Struct PackedSeqVec

pub struct PackedSeqVec {
    pub seq: Vec<u8>,
    pub len: usize,
}

A 2-bit packed owned sequence of DNA bases.

Fields

seq: Vec<u8>

len: usize

Trait Implementations

impl Clone for PackedSeqVec

fn clone(&self) -> PackedSeqVec

Returns a copy 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() -> PackedSeqVec

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 may be silently mapped into [0, 4) or panic. (TODO: Explicitly support different conversions.)

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: Optimize for non-BMI2 platforms. TODO: Support multiple ways of dealing with non-ACTG characters.

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 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 len(&self) -> usize

The length of the sequence in characters.

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

Create a SeqVec from ASCII input.