Struct MerDna 

pub struct MerDna { /* private fields */ }

A DNA k-mer stored as 2-bit packed encoding in u64 words.

This matches the Jellyfish MerDNA representation:

• Each base is 2 bits: A=0, C=1, G=2, T=3
• Bases are packed from LSB to MSB within each word
• Words are ordered from least significant to most significant

Examples

use jellyfish_reader::MerDna;

let mer: MerDna = "ACGT".parse().unwrap();
assert_eq!(mer.to_string(), "ACGT");
assert_eq!(mer.k(), 4);

let rc = mer.get_reverse_complement();
assert_eq!(rc.to_string(), "ACGT"); // ACGT is its own reverse complement

Implementations

impl MerDna

pub fn new(k: usize) -> Self

Create a new k-mer of the given length, initialized to all A’s.

pub fn from_words(words: Vec<u64>, k: usize) -> Self

Create a MerDna from raw word data and k-mer length.

The words should contain 2-bit packed bases matching Jellyfish’s encoding.

pub fn from_bytes(bytes: &[u8], k: usize) -> Self

Create a MerDna by reading packed bytes (as stored in Jellyfish binary files).

Bytes are read in order and packed into u64 words in little-endian byte order.

pub fn k(&self) -> usize

The k-mer length (number of bases).

pub fn words(&self) -> &[u64]

Access the raw u64 words.

pub fn get_base(&self, i: usize) -> u8

Get the base at position i (0-indexed from the right/LSB end).

Panics

Panics if i >= k.

pub fn set_base(&mut self, i: usize, base_code: u8)

Set the base at position i (0-indexed from the right/LSB end).

Panics

Panics if i >= k or if base_code is not in 0..4.

pub fn shift_left(&mut self, base: u8) -> Option<u8>

Shift the k-mer left by one position, inserting base at the right end.

Returns the base character that was shifted out from the left end.

pub fn shift_right(&mut self, base: u8) -> Option<u8>

Shift the k-mer right by one position, inserting base at the left end.

Returns the base character that was shifted out from the right end.

pub fn get_reverse_complement(&self) -> MerDna

Compute the reverse complement of this k-mer.

pub fn reverse_complement(&mut self)

Modify this k-mer in place to its reverse complement.

pub fn get_canonical(&self) -> MerDna

Get the canonical form (lexicographically smaller of self and reverse complement).

pub fn canonicalize(&mut self)

Modify this k-mer in place to its canonical form.

pub fn is_homopolymer(&self) -> bool

Check if this k-mer is a homopolymer (all same base).

pub fn poly_a(&mut self)

Set all bases to A.

pub fn poly_c(&mut self)

Set all bases to C.

pub fn poly_g(&mut self)

Set all bases to G.

pub fn poly_t(&mut self)

Set all bases to T.

Trait Implementations

impl Clone for MerDna

fn clone(&self) -> MerDna

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for MerDna

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

Formats the value using the given formatter.

impl Display for MerDna

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

Formats the value using the given formatter.

impl FromStr for MerDna

type Err = Error

The associated error which can be returned from parsing.

fn from_str(s: &str) -> Result<Self, Error>

Parses a string s to return a value of this type.

impl Hash for MerDna

fn hash<H: Hasher>(&self, state: &mut H)

Feeds this value into the given Hasher.

fn hash_slice<H>(data: &[Self], state: &mut H)

where H: Hasher, Self: Sized,

Feeds a slice of this type into the given Hasher.

impl Ord for MerDna

fn cmp(&self, other: &Self) -> Ordering

This method returns an Ordering between self and other.

fn max(self, other: Self) -> Self

where Self: Sized,

Compares and returns the maximum of two values.

fn min(self, other: Self) -> Self

where Self: Sized,

Compares and returns the minimum of two values.

fn clamp(self, min: Self, max: Self) -> Self

where Self: Sized,

Restrict a value to a certain interval.

impl PartialEq for MerDna

fn eq(&self, other: &Self) -> 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 PartialOrd for MerDna

fn partial_cmp(&self, other: &Self) -> Option<Ordering>

This method returns an ordering between self and other values if one exists.

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

Tests less than (for self and other) and is used by the < operator.

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

Tests less than or equal to (for self and other) and is used by the <= operator.

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

Tests greater than (for self and other) and is used by the > operator.

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

Tests greater than or equal to (for self and other) and is used by the >= operator.

impl Eq for MerDna