Enum google_api_proto::google::genomics::v1::cigar_unit::Operation

#[repr(i32)]
pub enum Operation {
    Unspecified = 0,
    AlignmentMatch = 1,
    Insert = 2,
    Delete = 3,
    Skip = 4,
    ClipSoft = 5,
    ClipHard = 6,
    Pad = 7,
    SequenceMatch = 8,
    SequenceMismatch = 9,
}

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

Variants

Unspecified = 0

AlignmentMatch = 1

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 = 2

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 = 3

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 = 4

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 = 5

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 = 6

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 = 7

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

SequenceMatch = 8

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

SequenceMismatch = 9

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>

👎Deprecated: Use the TryFrom<i32> implementation instead

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

impl Operation

pub fn as_str_name(&self) -> &'static str

String value of the enum field names used in the ProtoBuf definition.

The values are not transformed in any way and thus are considered stable (if the ProtoBuf definition does not change) and safe for programmatic use.

pub fn from_str_name(value: &str) -> Option<Self>

Creates an enum from field names used in the ProtoBuf definition.

Trait Implementations

impl Clone for Operation

fn clone(&self) -> Operation

Returns a copy of the value.

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

Performs copy-assignment from source.

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 From<Operation> for i32

fn from(value: Operation) -> i32

Converts to this type from the input type.

impl Hash for Operation

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 Ord for Operation

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

Restrict a value to a certain interval.

impl PartialEq for Operation

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

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

fn ne(&self, other: &Rhs) -> bool

This method tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl PartialOrd for Operation

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

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

fn lt(&self, other: &Rhs) -> bool

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

fn le(&self, other: &Rhs) -> bool

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

fn gt(&self, other: &Rhs) -> bool

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

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 TryFrom<i32> for Operation

type Error = DecodeError

The type returned in the event of a conversion error.

fn try_from(value: i32) -> Result<Operation, DecodeError>

Performs the conversion.

impl Copy for Operation

impl Eq for Operation

impl StructuralPartialEq for Operation