Struct PackedSeqVecBase 

pub struct PackedSeqVecBase<const B: usize>
where
    Bits<B>: SupportedBits,
{ /* private fields */ }

A variable-bit-width packed owned sequence of DNA bases.

Implementations

impl<const B: usize> PackedSeqVecBase<B>

where Bits<B>: SupportedBits,

pub fn from_raw_parts(seq: Vec<u8>, len: usize) -> Self

Creates a SeqVec from a vector of packed bytes and a length in bp.

The vector should have at least 48 bytes of padding after len. Otherwise, the vector will be resized to be padded with zeros.

impl PackedSeqVecBase<1>

pub fn with_len(n: usize) -> Self

pub fn random(len: usize, n_frac: f32) -> Self

Trait Implementations

impl<const B: usize> Clone for PackedSeqVecBase<B>

where Bits<B>: SupportedBits,

fn clone(&self) -> PackedSeqVecBase<B>

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl<const B: usize> CopyType for PackedSeqVecBase<B>

where Bits<B>: SupportedBits, Vec<u8>: MemSize, usize: MemSize,

type Copy = False

impl<const B: usize> Debug for PackedSeqVecBase<B>

where Bits<B>: SupportedBits,

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

Formats the value using the given formatter.

impl<const B: usize> Default for PackedSeqVecBase<B>

where Bits<B>: SupportedBits,

fn default() -> Self

Returns the “default value” for a type.

impl<const B: usize> MemDbgImpl for PackedSeqVecBase<B>

where Bits<B>: SupportedBits, Vec<u8>: MemDbgImpl, usize: MemDbgImpl,

fn _mem_dbg_rec_on( &self, _memdbg_writer: &mut impl Write, _memdbg_total_size: usize, _memdbg_max_depth: usize, _memdbg_prefix: &mut String, _memdbg_is_last: bool, _memdbg_flags: DbgFlags, ) -> Result

fn _mem_dbg_depth_on( &self, writer: &mut impl Write, total_size: usize, max_depth: usize, prefix: &mut String, field_name: Option<&str>, is_last: bool, padded_size: usize, flags: DbgFlags, ) -> Result<(), Error>

impl<const B: usize> MemSize for PackedSeqVecBase<B>

where Bits<B>: SupportedBits, Vec<u8>: MemSize, usize: MemSize,

fn mem_size(&self, _memsize_flags: SizeFlags) -> usize

Returns the (recursively computed) overall memory size of the structure in bytes.

impl<const B: usize> SeqVec for PackedSeqVecBase<B>

where Bits<B>: SupportedBits,

fn push_ascii(&mut self, seq: &[u8]) -> Range<usize>

For PackedSeqVec (2-bit encoding): map ASCII ACGT (and acgt) to DNA 0132 in that order. Other characters are silently mapped into 0..4.

Uses the BMI2 pext instruction when available, based on the n_to_bits_pext method described at https://github.com/Daniel-Liu-c0deb0t/cute-nucleotides.

For BitSeqVec (1-bit encoding): map ACGTacgt to 0, and everything else to 1.

type Seq<'s> = PackedSeqBase<'s, B>

fn into_raw(self) -> Vec<u8>

Convert into the underlying raw representation.

fn as_slice(&self) -> Self::Seq<'_>

Get a non-owning slice to the underlying sequence.

fn len(&self) -> usize

The length of the sequence in characters.

fn is_empty(&self) -> bool

Returns true if the sequence is empty.

fn clear(&mut self)

Empty the sequence.

fn push_seq<'a>(&mut self, seq: PackedSeqBase<'_, B>) -> Range<usize>

Append the given sequence to the underlying storage.

fn random(n: usize) -> Self

Generate a random sequence with the given number of characters.

fn slice(&self, range: Range<usize>) -> Self::Seq<'_>

Get a sub-slice of the sequence. Indices are character offsets.

fn read_kmer(&self, k: usize, pos: usize) -> u64

Extract a k-mer from this sequence.

fn read_revcomp_kmer(&self, k: usize, pos: usize) -> u64

Extract a k-mer from this sequence.

fn read_kmer_u128(&self, k: usize, pos: usize) -> u128

Extract a k-mer from this sequence.

fn read_revcomp_kmer_u128(&self, k: usize, pos: usize) -> u128

Extract a k-mer from this sequence.

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

Create a SeqVec from ASCII input.