Enum gapi_grpc::google::genomics::v1::cigar_unit::Operation

#[repr(i32)]pub enum Operation {
    Unspecified,
    AlignmentMatch,
    Insert,
    Delete,
    Skip,
    ClipSoft,
    ClipHard,
    Pad,
    SequenceMatch,
    SequenceMismatch,
}

Describes the different types of CIGAR alignment operations that exist. Used wherever CIGAR alignments are used.

Variants

Unspecified

AlignmentMatch

An alignment match indicates that a sequence can be aligned to the reference without evidence of an INDEL. Unlike the SEQUENCE_MATCH and SEQUENCE_MISMATCH operators, the ALIGNMENT_MATCH operator does not indicate whether the reference and read sequences are an exact match. This operator is equivalent to SAM’s M.

Insert

The insert operator indicates that the read contains evidence of bases being inserted into the reference. This operator is equivalent to SAM’s I.

Delete

The delete operator indicates that the read contains evidence of bases being deleted from the reference. This operator is equivalent to SAM’s D.

Skip

The skip operator indicates that this read skips a long segment of the reference, but the bases have not been deleted. This operator is commonly used when working with RNA-seq data, where reads may skip long segments of the reference between exons. This operator is equivalent to SAM’s N.

ClipSoft

The soft clip operator indicates that bases at the start/end of a read have not been considered during alignment. This may occur if the majority of a read maps, except for low quality bases at the start/end of a read. This operator is equivalent to SAM’s S. Bases that are soft clipped will still be stored in the read.

ClipHard

The hard clip operator indicates that bases at the start/end of a read have been omitted from this alignment. This may occur if this linear alignment is part of a chimeric alignment, or if the read has been trimmed (for example, during error correction or to trim poly-A tails for RNA-seq). This operator is equivalent to SAM’s H.

Pad

The pad operator indicates that there is padding in an alignment. This operator is equivalent to SAM’s P.

SequenceMatch

This operator indicates that this portion of the aligned sequence exactly matches the reference. This operator is equivalent to SAM’s =.

SequenceMismatch

This operator indicates that this portion of the aligned sequence is an alignment match to the reference, but a sequence mismatch. This can indicate a SNP or a read error. This operator is equivalent to SAM’s X.

Implementations

impl Operation

pub fn is_valid(value: i32) -> bool

Returns true if value is a variant of Operation.

pub fn from_i32(value: i32) -> Option<Operation>

Converts an i32 to a Operation, or None if value is not a valid variant.

Trait Implementations

impl Clone for Operation

fn clone(&self) -> Operation

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Copy for Operation

impl Debug for Operation

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

Formats the value using the given formatter.

impl Default for Operation

fn default() -> Operation

Returns the “default value” for a type.

impl Eq for Operation

impl From<Operation> for i32

fn from(value: Operation) -> i32

Performs the conversion.

impl Hash for Operation

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

Feeds this value into the given Hasher.

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

Feeds a slice of this type into the given Hasher.

impl Ord for Operation

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

This method returns an Ordering between self and other.

#[must_use]pub fn max(self, other: Self) -> Self

Compares and returns the maximum of two values.

#[must_use]pub fn min(self, other: Self) -> Self

Compares and returns the minimum of two values.

#[must_use]pub fn clamp(self, min: Self, max: Self) -> Self

Restrict a value to a certain interval.

impl PartialEq<Operation> for Operation

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

This method tests for self and other values to be equal, and is used by ==.

#[must_use]pub fn ne(&self, other: &Rhs) -> bool

This method tests for !=.

impl PartialOrd<Operation> for Operation

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

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

#[must_use]pub fn lt(&self, other: &Rhs) -> bool

This method tests less than (for self and other) and is used by the < operator.

#[must_use]pub fn le(&self, other: &Rhs) -> bool

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

#[must_use]pub fn gt(&self, other: &Rhs) -> bool

This method tests greater than (for self and other) and is used by the > operator.

#[must_use]pub fn ge(&self, other: &Rhs) -> bool

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

impl StructuralEq for Operation

impl StructuralPartialEq for Operation