Struct PackedSeq

pub struct PackedSeq<'s> { /* private fields */ }

A 2-bit packed non-owned slice of DNA bases.

Implementations

impl PackedSeq<'_>

pub fn normalize(&self) -> Self

Shrink seq to only just cover the data.

pub fn unpack(&self) -> Vec<u8>

Return a Vec<u8> of ASCII ACTG characters.

Trait Implementations

impl<'s> Clone for PackedSeq<'s>

fn clone(&self) -> PackedSeq<'s>

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl<'s> CopyType for PackedSeq<'s>

where &'s [u8]: MemSize, usize: MemSize,

type Copy = False

impl<'s> Debug for PackedSeq<'s>

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

Formats the value using the given formatter.

impl<'s> MemDbgImpl for PackedSeq<'s>

where &'s [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<'s> MemSize for PackedSeq<'s>

where &'s [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 Ord for PackedSeq<'_>

fn cmp(&self, other: &Self) -> Ordering

Compares 29 characters at a time.

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

where Self: Sized,

Compares and returns the maximum of two values.

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

where Self: Sized,

Compares and returns the minimum of two values.

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

where Self: Sized,

Restrict a value to a certain interval.

impl PartialEq for PackedSeq<'_>

fn eq(&self, other: &Self) -> bool

Compares 29 characters at a time.

fn ne(&self, other: &Rhs) -> bool

Tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl PartialOrd for PackedSeq<'_>

fn partial_cmp(&self, other: &Self) -> Option<Ordering>

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

fn lt(&self, other: &Rhs) -> bool

Tests less than (for self and other) and is used by the < operator.

fn le(&self, other: &Rhs) -> bool

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

fn gt(&self, other: &Rhs) -> bool

Tests greater than (for self and other) and is used by the > operator.

fn ge(&self, other: &Rhs) -> bool

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

impl<'s> Seq<'s> for PackedSeq<'s>

fn as_u64(&self) -> u64

Convert a short sequence (kmer) to a packed representation as usize. Panics if self is longer than 32 characters.

fn revcomp_as_u64(&self) -> u64

Convert a short sequence (kmer) to a packed representation of its reverse complement as usize. Panics if self is longer than 32 characters.

fn par_iter_bp_delayed( self, context: usize, delay: usize, ) -> (impl ExactSizeIterator<Item = (S, S)> + Clone, usize)

NOTE: When self starts does not start at a byte boundary, the ‘delayed’ character is not guaranteed to be 0.

fn par_iter_bp_delayed_2( self, context: usize, delay1: usize, delay2: usize, ) -> (impl ExactSizeIterator<Item = (S, S, S)> + Clone, usize)

NOTE: When self starts does not start at a byte boundary, the ‘delayed’ character is not guaranteed to be 0.

fn cmp_lcp(&self, other: &Self) -> (Ordering, usize)

Compares 29 characters at a time.

const BASES_PER_BYTE: usize = 4usize

Number of encoded characters per byte of memory of the Seq.

const BITS_PER_CHAR: usize = 2usize

Number of bits b to represent each character returned by iter_bp and variants..

type SeqVec = PackedSeqVec

The corresponding owned sequence type.

fn len(&self) -> usize

The length of the sequence in characters.

fn is_empty(&self) -> bool

Returns true if the sequence is empty.

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

Get the character at the given index.

fn get_ascii(&self, index: usize) -> u8

Get the ASCII character at the given index, without mapping to b-bit values.

fn to_vec(&self) -> PackedSeqVec

Convert to an owned version.

fn to_revcomp(&self) -> PackedSeqVec

Compute the reverse complement of this sequence.

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

Get a sub-slice of the sequence. range indicates character indices.

fn iter_bp(self) -> impl ExactSizeIterator<Item = u8> + Clone

Iterate over the b-bit characters of the sequence.

fn par_iter_bp( self, context: usize, ) -> (impl ExactSizeIterator<Item = S> + Clone, usize)

Iterate over 8 chunks of b-bit characters of the sequence in parallel.

fn bits_per_char(&self) -> usize

Convenience function that returns b=Self::BITS_PER_CHAR.

fn to_word(&self) -> usize

👎Deprecated: Prefer to_u64.

Convert a short sequence (kmer) to a packed representation as usize.

fn to_word_revcomp(&self) -> usize

👎Deprecated: Prefer revcomp_to_u64.

Convert a short sequence (kmer) to a packed representation of its reverse complement as usize.

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 reverse complement k-mer from this sequence.

impl<'s> Copy for PackedSeq<'s>

impl Eq for PackedSeq<'_>