Struct AsciiSeq

pub struct AsciiSeq<'s>(pub &'s [u8]);

A &[u8] representing an ASCII-encoded DNA sequence of ACGTacgt.

Other characters will be mapped into [0, 4) via (c>>1)&3, or may cause panics.

Tuple Fields

0: &'s [u8]

Trait Implementations

impl<'s> Clone for AsciiSeq<'s>

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

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl<'s> CopyType for AsciiSeq<'s>

where &'s [u8]: MemSize,

type Copy = False

impl<'s> Debug for AsciiSeq<'s>

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

Formats the value using the given formatter.

impl<'s> MemDbgImpl for AsciiSeq<'s>

where &'s [u8]: 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 AsciiSeq<'s>

where &'s [u8]: MemSize,

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

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

impl<'s> Ord for AsciiSeq<'s>

fn cmp(&self, other: &AsciiSeq<'s>) -> Ordering

This method returns an Ordering between self and other.

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<'s> PartialEq for AsciiSeq<'s>

fn eq(&self, other: &AsciiSeq<'s>) -> bool

Tests for self and other values to be equal, and is used by ==.

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<'s> PartialOrd for AsciiSeq<'s>

fn partial_cmp(&self, other: &AsciiSeq<'s>) -> 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 AsciiSeq<'s>

Maps ASCII to [0, 4) on the fly. Prefer first packing into a PackedSeqVec for storage.

const BASES_PER_BYTE: usize = 1usize

Each input byte stores a single character.

const BITS_PER_CHAR: usize = 2usize

But each output bp only takes 2 bits!

fn to_vec(&self) -> AsciiSeqVec

Convert to an owned version.

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

Iterate the basepairs in the sequence, assuming values in 0..4.

NOTE: This is only efficient on x86_64 with BMI2 support for pext.

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

Iterate the basepairs in the sequence in 8 parallel streams, assuming values in 0..4.

type SeqVec = AsciiSeqVec

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 as_u64(&self) -> u64

Convert a short sequence (kmer) to a packed representation as u64.

fn revcomp_as_u64(&self) -> u64

Convert a short sequence (kmer) to a packed representation of its reverse complement as u64.

fn to_revcomp(&self) -> AsciiSeqVec

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

Iterate over 8 chunks of the sequence in parallel, returning two characters offset by delay positions.

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

Iterate over 8 chunks of the sequence in parallel, returning three characters: the char added, the one delay positions before, and the one delay2 positions before.

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

Compare and return the LCP of the two sequences.

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 AsciiSeq<'s>

impl<'s> Eq for AsciiSeq<'s>

impl<'s> StructuralPartialEq for AsciiSeq<'s>