Path

pub fn contig_keys(&self) -> &[String]

pub fn get_slice(&self, chromosome: &str, start: usize, end: usize) -> &[u8]

Retrieves a reference slice from a given 0-based coordinates. If start or end goes past the full contig length, it will be truncated to the full contig length.

Arguments

• chromosome - the chromosome to slice from
• start - the 0-based start index (included)
• end - the 0-based end index (excluded)

Panics

• if chromosome was not in the FASTA file
• if start > end

pub fn get_full_chromosome(&self, chromosome: &str) -> &[u8]

Retrieves a full chromosome by name

Arguments

• chromosome - the chromosome to slice from

Panics

• if chromosome was not in the FASTA file