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>

Loads a reference genome from a given FASTA file

Arguments

• fasta_fn - the FASTA filename, gzip is allowed

Errors

• if the FASTA file cannot be opened or read
• if a FASTA record cannot be parsed
• if a contig key is duplicated in the FASTA file

pub fn add_contig( &mut self, contig_key: String, contig_sequence: Vec<u8>, ) -> Result<()>

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 in place

Errors

• if contig_key is already in the reference genome

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

Adds a new contig from a UTF-8 string by converting it to bytes and calling Self::add_contig.

Arguments

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

Errors

• if contig_key is already in the reference genome

pub fn filename(&self) -> &Path

Returns the filename of the reference genome.

pub fn contig_keys(&self) -> impl Iterator<Item = &String>

Returns an iterator over the contig keys in the reference genome. The order of the contig keys is guaranteed to be the same as the order as they were added to the reference genome.

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

Errors

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

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

Retrieves a full chromosome by name

Arguments

• chromosome - the chromosome to slice from

Errors

• if chromosome was not in the FASTA file