Struct Reference 

pub struct Reference { /* private fields */ }

Reference sequence storage

Loads and stores reference sequences from .3.rai and .4.rai RustAlign index files. The reference is stored in bit-packed format (2 bits per nucleotide).

Implementations

impl Reference

pub fn load<P: AsRef<Path>>(path_base: P) -> AlignResult<Self>

Load reference from .3.rai and .4.rai files

Arguments

• path_base - Path to the index base (without extensions)

pub fn n_refs(&self) -> u32

Get the number of reference sequences

pub fn approx_len(&self, tidx: u32) -> u64

Get the approximate length of a reference sequence

pub fn get_stretch( &self, buf: &[u8], tidx: u32, toff: u64, count: usize, ) -> AlignResult<Vec<Nuc>>

Extract a stretch of reference sequence

Arguments

• buf - The bit-packed reference buffer from .4.rai file
• tidx - Reference sequence index (chromosome index)
• toff - Offset within the reference sequence
• count - Number of bases to extract

Returns

A vector of nucleotides

pub fn buf_sz(&self) -> u64

Get the buffer size needed