Enum ReadsPaired 

pub enum ReadsPaired<D> {
    Empty,
    Unpaired {
        reads: Reads<D>,
    },
    Paired {
        paired1: Reads<D>,
        paired2: Reads<D>,
    },
    Combined {
        paired1: Reads<D>,
        paired2: Reads<D>,
        unpaired: Reads<D>,
    },
}

Variants

Empty

Unpaired

Fields

reads: Reads<D>

Paired

Fields

paired1: Reads<D>

paired2: Reads<D>

Combined

Fields

paired1: Reads<D>

paired2: Reads<D>

unpaired: Reads<D>

Implementations

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

pub fn iterable(&self) -> Vec<&Reads<D>>

return an iterable element (Vec) with all contained Reads

pub fn n_reads(&self) -> usize

the overall number of reads

pub fn n_read_pairs(&self) -> usize

the number of paired reads

pub fn n_unpaired_reads(&self) -> usize

the number of unpaired reads

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

get the read with the index i from the ReadsPaired - with multiple underlying Reads its is counted linearly trough paired1, paired2, unpaired

pub fn get_paired_read(&self, i: usize) -> Option<PairedRead<D>>

pub fn mem(&self) -> usize

pub fn from_reads( (paired1, paired2, unpaired): (Reads<D>, Reads<D>, Reads<D>), ) -> Self

transform a tuple of two paired Reads and one unpaired Reads into a ReadsPaired depending on the contents of the Reads

pub fn iter(&self) -> Box<dyn Iterator<Item = Read<D>> + '_>

pub fn iter_partial( &self, range: Range<usize>, ) -> Box<dyn Iterator<Item = Read<D>> + '_>

pub fn decombine(&mut self) -> usize

if the ReadsPaired is of Combined type, remove the unpaired reads, returns the number of reads that were removed

impl<DI: ReadData> ReadsPaired<DI>

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

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

pub fn tag_kmers_vec(&self, k: usize, n_samples: usize) -> Vec<u64>

return the number of k-mers occuring with each u8-encoded tag, with the tag as the index if there are no tags saved in the Readspauired, it returns a vector of the length n_sampeles, filles with zeroes

Trait Implementations

impl<D: Clone> Clone for ReadsPaired<D>

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

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl<D: Debug> Debug for ReadsPaired<D>

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

Formats the value using the given formatter.

impl<'de, D> Deserialize<'de> for ReadsPaired<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> Display for ReadsPaired<D>

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

Formats the value using the given formatter.

impl<D: Hash> Hash for ReadsPaired<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 ReadsPaired<D>

fn cmp(&self, other: &ReadsPaired<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 ReadsPaired<D>

fn eq(&self, other: &ReadsPaired<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 ReadsPaired<D>

fn partial_cmp(&self, other: &ReadsPaired<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 ReadsPaired<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 ReadsPaired<D>

impl<D> StructuralPartialEq for ReadsPaired<D>