Struct Ebwt 

pub struct Ebwt { /* private fields */ }

Extended Burrows-Wheeler Transform (FM-index)

This is the main data structure used by RustAlign for ultrafast sequence alignment. It is memory-mapped from .rai index files.

Implementations

impl Ebwt

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

Load an existing index from disk

Arguments

• path_base - Path to the index (without .1.rai, .2.rai, etc. extensions)

Errors

Returns an error if the index files don’t exist or are corrupted.

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

Load a “large” index variant

pub fn params(&self) -> &EbwtParams

Get the index parameters

pub fn path(&self) -> &Path

Get the path to this index

pub fn is_large(&self) -> bool

Check if this is a large index

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

Get the chromosome names

pub fn n_pat(&self) -> u32

Get the number of chromosomes

pub fn n_frag(&self) -> u32

Get the number of fragments

pub fn rstarts(&self) -> &[u32]

Get the rstarts array

pub fn plen(&self) -> &[u32]

Get chromosome lengths

pub fn z_off(&self) -> u32

Get the zOff value (position of $ in BWT)

pub fn get_offset(&self, row: u64) -> AlignResult<u64>

Convert a BWT row to a genome offset using suffix array samples and LF-mapping.

This implements RustAlign’s getOffset() algorithm:

1. If row is zOff, return 0
2. If row is at a sampled position, return the sampled offset
3. Otherwise, walk back using LF-mapping until hitting zOff or a sampled row

pub fn joined_to_text_off( &self, qlen: u64, off: u64, fw: bool, ) -> AlignResult<(u32, u64, u64)>

Convert a genome offset to chromosome index and position.

This implements RustAlign’s joinedToTextOff() algorithm using binary search on the rstarts array.

Returns (chromosome_index, position_in_chromosome, chromosome_length)

pub fn resolve_position( &self, row: u64, qlen: u64, fw: bool, ) -> AlignResult<(String, u64, u64)>

Resolve a BWT row to chromosome name and position.

This combines getOffset() and joinedToTextOff() to convert a BWT row directly to a chromosome name and position.

Returns (chromosome_name, position, chromosome_length)

Trait Implementations

impl FmIndex for Ebwt

fn exact_match(&self, pattern: &[Nuc]) -> AlignResult<Vec<usize>>

Exact match search using backward search on FM-index

This implements the classic FM-index backward search algorithm:

1. Initialize range using ftab for the last ftabChars nucleotides
2. Extend left through remaining characters using LF-mapping
3. Return all positions in the final range

fn len(&self) -> usize

Get the length of the indexed text

fn is_empty(&self) -> bool

Check if the index is empty

fn bwt(&self, pos: usize) -> AlignResult<NucPair>

Get forward BWT character at position

fn rank(&self, c: Nuc, _pos: usize) -> AlignResult<usize>

Rank operation - count occurrences of character up to position

fn select(&self, c: Nuc, _k: usize) -> AlignResult<usize>

Select operation - find position of k-th occurrence of character