Struct PackedSeqVec 

pub struct PackedSeqVec { /* private fields */ }

A 2-bit packed owned sequence of DNA bases.

Trait Implementations

impl Clone for PackedSeqVec

fn clone(&self) -> PackedSeqVec

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl CopyType for PackedSeqVec

where Vec<u8>: MemSize, usize: MemSize,

type Copy = False

impl Debug for PackedSeqVec

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

Formats the value using the given formatter.

impl Default for PackedSeqVec

fn default() -> Self

Returns the “default value” for a type.

impl MemDbgImpl for PackedSeqVec

where 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 MemSize for PackedSeqVec

where 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 SeqVec for PackedSeqVec

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

Push an ASCII sequence to an PackedSeqVec. Aa map to 0, Cc to 1, Gg to 3, and Tt to 2. 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.

TODO: Support multiple ways of dealing with non-ACTG characters:

• panic on non-ACGT,
• filter out non-ACGT.

type Seq<'s> = PackedSeq<'s>

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: PackedSeq<'_>) -> 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 from_ascii(seq: &[u8]) -> Self

Create a SeqVec from ASCII input.