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EbwtWithRef

rustalign_fmindex

Struct EbwtWithRef 

Source 
pub struct EbwtWithRef {
    pub ebwt: Ebwt,
    pub reference: Reference,
    /* private fields */
}
Expand description

Combined structure for FM-index with reference

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§ebwt: Ebwt

The FM-index

§reference: Reference

The reference sequence metadata

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impl EbwtWithRef

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

Load both FM-index and reference

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pub fn get_reference( &self, chr_idx: u32, pos: u64, len: usize, ) -> AlignResult<Vec<Nuc>>

Extract reference sequence for a given chromosome and position

Note: pos should be 0-based position within the chromosome

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pub fn ebwt(&self) -> &Ebwt

Get the underlying Ebwt

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