Struct EbwtParams 

pub struct EbwtParams {

    pub len: u64,
    pub bwt_len: u64,
    pub sz: u64,
    pub bwt_sz: u64,
    pub line_rate: i32,
    pub orig_off_rate: i32,
    pub off_rate: i32,
    pub off_mask: u64,
    pub ftab_chars: i32,
    pub eftab_len: u32,
    pub eftab_sz: u32,
    pub ftab_len: u64,
    pub ftab_sz: u64,
    pub offs_len: u64,
    pub offs_sz: u64,
    pub line_sz: u32,
    pub side_sz: u32,
    pub side_bwt_sz: u32,
    pub side_bwt_len: u32,
    pub num_sides: u64,
    pub num_lines: u64,
    pub ebwt_tot_len: u64,
    pub ebwt_tot_sz: u64,
    pub color: bool,
    pub entire_reverse: bool,
}

Parameters describing an FM-index structure

This corresponds to the EbwtParams class in the original C++ code. All fields match the C++ implementation for binary compatibility.

Fields

len: u64

Length of reference sequence

bwt_len: u64

BWT length (len + 1 for terminating symbol)

sz: u64

Size in 32-bit words (len+3)/4

bwt_sz: u64

BWT size in 32-bit words (len/4 + 1)

line_rate: i32

Log2 of line size (for side calculation)

orig_off_rate: i32

Original offset rate (from constructor)

off_rate: i32

Suffix array sample rate (log2)

off_mask: u64

Mask for offset calculations

ftab_chars: i32

Number of characters in ftab

eftab_len: u32

Extended ftab length (ftabChars*2)

eftab_sz: u32

Extended ftab size in bytes

ftab_len: u64

Ftab length (1 << (ftabChars*2)) + 1

ftab_sz: u64

Ftab size in bytes

offs_len: u64

Offsets array length

offs_sz: u64

Offsets array size in bytes

line_sz: u32

Line size (1 << lineRate)

side_sz: u32

Size of each side in bytes

side_bwt_sz: u32

Size of BWT portion in each side

side_bwt_len: u32

Length of BWT portion in each side

num_sides: u64

Number of sides in the index

num_lines: u64

Number of lines

ebwt_tot_len: u64

Total ebwt length

ebwt_tot_sz: u64

Total ebwt size in bytes

color: bool

Colorspace mode (not used in DNA mode)

entire_reverse: bool

Entire reverse mode

Implementations

impl EbwtParams

pub fn new(ref_len: u64) -> Self

Create default parameters for a given reference length

pub fn with_options( ref_len: u64, line_rate: i32, off_rate: i32, ftab_chars: i32, color: bool, entire_reverse: bool, ) -> Self

Create parameters with specific options (matches C++ EbwtParams::init)

pub fn set_off_rate(&mut self, off_rate: i32)

Set a new suffix-array sampling rate (matches C++ setOffRate)

pub fn side_size(&self) -> u32

Get size of a side in bytes

pub fn pos_to_side(&self, pos: u64) -> u64

Calculate which side a BWT position is on

pub fn is_valid(&self) -> bool

Check if parameters are valid (matches C++ repOk)

pub fn total_size(&self) -> u64

Get total size in bytes

Trait Implementations

impl Clone for EbwtParams

fn clone(&self) -> EbwtParams

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for EbwtParams

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

Formats the value using the given formatter.

impl Default for EbwtParams

fn default() -> Self

Returns the “default value” for a type.

impl PartialEq for EbwtParams

fn eq(&self, other: &EbwtParams) -> bool

Tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Rhs) -> bool

Tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl Eq for EbwtParams

impl StructuralPartialEq for EbwtParams