1// Copyright 2016 Google Inc. 2// 3// Licensed under the Apache License, Version 2.0 (the "License"); 4// you may not use this file except in compliance with the License. 5// You may obtain a copy of the License at 6// 7// http://www.apache.org/licenses/LICENSE-2.0 8// 9// Unless required by applicable law or agreed to in writing, software 10// distributed under the License is distributed on an "AS IS" BASIS, 11// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12// See the License for the specific language governing permissions and 13// limitations under the License. 14 15// Code generated by protoc-gen-go. DO NOT EDIT. 16// versions: 17// protoc-gen-go v1.25.0 18// protoc v3.13.0 19// source: google/genomics/v1/cigar.proto 20 21package genomics 22 23import ( 24 reflect "reflect" 25 sync "sync" 26 27 proto "github.com/golang/protobuf/proto" 28 _ "google.golang.org/genproto/googleapis/api/annotations" 29 protoreflect "google.golang.org/protobuf/reflect/protoreflect" 30 protoimpl "google.golang.org/protobuf/runtime/protoimpl" 31) 32 33const ( 34 // Verify that this generated code is sufficiently up-to-date. 35 _ = protoimpl.EnforceVersion(20 - protoimpl.MinVersion) 36 // Verify that runtime/protoimpl is sufficiently up-to-date. 37 _ = protoimpl.EnforceVersion(protoimpl.MaxVersion - 20) 38) 39 40// This is a compile-time assertion that a sufficiently up-to-date version 41// of the legacy proto package is being used. 42const _ = proto.ProtoPackageIsVersion4 43 44// Describes the different types of CIGAR alignment operations that exist. 45// Used wherever CIGAR alignments are used. 46type CigarUnit_Operation int32 47 48const ( 49 CigarUnit_OPERATION_UNSPECIFIED CigarUnit_Operation = 0 50 // An alignment match indicates that a sequence can be aligned to the 51 // reference without evidence of an INDEL. Unlike the 52 // `SEQUENCE_MATCH` and `SEQUENCE_MISMATCH` operators, 53 // the `ALIGNMENT_MATCH` operator does not indicate whether the 54 // reference and read sequences are an exact match. This operator is 55 // equivalent to SAM's `M`. 56 CigarUnit_ALIGNMENT_MATCH CigarUnit_Operation = 1 57 // The insert operator indicates that the read contains evidence of bases 58 // being inserted into the reference. This operator is equivalent to SAM's 59 // `I`. 60 CigarUnit_INSERT CigarUnit_Operation = 2 61 // The delete operator indicates that the read contains evidence of bases 62 // being deleted from the reference. This operator is equivalent to SAM's 63 // `D`. 64 CigarUnit_DELETE CigarUnit_Operation = 3 65 // The skip operator indicates that this read skips a long segment of the 66 // reference, but the bases have not been deleted. This operator is commonly 67 // used when working with RNA-seq data, where reads may skip long segments 68 // of the reference between exons. This operator is equivalent to SAM's 69 // `N`. 70 CigarUnit_SKIP CigarUnit_Operation = 4 71 // The soft clip operator indicates that bases at the start/end of a read 72 // have not been considered during alignment. This may occur if the majority 73 // of a read maps, except for low quality bases at the start/end of a read. 74 // This operator is equivalent to SAM's `S`. Bases that are soft 75 // clipped will still be stored in the read. 76 CigarUnit_CLIP_SOFT CigarUnit_Operation = 5 77 // The hard clip operator indicates that bases at the start/end of a read 78 // have been omitted from this alignment. This may occur if this linear 79 // alignment is part of a chimeric alignment, or if the read has been 80 // trimmed (for example, during error correction or to trim poly-A tails for 81 // RNA-seq). This operator is equivalent to SAM's `H`. 82 CigarUnit_CLIP_HARD CigarUnit_Operation = 6 83 // The pad operator indicates that there is padding in an alignment. This 84 // operator is equivalent to SAM's `P`. 85 CigarUnit_PAD CigarUnit_Operation = 7 86 // This operator indicates that this portion of the aligned sequence exactly 87 // matches the reference. This operator is equivalent to SAM's `=`. 88 CigarUnit_SEQUENCE_MATCH CigarUnit_Operation = 8 89 // This operator indicates that this portion of the aligned sequence is an 90 // alignment match to the reference, but a sequence mismatch. This can 91 // indicate a SNP or a read error. This operator is equivalent to SAM's 92 // `X`. 93 CigarUnit_SEQUENCE_MISMATCH CigarUnit_Operation = 9 94) 95 96// Enum value maps for CigarUnit_Operation. 97var ( 98 CigarUnit_Operation_name = map[int32]string{ 99 0: "OPERATION_UNSPECIFIED", 100 1: "ALIGNMENT_MATCH", 101 2: "INSERT", 102 3: "DELETE", 103 4: "SKIP", 104 5: "CLIP_SOFT", 105 6: "CLIP_HARD", 106 7: "PAD", 107 8: "SEQUENCE_MATCH", 108 9: "SEQUENCE_MISMATCH", 109 } 110 CigarUnit_Operation_value = map[string]int32{ 111 "OPERATION_UNSPECIFIED": 0, 112 "ALIGNMENT_MATCH": 1, 113 "INSERT": 2, 114 "DELETE": 3, 115 "SKIP": 4, 116 "CLIP_SOFT": 5, 117 "CLIP_HARD": 6, 118 "PAD": 7, 119 "SEQUENCE_MATCH": 8, 120 "SEQUENCE_MISMATCH": 9, 121 } 122) 123 124func (x CigarUnit_Operation) Enum() *CigarUnit_Operation { 125 p := new(CigarUnit_Operation) 126 *p = x 127 return p 128} 129 130func (x CigarUnit_Operation) String() string { 131 return protoimpl.X.EnumStringOf(x.Descriptor(), protoreflect.EnumNumber(x)) 132} 133 134func (CigarUnit_Operation) Descriptor() protoreflect.EnumDescriptor { 135 return file_google_genomics_v1_cigar_proto_enumTypes[0].Descriptor() 136} 137 138func (CigarUnit_Operation) Type() protoreflect.EnumType { 139 return &file_google_genomics_v1_cigar_proto_enumTypes[0] 140} 141 142func (x CigarUnit_Operation) Number() protoreflect.EnumNumber { 143 return protoreflect.EnumNumber(x) 144} 145 146// Deprecated: Use CigarUnit_Operation.Descriptor instead. 147func (CigarUnit_Operation) EnumDescriptor() ([]byte, []int) { 148 return file_google_genomics_v1_cigar_proto_rawDescGZIP(), []int{0, 0} 149} 150 151// A single CIGAR operation. 152type CigarUnit struct { 153 state protoimpl.MessageState 154 sizeCache protoimpl.SizeCache 155 unknownFields protoimpl.UnknownFields 156 157 Operation CigarUnit_Operation `protobuf:"varint,1,opt,name=operation,proto3,enum=google.genomics.v1.CigarUnit_Operation" json:"operation,omitempty"` 158 // The number of genomic bases that the operation runs for. Required. 159 OperationLength int64 `protobuf:"varint,2,opt,name=operation_length,json=operationLength,proto3" json:"operation_length,omitempty"` 160 // `referenceSequence` is only used at mismatches 161 // (`SEQUENCE_MISMATCH`) and deletions (`DELETE`). 162 // Filling this field replaces SAM's MD tag. If the relevant information is 163 // not available, this field is unset. 164 ReferenceSequence string `protobuf:"bytes,3,opt,name=reference_sequence,json=referenceSequence,proto3" json:"reference_sequence,omitempty"` 165} 166 167func (x *CigarUnit) Reset() { 168 *x = CigarUnit{} 169 if protoimpl.UnsafeEnabled { 170 mi := &file_google_genomics_v1_cigar_proto_msgTypes[0] 171 ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) 172 ms.StoreMessageInfo(mi) 173 } 174} 175 176func (x *CigarUnit) String() string { 177 return protoimpl.X.MessageStringOf(x) 178} 179 180func (*CigarUnit) ProtoMessage() {} 181 182func (x *CigarUnit) ProtoReflect() protoreflect.Message { 183 mi := &file_google_genomics_v1_cigar_proto_msgTypes[0] 184 if protoimpl.UnsafeEnabled && x != nil { 185 ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) 186 if ms.LoadMessageInfo() == nil { 187 ms.StoreMessageInfo(mi) 188 } 189 return ms 190 } 191 return mi.MessageOf(x) 192} 193 194// Deprecated: Use CigarUnit.ProtoReflect.Descriptor instead. 195func (*CigarUnit) Descriptor() ([]byte, []int) { 196 return file_google_genomics_v1_cigar_proto_rawDescGZIP(), []int{0} 197} 198 199func (x *CigarUnit) GetOperation() CigarUnit_Operation { 200 if x != nil { 201 return x.Operation 202 } 203 return CigarUnit_OPERATION_UNSPECIFIED 204} 205 206func (x *CigarUnit) GetOperationLength() int64 { 207 if x != nil { 208 return x.OperationLength 209 } 210 return 0 211} 212 213func (x *CigarUnit) GetReferenceSequence() string { 214 if x != nil { 215 return x.ReferenceSequence 216 } 217 return "" 218} 219 220var File_google_genomics_v1_cigar_proto protoreflect.FileDescriptor 221 222var file_google_genomics_v1_cigar_proto_rawDesc = []byte{ 223 0x0a, 0x1e, 0x67, 0x6f, 0x6f, 0x67, 0x6c, 0x65, 0x2f, 0x67, 0x65, 0x6e, 0x6f, 0x6d, 0x69, 0x63, 224 0x73, 0x2f, 0x76, 0x31, 0x2f, 0x63, 0x69, 0x67, 0x61, 0x72, 0x2e, 0x70, 0x72, 0x6f, 0x74, 0x6f, 225 0x12, 0x12, 0x67, 0x6f, 0x6f, 0x67, 0x6c, 0x65, 0x2e, 0x67, 0x65, 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(*CigarUnit)(nil), // 1: google.genomics.v1.CigarUnit 277} 278var file_google_genomics_v1_cigar_proto_depIdxs = []int32{ 279 0, // 0: google.genomics.v1.CigarUnit.operation:type_name -> google.genomics.v1.CigarUnit.Operation 280 1, // [1:1] is the sub-list for method output_type 281 1, // [1:1] is the sub-list for method input_type 282 1, // [1:1] is the sub-list for extension type_name 283 1, // [1:1] is the sub-list for extension extendee 284 0, // [0:1] is the sub-list for field type_name 285} 286 287func init() { file_google_genomics_v1_cigar_proto_init() } 288func file_google_genomics_v1_cigar_proto_init() { 289 if File_google_genomics_v1_cigar_proto != nil { 290 return 291 } 292 if !protoimpl.UnsafeEnabled { 293 file_google_genomics_v1_cigar_proto_msgTypes[0].Exporter = func(v interface{}, i int) interface{} { 294 switch v := v.(*CigarUnit); i { 295 case 0: 296 return &v.state 297 case 1: 298 return &v.sizeCache 299 case 2: 300 return &v.unknownFields 301 default: 302 return nil 303 } 304 } 305 } 306 type x struct{} 307 out := protoimpl.TypeBuilder{ 308 File: protoimpl.DescBuilder{ 309 GoPackagePath: reflect.TypeOf(x{}).PkgPath(), 310 RawDescriptor: file_google_genomics_v1_cigar_proto_rawDesc, 311 NumEnums: 1, 312 NumMessages: 1, 313 NumExtensions: 0, 314 NumServices: 0, 315 }, 316 GoTypes: file_google_genomics_v1_cigar_proto_goTypes, 317 DependencyIndexes: file_google_genomics_v1_cigar_proto_depIdxs, 318 EnumInfos: file_google_genomics_v1_cigar_proto_enumTypes, 319 MessageInfos: file_google_genomics_v1_cigar_proto_msgTypes, 320 }.Build() 321 File_google_genomics_v1_cigar_proto = out.File 322 file_google_genomics_v1_cigar_proto_rawDesc = nil 323 file_google_genomics_v1_cigar_proto_goTypes = nil 324 file_google_genomics_v1_cigar_proto_depIdxs = nil 325} 326