Struct Kmer 

pub struct Kmer(pub u64);

A k-length nucleotide sequence represented as a 64-bit integer.

Tuple Fields

0: u64

Implementations

impl Kmer

pub fn from_u64(value: u64) -> Kmer

Construct a k-mer from an unsigned integer

pub fn make(seq: &str) -> Option<Kmer>

convert a k-length string into a k-mer.

If k > 32 or the string contains letters other than “A”, “C”, “G”, “T”, or “U”, None is returned.

pub fn make_many(k: usize, seq: &str) -> Vec<Kmer>

Extract k-mers from a string.

Traverse the string seq and put all the valid k-mers in a vector.

pub fn with_many<S, F>(k: usize, seq: &S, f: F)

where S: AsRef<[u8]>, F: FnMut(&Kmer),

Extract k-mers from a byte sequence and pass them to a closure.

pub fn with_many_both<S, F>(k: usize, seq: &S, f: F)

where S: AsRef<[u8]>, F: FnMut(&Kmer, &Kmer),

Extract k-mers from both strands of a byte sequence.

pub fn base(c: char) -> Option<Kmer>

Convert a character to a 1-mer.

pub fn byte(c: u8) -> Option<Kmer>

Convert an ASCII byte to a 1-mer.

pub fn rev(&self, k: usize) -> Kmer

Create a reversed k-mer.

pub fn rev_comp(&self, k: usize) -> Kmer

Create a reverse-complement k-mer.

pub fn render(&self, k: usize) -> String

Convert a k-mer to a string.

pub fn ham(x: &Kmer, y: &Kmer) -> usize

Compute the Hamming distance between two k-mers.

pub fn frequency_vector<S>(k: usize, seq: &S) -> Vec<usize>

where S: AsRef<[u8]>,

Compute the frequency of k-mers on the forward strand of a sequence.

Compute a frequency vector with the number of instances in seq of each of the 4**k possible k-mers.

Note that this is a dense representation, so the vector will have 4**k elements.

pub fn frequency_vector_both<S>(k: usize, seq: &S) -> Vec<usize>

where S: AsRef<[u8]>,

Compute the frequency of k-mers on both strands of a sequence.

Compute a frequency vector with the number of instances in seq of each of the 4**k possible k-mers.

Note that this is a dense representation, so the vector will have 4**k elements.

Trait Implementations

impl Clone for Kmer

fn clone(&self) -> Kmer

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for Kmer

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

Formats the value using the given formatter.

impl Hash for Kmer

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 Kmer

fn cmp(&self, other: &Kmer) -> 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 Kmer

fn eq(&self, other: &Kmer) -> 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 Kmer

fn partial_cmp(&self, other: &Kmer) -> 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 Kmer

impl StructuralPartialEq for Kmer