Struct PackedNSeqVec 

pub struct PackedNSeqVec {
    pub seq: PackedSeqVec,
    pub ambiguous: BitSeqVec,
}

Fields

seq: PackedSeqVec

ambiguous: BitSeqVec

Implementations

impl PackedNSeqVec

Implement a subset of SeqVec for PackedNSeqVec.

pub fn clear(&mut self)

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

Available on crate feature rand only.

pub fn as_slice(&self) -> PackedNSeq<'_>

pub fn slice(&self, range: Range<usize>) -> PackedNSeq<'_>

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

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

pub fn from_ascii_and_quality( seq: &[u8], quality: &[u8], threshold: usize, ) -> Self

Create a mask that is 1 for all non-ACGT bases and for all low-quality bases with quality <threshold.

pub fn push_from_ascii_and_quality( &mut self, seq: &[u8], quality: &[u8], min_qual: u8, )

Create a mask that is 1 for all non-ACGT bases and for all low-quality bases with quality <threshold.

pub fn from_fastx(path: &Path) -> Self

Available on crate feature file_io only.

Read a fasta/fastq file at the given path into a PackedNSeq, separating records with N.

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

Available on crate feature file_io only.

Read FASTA/FASTQ using Helicase’s parallel reader, separating records with N.

Does not preserve the order or records!

Chunk boundaries may contain extra Ns for byte alignment.

pub fn from_fastq_with_quality(path: &Path, min_qual: u8) -> Self

Available on crate feature file_io only.

Read a fasta/fastq file at the given path into a PackedNSeq, separating records with N. Low-quality bases are masked out.

pub fn from_fastq_with_quality_parallel( path: &Path, min_qual: u8, num_threads: usize, ) -> Self

Available on crate feature file_io only.

Read FASTQ using Helicase’s parallel reader, separating records with N.

Masks non-ACGT bases and qualities below min_qual. Does not preserve the order or records! Chunk boundaries may contain extra Ns for byte alignment.

Trait Implementations

impl Clone for PackedNSeqVec

fn clone(&self) -> Self

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for PackedNSeqVec

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

Formats the value using the given formatter.

impl Default for PackedNSeqVec

fn default() -> Self

Returns the “default value” for a type.

impl FlatType for PackedNSeqVec

where PackedSeqVec: MemSize + FlatType, BitSeqVec: MemSize + FlatType,

type Flat = False

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

impl MemDbgImpl for PackedNSeqVec

where PackedSeqVec: MemDbgImpl + FlatType, BitSeqVec: 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 MemSize for PackedNSeqVec

where PackedSeqVec: MemSize + FlatType, BitSeqVec: 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.