Struct PackedSeqVecBase 

pub struct PackedSeqVecBase<const B: usize> { /* private fields */ }

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

Implementations

impl PackedSeqVecBase<2>

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.

pub fn from_fastx(path: &Path) -> (Self, Vec<Range<usize>>)

Available on crate feature file_io only.

Read a fasta/fastq file at the given path into a PackedSeq. Returns the sequence as well as the slices of all records.

Currently, all slices are bit-packed, without any padding.

pub fn from_fastx_parallel( path: &Path, num_threads: usize, ) -> (Self, Vec<Range<usize>>)

Available on crate feature file_io only.

Read a plain FASTA/FASTQ file using num_threads workers. NOTE: This may return data out-of-order!

Returns the sequence and record ranges in chunk completion order. There may be padding between chunks; use the returned ranges to access records. A thread count of zero disables multi-threading. Compression formats without parallel decoding support are read sequentially.

impl PackedSeqVecBase<1>

pub fn with_len(n: usize) -> Self

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

Available on crate feature rand only.

Trait Implementations

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

fn clone(&self) -> Self

Returns a duplicate of the value.

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

Performs copy-assignment from source.

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

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> FlatType for PackedSeqVecBase<B>

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

type Flat = False

Whether the type is flat (True) or not (False).

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

where Vec<u8>: MemDbgImpl + FlatType, usize: MemDbgImpl + FlatType,

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, _memdbg_refs: &mut HashSet<usize>, ) -> Result

Recursively displays the fields of self below the current line.

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, dbg_refs: &mut HashSet<usize>, ) -> Result<(), Error>

Displays self at the given depth without any reference-address annotation; forwards to _mem_dbg_depth_on_impl with RefDisplay::None.

fn _mem_dbg_depth_on_impl( &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, dbg_refs: &mut HashSet<usize>, ref_display: RefDisplay, ) -> Result<(), Error>

Internal implementation for depth display.

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

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

fn mem_size_rec( &self, _memsize_flags: SizeFlags, _memsize_refs: &mut HashMap<usize, usize>, ) -> usize

Recursive implementation that tracks visited references for deduplication.

fn mem_size(&self, 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.

Returns the range of the newly added sequence in the packed representation.

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

Available on crate feature rand only.

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.