Struct Reads 

pub struct Reads<D> { /* private fields */ }

Store many DNA sequences together with an Exts and data each compactly packed together

fields:

• storage: Vec with 2-bit encoded DNA bases of all sequences
• ends: Vec with the ends (exclusive) of the separate sequences in the Reads
• exts: Option<Vec> with one Exts for each sequence
• data: Vec with data for each sequence
• len: length of all sequences together
• stranded: [Stranded] conveying the strandedness and direction of the reads

Implementations

impl<D: Clone + Copy> Reads<D>

pub fn new(stranded: Strandedness) -> Self

Returns a new Reads

pub fn new_with_quality(stranded: Strandedness) -> Self

pub fn stranded(&self) -> Strandedness

pub fn n_reads(&self) -> usize

Returns the number of reads stored

pub fn mem(&self) -> usize

get the memory required for the reads

pub fn set_stranded(&mut self, stranded: Strandedness)

set the strandedness and the direction of the reads

pub fn set_custom_quality_bins(&mut self, quality_bins: QualityBins)

set custom quality bins

pub fn add_read<V: Vmer>( &mut self, seq: V, exts: Option<Exts>, data: D, quality_scores: Option<&[u8]>, )

Adds a new read to the Reads

pub fn from_vmer_vec<V: Vmer, S: IntoIterator<Item = (V, Exts, D)>>( vec_iter: S, stranded: Strandedness, ) -> Self

Transforms a [(vmer, exts, data)] into a Reads - watch for memory usage

pub fn add_from_bytes(&mut self, bytes: &[u8], exts: Option<Exts>, data: D)

add ASCII encoded bases to the Reads

will transform all ascii characters outside of ACGTacgt into A

if Reads previously contained no exts, no new exts will be added see also: Reads::add_from_bytes_checked

pub fn add_from_bytes_checked( &mut self, bytes: &[u8], exts: Option<Exts>, data: D, ) -> bool

add ASCII encoded bases to the Reads

will return false if the bytes contained characters outside of ACGTacgt, otherwise return true and add the bases see also: Reads::add_from_bytes

pub fn get_read(&self, i: usize) -> Option<Read<D>>

get the ith read in a Reads

pub fn shrink_to_fit(&mut self)

shrink the vectors’ capacity to fit the length

use sparsely

pub fn iter(&self) -> ReadsIter<'_, D>

Iterate over the reads as (DnaString, Exts, D).

pub fn partial_iter(&self, range: Range<usize>) -> ReadsIter<'_, D>

Iterate over a range start reads as (DnaString, Exts, D).

pub fn info(&self) -> String

impl<D: ReadData> Reads<D>

pub fn tag_kmers(&self, k: usize) -> HashMap<Tag, usize>

get the number of k-mers for each unique data value

Trait Implementations

impl<D: Clone> Clone for Reads<D>

fn clone(&self) -> Reads<D>

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl<D: Debug> Debug for Reads<D>

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

Formats the value using the given formatter.

impl<D: Clone + Copy> Default for Reads<D>

fn default() -> Self

Returns the “default value” for a type.

impl<'de, D> Deserialize<'de> for Reads<D>

where D: Deserialize<'de>,

fn deserialize<__D>(__deserializer: __D) -> Result<Self, __D::Error>

where __D: Deserializer<'de>,

Deserialize this value from the given Serde deserializer.

impl<D: Clone + Copy + Debug> Display for Reads<D>

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

Formats the value using the given formatter.

impl<D: Hash> Hash for Reads<D>

fn hash<__H: Hasher>(&self, state: &mut __H)

Feeds this value into the given Hasher.

fn hash_slice<H>(data: &[Self], state: &mut H)

where H: Hasher, Self: Sized,

Feeds a slice of this type into the given Hasher.

impl<D: Ord> Ord for Reads<D>

fn cmp(&self, other: &Reads<D>) -> 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<D: PartialEq> PartialEq for Reads<D>

fn eq(&self, other: &Reads<D>) -> 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<D: PartialOrd> PartialOrd for Reads<D>

fn partial_cmp(&self, other: &Reads<D>) -> 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<D> Serialize for Reads<D>

where D: Serialize,

fn serialize<__S>(&self, __serializer: __S) -> Result<__S::Ok, __S::Error>

where __S: Serializer,

Serialize this value into the given Serde serializer.

impl<D: Eq> Eq for Reads<D>

impl<D> StructuralPartialEq for Reads<D>