// Code generated by protoc-gen-go. DO NOT EDIT.
// source: google/genomics/v1/cigar.proto

package genomics // import "google.golang.org/genproto/googleapis/genomics/v1"

import proto "github.com/golang/protobuf/proto"
import fmt "fmt"
import math "math"
import _ "google.golang.org/genproto/googleapis/api/annotations"

// Reference imports to suppress errors if they are not otherwise used.
var _ = proto.Marshal
var _ = fmt.Errorf
var _ = math.Inf

// This is a compile-time assertion to ensure that this generated file
// is compatible with the proto package it is being compiled against.
// A compilation error at this line likely means your copy of the
// proto package needs to be updated.
const _ = proto.ProtoPackageIsVersion2 // please upgrade the proto package

// Describes the different types of CIGAR alignment operations that exist.
// Used wherever CIGAR alignments are used.
type CigarUnit_Operation int32

const (
	CigarUnit_OPERATION_UNSPECIFIED CigarUnit_Operation = 0
	// 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`.
	CigarUnit_ALIGNMENT_MATCH CigarUnit_Operation = 1
	// The insert operator indicates that the read contains evidence of bases
	// being inserted into the reference. This operator is equivalent to SAM's
	// `I`.
	CigarUnit_INSERT CigarUnit_Operation = 2
	// The delete operator indicates that the read contains evidence of bases
	// being deleted from the reference. This operator is equivalent to SAM's
	// `D`.
	CigarUnit_DELETE CigarUnit_Operation = 3
	// 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`.
	CigarUnit_SKIP CigarUnit_Operation = 4
	// 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.
	CigarUnit_CLIP_SOFT CigarUnit_Operation = 5
	// 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`.
	CigarUnit_CLIP_HARD CigarUnit_Operation = 6
	// The pad operator indicates that there is padding in an alignment. This
	// operator is equivalent to SAM's `P`.
	CigarUnit_PAD CigarUnit_Operation = 7
	// This operator indicates that this portion of the aligned sequence exactly
	// matches the reference. This operator is equivalent to SAM's `=`.
	CigarUnit_SEQUENCE_MATCH CigarUnit_Operation = 8
	// 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`.
	CigarUnit_SEQUENCE_MISMATCH CigarUnit_Operation = 9
)

var CigarUnit_Operation_name = map[int32]string{
	0: "OPERATION_UNSPECIFIED",
	1: "ALIGNMENT_MATCH",
	2: "INSERT",
	3: "DELETE",
	4: "SKIP",
	5: "CLIP_SOFT",
	6: "CLIP_HARD",
	7: "PAD",
	8: "SEQUENCE_MATCH",
	9: "SEQUENCE_MISMATCH",
}
var CigarUnit_Operation_value = map[string]int32{
	"OPERATION_UNSPECIFIED": 0,
	"ALIGNMENT_MATCH":       1,
	"INSERT":                2,
	"DELETE":                3,
	"SKIP":                  4,
	"CLIP_SOFT":             5,
	"CLIP_HARD":             6,
	"PAD":                   7,
	"SEQUENCE_MATCH":        8,
	"SEQUENCE_MISMATCH":     9,
}

func (x CigarUnit_Operation) String() string {
	return proto.EnumName(CigarUnit_Operation_name, int32(x))
}
func (CigarUnit_Operation) EnumDescriptor() ([]byte, []int) {
	return fileDescriptor_cigar_6b0f6bba324393a8, []int{0, 0}
}

// A single CIGAR operation.
type CigarUnit struct {
	Operation CigarUnit_Operation `protobuf:"varint,1,opt,name=operation,proto3,enum=google.genomics.v1.CigarUnit_Operation" json:"operation,omitempty"`
	// The number of genomic bases that the operation runs for. Required.
	OperationLength int64 `protobuf:"varint,2,opt,name=operation_length,json=operationLength,proto3" json:"operation_length,omitempty"`
	// `referenceSequence` is only used at mismatches
	// (`SEQUENCE_MISMATCH`) and deletions (`DELETE`).
	// Filling this field replaces SAM's MD tag. If the relevant information is
	// not available, this field is unset.
	ReferenceSequence    string   `protobuf:"bytes,3,opt,name=reference_sequence,json=referenceSequence,proto3" json:"reference_sequence,omitempty"`
	XXX_NoUnkeyedLiteral struct{} `json:"-"`
	XXX_unrecognized     []byte   `json:"-"`
	XXX_sizecache        int32    `json:"-"`
}

func (m *CigarUnit) Reset()         { *m = CigarUnit{} }
func (m *CigarUnit) String() string { return proto.CompactTextString(m) }
func (*CigarUnit) ProtoMessage()    {}
func (*CigarUnit) Descriptor() ([]byte, []int) {
	return fileDescriptor_cigar_6b0f6bba324393a8, []int{0}
}
func (m *CigarUnit) XXX_Unmarshal(b []byte) error {
	return xxx_messageInfo_CigarUnit.Unmarshal(m, b)
}
func (m *CigarUnit) XXX_Marshal(b []byte, deterministic bool) ([]byte, error) {
	return xxx_messageInfo_CigarUnit.Marshal(b, m, deterministic)
}
func (dst *CigarUnit) XXX_Merge(src proto.Message) {
	xxx_messageInfo_CigarUnit.Merge(dst, src)
}
func (m *CigarUnit) XXX_Size() int {
	return xxx_messageInfo_CigarUnit.Size(m)
}
func (m *CigarUnit) XXX_DiscardUnknown() {
	xxx_messageInfo_CigarUnit.DiscardUnknown(m)
}

var xxx_messageInfo_CigarUnit proto.InternalMessageInfo

func (m *CigarUnit) GetOperation() CigarUnit_Operation {
	if m != nil {
		return m.Operation
	}
	return CigarUnit_OPERATION_UNSPECIFIED
}

func (m *CigarUnit) GetOperationLength() int64 {
	if m != nil {
		return m.OperationLength
	}
	return 0
}

func (m *CigarUnit) GetReferenceSequence() string {
	if m != nil {
		return m.ReferenceSequence
	}
	return ""
}

func init() {
	proto.RegisterType((*CigarUnit)(nil), "google.genomics.v1.CigarUnit")
	proto.RegisterEnum("google.genomics.v1.CigarUnit_Operation", CigarUnit_Operation_name, CigarUnit_Operation_value)
}

func init() {
	proto.RegisterFile("google/genomics/v1/cigar.proto", fileDescriptor_cigar_6b0f6bba324393a8)
}

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