googleapis/genomics/v1/cigar.pb.go - third_party/github.com/googleapis/go-genproto - Git at Google

 // Copyright 2016 Google Inc.
 //
 // Licensed under the Apache License, Version 2.0 (the "License");
 // you may not use this file except in compliance with the License.
 // You may obtain a copy of the License at
 //
 //     http://www.apache.org/licenses/LICENSE-2.0
 //
 // Unless required by applicable law or agreed to in writing, software
 // distributed under the License is distributed on an "AS IS" BASIS,
 // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 // See the License for the specific language governing permissions and
 // limitations under the License.

 // Code generated by protoc-gen-go. DO NOT EDIT.
 // versions:
 // 	protoc-gen-go v1.22.0
 // 	protoc        v3.12.2
 // source: google/genomics/v1/cigar.proto

 package genomics

 import (
 	reflect "reflect"
 	sync "sync"

 	proto "github.com/golang/protobuf/proto"
 	_ "google.golang.org/genproto/googleapis/api/annotations"
 	protoreflect "google.golang.org/protobuf/reflect/protoreflect"
 	protoimpl "google.golang.org/protobuf/runtime/protoimpl"
 )

 const (
 	// Verify that this generated code is sufficiently up-to-date.
 	_ = protoimpl.EnforceVersion(20 - protoimpl.MinVersion)
 	// Verify that runtime/protoimpl is sufficiently up-to-date.
 	_ = protoimpl.EnforceVersion(protoimpl.MaxVersion - 20)
 )

 // This is a compile-time assertion that a sufficiently up-to-date version
 // of the legacy proto package is being used.
 const _ = proto.ProtoPackageIsVersion4

 // 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
 )

 // Enum value maps for CigarUnit_Operation.
 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",
 	}
 	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) Enum() *CigarUnit_Operation {
 	p := new(CigarUnit_Operation)
 	*p = x
 	return p
 }

 func (x CigarUnit_Operation) String() string {
 	return protoimpl.X.EnumStringOf(x.Descriptor(), protoreflect.EnumNumber(x))
 }

 func (CigarUnit_Operation) Descriptor() protoreflect.EnumDescriptor {
 	return file_google_genomics_v1_cigar_proto_enumTypes[0].Descriptor()
 }

 func (CigarUnit_Operation) Type() protoreflect.EnumType {
 	return &file_google_genomics_v1_cigar_proto_enumTypes[0]
 }

 func (x CigarUnit_Operation) Number() protoreflect.EnumNumber {
 	return protoreflect.EnumNumber(x)
 }

 // Deprecated: Use CigarUnit_Operation.Descriptor instead.
 func (CigarUnit_Operation) EnumDescriptor() ([]byte, []int) {
 	return file_google_genomics_v1_cigar_proto_rawDescGZIP(), []int{0, 0}
 }

 // A single CIGAR operation.
 type CigarUnit struct {
 	state         protoimpl.MessageState
 	sizeCache     protoimpl.SizeCache
 	unknownFields protoimpl.UnknownFields

 	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"`
 }

 func (x *CigarUnit) Reset() {
 	*x = CigarUnit{}
 	if protoimpl.UnsafeEnabled {
 		mi := &file_google_genomics_v1_cigar_proto_msgTypes[0]
 		ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x))
 		ms.StoreMessageInfo(mi)
 	}
 }

 func (x *CigarUnit) String() string {
 	return protoimpl.X.MessageStringOf(x)
 }

 func (*CigarUnit) ProtoMessage() {}

 func (x *CigarUnit) ProtoReflect() protoreflect.Message {
 	mi := &file_google_genomics_v1_cigar_proto_msgTypes[0]
 	if protoimpl.UnsafeEnabled && x != nil {
 		ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x))
 		if ms.LoadMessageInfo() == nil {
 			ms.StoreMessageInfo(mi)
 		}
 		return ms
 	}
 	return mi.MessageOf(x)
 }

 // Deprecated: Use CigarUnit.ProtoReflect.Descriptor instead.
 func (*CigarUnit) Descriptor() ([]byte, []int) {
 	return file_google_genomics_v1_cigar_proto_rawDescGZIP(), []int{0}
 }

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

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

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

 var File_google_genomics_v1_cigar_proto protoreflect.FileDescriptor

 var file_google_genomics_v1_cigar_proto_rawDesc = []byte{
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 }

 var (
 	file_google_genomics_v1_cigar_proto_rawDescOnce sync.Once
 	file_google_genomics_v1_cigar_proto_rawDescData = file_google_genomics_v1_cigar_proto_rawDesc
 )

 func file_google_genomics_v1_cigar_proto_rawDescGZIP() []byte {
 	file_google_genomics_v1_cigar_proto_rawDescOnce.Do(func() {
 		file_google_genomics_v1_cigar_proto_rawDescData = protoimpl.X.CompressGZIP(file_google_genomics_v1_cigar_proto_rawDescData)
 	})
 	return file_google_genomics_v1_cigar_proto_rawDescData
 }

 var file_google_genomics_v1_cigar_proto_enumTypes = make([]protoimpl.EnumInfo, 1)
 var file_google_genomics_v1_cigar_proto_msgTypes = make([]protoimpl.MessageInfo, 1)
 var file_google_genomics_v1_cigar_proto_goTypes = []interface{}{
 	(CigarUnit_Operation)(0), // 0: google.genomics.v1.CigarUnit.Operation
 	(*CigarUnit)(nil),        // 1: google.genomics.v1.CigarUnit
 }
 var file_google_genomics_v1_cigar_proto_depIdxs = []int32{
 	0, // 0: google.genomics.v1.CigarUnit.operation:type_name -> google.genomics.v1.CigarUnit.Operation
 	1, // [1:1] is the sub-list for method output_type
 	1, // [1:1] is the sub-list for method input_type
 	1, // [1:1] is the sub-list for extension type_name
 	1, // [1:1] is the sub-list for extension extendee
 	0, // [0:1] is the sub-list for field type_name
 }

 func init() { file_google_genomics_v1_cigar_proto_init() }
 func file_google_genomics_v1_cigar_proto_init() {
 	if File_google_genomics_v1_cigar_proto != nil {
 		return
 	}
 	if !protoimpl.UnsafeEnabled {
 		file_google_genomics_v1_cigar_proto_msgTypes[0].Exporter = func(v interface{}, i int) interface{} {
 			switch v := v.(*CigarUnit); i {
 			case 0:
 				return &v.state
 			case 1:
 				return &v.sizeCache
 			case 2:
 				return &v.unknownFields
 			default:
 				return nil
 			}
 		}
 	}
 	type x struct{}
 	out := protoimpl.TypeBuilder{
 		File: protoimpl.DescBuilder{
 			GoPackagePath: reflect.TypeOf(x{}).PkgPath(),
 			RawDescriptor: file_google_genomics_v1_cigar_proto_rawDesc,
 			NumEnums:      1,
 			NumMessages:   1,
 			NumExtensions: 0,
 			NumServices:   0,
 		},
 		GoTypes:           file_google_genomics_v1_cigar_proto_goTypes,
 		DependencyIndexes: file_google_genomics_v1_cigar_proto_depIdxs,
 		EnumInfos:         file_google_genomics_v1_cigar_proto_enumTypes,
 		MessageInfos:      file_google_genomics_v1_cigar_proto_msgTypes,
 	}.Build()
 	File_google_genomics_v1_cigar_proto = out.File
 	file_google_genomics_v1_cigar_proto_rawDesc = nil
 	file_google_genomics_v1_cigar_proto_goTypes = nil
 	file_google_genomics_v1_cigar_proto_depIdxs = nil
 }
	// Copyright 2016 Google Inc.
	//
	// Licensed under the Apache License, Version 2.0 (the "License");
	// you may not use this file except in compliance with the License.
	// You may obtain a copy of the License at
	//
	// http://www.apache.org/licenses/LICENSE-2.0
	//
	// Unless required by applicable law or agreed to in writing, software
	// distributed under the License is distributed on an "AS IS" BASIS,
	// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
	// See the License for the specific language governing permissions and
	// limitations under the License.

	// Code generated by protoc-gen-go. DO NOT EDIT.
	// versions:
	// protoc-gen-go v1.22.0
	// protoc v3.12.2
	// source: google/genomics/v1/cigar.proto

	package genomics

	import (
	reflect "reflect"
	sync "sync"

	proto "github.com/golang/protobuf/proto"
	_ "google.golang.org/genproto/googleapis/api/annotations"
	protoreflect "google.golang.org/protobuf/reflect/protoreflect"
	protoimpl "google.golang.org/protobuf/runtime/protoimpl"
	)

	const (
	// Verify that this generated code is sufficiently up-to-date.
	_ = protoimpl.EnforceVersion(20 - protoimpl.MinVersion)
	// Verify that runtime/protoimpl is sufficiently up-to-date.
	_ = protoimpl.EnforceVersion(protoimpl.MaxVersion - 20)
	)

	// This is a compile-time assertion that a sufficiently up-to-date version
	// of the legacy proto package is being used.
	const _ = proto.ProtoPackageIsVersion4

	// 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
	)

	// Enum value maps for CigarUnit_Operation.
	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",
	}
	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) Enum() *CigarUnit_Operation {
	p := new(CigarUnit_Operation)
	*p = x
	return p
	}

	func (x CigarUnit_Operation) String() string {
	return protoimpl.X.EnumStringOf(x.Descriptor(), protoreflect.EnumNumber(x))
	}

	func (CigarUnit_Operation) Descriptor() protoreflect.EnumDescriptor {
	return file_google_genomics_v1_cigar_proto_enumTypes[0].Descriptor()
	}

	func (CigarUnit_Operation) Type() protoreflect.EnumType {
	return &file_google_genomics_v1_cigar_proto_enumTypes[0]
	}

	func (x CigarUnit_Operation) Number() protoreflect.EnumNumber {
	return protoreflect.EnumNumber(x)
	}

	// Deprecated: Use CigarUnit_Operation.Descriptor instead.
	func (CigarUnit_Operation) EnumDescriptor() ([]byte, []int) {
	return file_google_genomics_v1_cigar_proto_rawDescGZIP(), []int{0, 0}
	}

	// A single CIGAR operation.
	type CigarUnit struct {
	state protoimpl.MessageState
	sizeCache protoimpl.SizeCache
	unknownFields protoimpl.UnknownFields

	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"`
	}

	func (x *CigarUnit) Reset() {
	*x = CigarUnit{}
	if protoimpl.UnsafeEnabled {
	mi := &file_google_genomics_v1_cigar_proto_msgTypes[0]
	ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x))
	ms.StoreMessageInfo(mi)
	}
	}

	func (x *CigarUnit) String() string {
	return protoimpl.X.MessageStringOf(x)
	}

	func (*CigarUnit) ProtoMessage() {}

	func (x *CigarUnit) ProtoReflect() protoreflect.Message {
	mi := &file_google_genomics_v1_cigar_proto_msgTypes[0]
	if protoimpl.UnsafeEnabled && x != nil {
	ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x))
	if ms.LoadMessageInfo() == nil {
	ms.StoreMessageInfo(mi)
	}
	return ms
	}
	return mi.MessageOf(x)
	}

	// Deprecated: Use CigarUnit.ProtoReflect.Descriptor instead.
	func (*CigarUnit) Descriptor() ([]byte, []int) {
	return file_google_genomics_v1_cigar_proto_rawDescGZIP(), []int{0}
	}

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

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

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

	var File_google_genomics_v1_cigar_proto protoreflect.FileDescriptor

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	}

	var (
	file_google_genomics_v1_cigar_proto_rawDescOnce sync.Once
	file_google_genomics_v1_cigar_proto_rawDescData = file_google_genomics_v1_cigar_proto_rawDesc
	)

	func file_google_genomics_v1_cigar_proto_rawDescGZIP() []byte {
	file_google_genomics_v1_cigar_proto_rawDescOnce.Do(func() {
	file_google_genomics_v1_cigar_proto_rawDescData = protoimpl.X.CompressGZIP(file_google_genomics_v1_cigar_proto_rawDescData)
	})
	return file_google_genomics_v1_cigar_proto_rawDescData
	}

	var file_google_genomics_v1_cigar_proto_enumTypes = make([]protoimpl.EnumInfo, 1)
	var file_google_genomics_v1_cigar_proto_msgTypes = make([]protoimpl.MessageInfo, 1)
	var file_google_genomics_v1_cigar_proto_goTypes = []interface{}{
	(CigarUnit_Operation)(0), // 0: google.genomics.v1.CigarUnit.Operation
	(*CigarUnit)(nil), // 1: google.genomics.v1.CigarUnit
	}
	var file_google_genomics_v1_cigar_proto_depIdxs = []int32{
	0, // 0: google.genomics.v1.CigarUnit.operation:type_name -> google.genomics.v1.CigarUnit.Operation
	1, // [1:1] is the sub-list for method output_type
	1, // [1:1] is the sub-list for method input_type
	1, // [1:1] is the sub-list for extension type_name
	1, // [1:1] is the sub-list for extension extendee
	0, // [0:1] is the sub-list for field type_name
	}

	func init() { file_google_genomics_v1_cigar_proto_init() }
	func file_google_genomics_v1_cigar_proto_init() {
	if File_google_genomics_v1_cigar_proto != nil {
	return
	}
	if !protoimpl.UnsafeEnabled {
	file_google_genomics_v1_cigar_proto_msgTypes[0].Exporter = func(v interface{}, i int) interface{} {
	switch v := v.(*CigarUnit); i {
	case 0:
	return &v.state
	case 1:
	return &v.sizeCache
	case 2:
	return &v.unknownFields
	default:
	return nil
	}
	}
	}
	type x struct{}
	out := protoimpl.TypeBuilder{
	File: protoimpl.DescBuilder{
	GoPackagePath: reflect.TypeOf(x{}).PkgPath(),
	RawDescriptor: file_google_genomics_v1_cigar_proto_rawDesc,
	NumEnums: 1,
	NumMessages: 1,
	NumExtensions: 0,
	NumServices: 0,
	},
	GoTypes: file_google_genomics_v1_cigar_proto_goTypes,
	DependencyIndexes: file_google_genomics_v1_cigar_proto_depIdxs,
	EnumInfos: file_google_genomics_v1_cigar_proto_enumTypes,
	MessageInfos: file_google_genomics_v1_cigar_proto_msgTypes,
	}.Build()
	File_google_genomics_v1_cigar_proto = out.File
	file_google_genomics_v1_cigar_proto_rawDesc = nil
	file_google_genomics_v1_cigar_proto_goTypes = nil
	file_google_genomics_v1_cigar_proto_depIdxs = nil
	}