Struct debruijn::kmer::VarIntKmer

pub struct VarIntKmer<T: PrimInt + FromPrimitive + IntHelp, KS: KmerSize> {
    pub storage: T,
    pub phantom: PhantomData<KS>,
}

A fixed-length Kmer sequence that may not fill the bits of T

side: L R bases: 0 0 0 A C G T T bits: H ........ L bit : 14 12 10 8 6 4 2 0

sorting the integer will give a lexicographic sorting of the corresponding string. kmers that don't fill storage are always aligned to the least signifcant bits

Fields

storage: T

phantom: PhantomData<KS>

Methods

impl<T: PrimInt + FromPrimitive + Hash + IntHelp, KS: KmerSize> VarIntKmer<T, KS>

pub fn top_mask(n_bases: usize) -> T

pub fn bottom_mask(n_bases: usize) -> T

Trait Implementations

impl<T: PrimInt + FromPrimitive + Hash + IntHelp, KS: KmerSize> Mer for VarIntKmer<T, KS>

fn len(&self) -> usize

Length of DNA sequence

fn get(&self, pos: usize) -> u8

Get the letter at the given position.

fn set_mut(&mut self, pos: usize, v: u8)

Set base at pos to 2-bit encoded base val

fn set_slice_mut(&mut self, pos: usize, n_bases: usize, value: u64)

Set a slice of bases in the kmer, using the packed representation in value. Sets n_bases, starting at pos. Incoming bases must always be packed into the upper-most bits of the value.

fn rc(&self) -> Self

Return the reverse complement of this kmer

Important traits for MerIter<'a, M>

impl<'a, M: 'a + Mer> Iterator for MerIter<'a, M> type Item = u8;

fn iter<'a>(&'a self) -> MerIter<'a, Self>

Iterate over the bases in the sequence

impl<T: PrimInt + FromPrimitive + Hash + IntHelp, KS: KmerSize> Kmer for VarIntKmer<T, KS>

fn empty() -> Self

Create a Kmer initialized to all A's

fn k() -> usize

K value for this concrete type.

fn to_u64(&self) -> u64

Return the rank of this kmer in an lexicographic ordering of all kmers E.g. 'AAAA' -> 0, 'AAAT' -> 1, etc. This will panic if K > 32.

fn from_u64(v: u64) -> Self

fn extend_left(&self, v: u8) -> Self

Shift the base v into the left end of the kmer

fn extend_right(&self, v: u8) -> Self

Add the base v to the right side of the sequence, and remove the leftmost base

fn extend(&self, v: u8, dir: Dir) -> Self

Add the base v to the side of sequence given by dir, and remove a base at the opposite side

fn get_extensions(&self, exts: Exts, dir: Dir) -> Vec<Self>

Generate all the extension of this sequence given by exts in direction Dir

fn min_rc_flip(&self) -> (Self, bool)

Return the minimum of the kmer and it's reverse complement, and a flag indicating if sequence was flipped

fn min_rc(&self) -> Self

fn is_palindrome(&self) -> bool

Test if this Kmer and it's reverse complement are the same

fn from_bytes(bytes: &[u8]) -> Self

Create a Kmer from the first K bytes of bytes, which must be encoded as the integers 0-4.

fn from_ascii(bytes: &[u8]) -> Self

Create a Kmer from the first K bytes of bytes, which must be encoded as ASCII letters A,C,G, or T.

fn to_string(&self) -> String

Return String containing Kmer sequence

fn kmers_from_bytes(str: &[u8]) -> Vec<Self>

Generate vector of all kmers contained in str encoded as 0-4.

fn kmers_from_ascii(str: &[u8]) -> Vec<Self>

Generate vector of all kmers contained in str, encoded as ASCII ACGT.

impl<T: PartialEq + PrimInt + FromPrimitive + IntHelp, KS: PartialEq + KmerSize> PartialEq<VarIntKmer<T, KS>> for VarIntKmer<T, KS>

fn eq(&self, other: &VarIntKmer<T, KS>) -> bool

This method tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &VarIntKmer<T, KS>) -> bool

This method tests for !=.

impl<T: Clone + PrimInt + FromPrimitive + IntHelp, KS: Clone + KmerSize> Clone for VarIntKmer<T, KS>

fn clone(&self) -> VarIntKmer<T, KS>

Returns a copy of the value.

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

Performs copy-assignment from source.

impl<T: Ord + PrimInt + FromPrimitive + IntHelp, KS: Ord + KmerSize> Ord for VarIntKmer<T, KS>

fn cmp(&self, other: &VarIntKmer<T, KS>) -> Ordering

This method returns an Ordering between self and other.

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

Compares and returns the maximum of two values.

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

Compares and returns the minimum of two values.

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

🔬 This is a nightly-only experimental API. (clamp)

Restrict a value to a certain interval.

impl<T: Eq + PrimInt + FromPrimitive + IntHelp, KS: Eq + KmerSize> Eq for VarIntKmer<T, KS>

impl<T: PartialOrd + PrimInt + FromPrimitive + IntHelp, KS: PartialOrd + KmerSize> PartialOrd<VarIntKmer<T, KS>> for VarIntKmer<T, KS>

fn partial_cmp(&self, other: &VarIntKmer<T, KS>) -> Option<Ordering>

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

fn lt(&self, other: &VarIntKmer<T, KS>) -> bool

This method tests less than (for self and other) and is used by the < operator.

fn le(&self, other: &VarIntKmer<T, KS>) -> bool

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

fn gt(&self, other: &VarIntKmer<T, KS>) -> bool

This method tests greater than (for self and other) and is used by the > operator.

fn ge(&self, other: &VarIntKmer<T, KS>) -> bool

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

impl<T: Copy + PrimInt + FromPrimitive + IntHelp, KS: Copy + KmerSize> Copy for VarIntKmer<T, KS>

impl<T: PrimInt + FromPrimitive + Hash + IntHelp, KS: KmerSize> Debug for VarIntKmer<T, KS>

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

Formats the value using the given formatter.

impl<T: Hash + PrimInt + FromPrimitive + IntHelp, KS: Hash + KmerSize> Hash for VarIntKmer<T, KS>

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

Feeds this value into the given [Hasher].

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

Feeds a slice of this type into the given [Hasher].

impl<T: PrimInt + FromPrimitive + IntHelp, KS: KmerSize> Serialize for VarIntKmer<T, KS> where
    T: Serialize, 

fn serialize<__S>(&self, __serializer: __S) -> Result<__S::Ok, __S::Error> where
    __S: Serializer, 

Serialize this value into the given Serde serializer.

impl<'de, T: PrimInt + FromPrimitive + IntHelp, KS: KmerSize> Deserialize<'de> for VarIntKmer<T, KS> where
    T: Deserialize<'de>, 

fn deserialize<__D>(__deserializer: __D) -> Result<Self, __D::Error> where
    __D: Deserializer<'de>, 

Deserialize this value from the given Serde deserializer.