Struct ReferenceReader 

pub struct ReferenceReader {
    pub current_sequence: Vec<u8>,
    pub genomes_and_contigs: GenomesAndContigs,
    pub target_lens: HashMap<usize, u64>,
    /* private fields */
}

Struct handling methods to read and handle information for references indexed_reader represents the #IndexedReader current_sequence is the byte array current being read from the indexed_reader file genomes_and_contigs holds the #GenomesAndContigs struct matching contig string names to tids reference index to tid holds a reference index matched to a LinkedHashSet of all associated tids target_names matches the tid to a byte array representation of the contigs name in the Fasta file target_lens matches the tid of a contig to its observed length in the Fasta file in base pairs

Fields

current_sequence: Vec<u8>

genomes_and_contigs: GenomesAndContigs

target_lens: HashMap<usize, u64>

Implementations

impl ReferenceReader

pub fn new( concatenated_genomes: &Option<String>, genomes_and_contigs: GenomesAndContigs, _number_of_contigs: usize, ) -> ReferenceReader

pub fn new_with_target_names( concatenated_genomes: &Option<String>, genomes_and_contigs: GenomesAndContigs, target_names: Vec<&[u8]>, ) -> Self

pub fn new_from_reader_with_reference_index( reader: &Self, ref_idx: usize, ) -> Self

Somewhat efficient cloning function. Only takes the info needed for a given ref idx

pub fn new_from_reader_with_tid_and_rid( reader: &ReferenceReader, ref_idx: usize, tid: usize, ) -> Self

pub fn get_target_name(&self, tid: usize) -> &[u8]

pub fn add_target(&mut self, target: &[u8], tid: usize)

pub fn update_ref_index_tids(&mut self, ref_index: usize, tid: usize) -> usize

pub fn retrieve_tids_for_ref_index( &self, ref_index: usize, ) -> Option<&LinkedHashSet<usize>>

pub fn add_length(&mut self, tid: usize, length: u64)

pub fn add_lengths(&mut self, target_lengths: HashMap<usize, u64>)

pub fn get_contig_length(&self, tid: usize) -> u64

pub fn retrieve_reference_stem(&self, ref_idx: usize) -> String

pub fn update_current_sequence_capacity(&mut self, size: usize)

pub fn update_current_sequence_without_capacity(&mut self)

pub fn retrieve_contig_name_from_tid(&self, tid: usize) -> Option<&Vec<u8>>

pub fn fetch_contig_from_reference_by_contig_name( &mut self, contig_name: &[u8], ref_idx: usize, )

pub fn fetch_contig_from_reference_by_tid( &mut self, tid: usize, ref_idx: usize, ) -> Result<(), Error>

pub fn fetch_reference_context( &mut self, ref_idx: usize, interval: &SimpleInterval, )

Fetches the reference sequence from a given SimpleInterval The return position is 0-base start and stop inclusive

pub fn read_sequence_to_vec(&mut self)

pub fn split_contig_name<'b>(contig_name: &'b [u8], separator: u8) -> &'b [u8]

Takes a contig name &u8 and splits around a suspected separator character

Trait Implementations

impl Clone for ReferenceReader

fn clone(&self) -> Self

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for ReferenceReader

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

Formats the value using the given formatter.