| // 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 v3.12.3 |
| // 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 |
| } |