cigar.pb.go

Documentation: google.golang.org/genproto/googleapis/genomics/v1

     1  // Copyright 2024 Google LLC
     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 v1.26.0
    18  // 	protoc        v4.24.4
    19  // source: google/genomics/v1/cigar.proto
    20  
    21  package genomics
    22  
    23  import (
    24  	reflect "reflect"
    25  	sync "sync"
    26  
    27  	_ "google.golang.org/genproto/googleapis/api/annotations"
    28  	protoreflect "google.golang.org/protobuf/reflect/protoreflect"
    29  	protoimpl "google.golang.org/protobuf/runtime/protoimpl"
    30  )
    31  
    32  const (
    33  	// Verify that this generated code is sufficiently up-to-date.
    34  	_ = protoimpl.EnforceVersion(20 - protoimpl.MinVersion)
    35  	// Verify that runtime/protoimpl is sufficiently up-to-date.
    36  	_ = protoimpl.EnforceVersion(protoimpl.MaxVersion - 20)
    37  )
    38  
    39  // Describes the different types of CIGAR alignment operations that exist.
    40  // Used wherever CIGAR alignments are used.
    41  type CigarUnit_Operation int32
    42  
    43  const (
    44  	CigarUnit_OPERATION_UNSPECIFIED CigarUnit_Operation = 0
    45  	// An alignment match indicates that a sequence can be aligned to the
    46  	// reference without evidence of an INDEL. Unlike the
    47  	// `SEQUENCE_MATCH` and `SEQUENCE_MISMATCH` operators,
    48  	// the `ALIGNMENT_MATCH` operator does not indicate whether the
    49  	// reference and read sequences are an exact match. This operator is
    50  	// equivalent to SAM's `M`.
    51  	CigarUnit_ALIGNMENT_MATCH CigarUnit_Operation = 1
    52  	// The insert operator indicates that the read contains evidence of bases
    53  	// being inserted into the reference. This operator is equivalent to SAM's
    54  	// `I`.
    55  	CigarUnit_INSERT CigarUnit_Operation = 2
    56  	// The delete operator indicates that the read contains evidence of bases
    57  	// being deleted from the reference. This operator is equivalent to SAM's
    58  	// `D`.
    59  	CigarUnit_DELETE CigarUnit_Operation = 3
    60  	// The skip operator indicates that this read skips a long segment of the
    61  	// reference, but the bases have not been deleted. This operator is commonly
    62  	// used when working with RNA-seq data, where reads may skip long segments
    63  	// of the reference between exons. This operator is equivalent to SAM's
    64  	// `N`.
    65  	CigarUnit_SKIP CigarUnit_Operation = 4
    66  	// The soft clip operator indicates that bases at the start/end of a read
    67  	// have not been considered during alignment. This may occur if the majority
    68  	// of a read maps, except for low quality bases at the start/end of a read.
    69  	// This operator is equivalent to SAM's `S`. Bases that are soft
    70  	// clipped will still be stored in the read.
    71  	CigarUnit_CLIP_SOFT CigarUnit_Operation = 5
    72  	// The hard clip operator indicates that bases at the start/end of a read
    73  	// have been omitted from this alignment. This may occur if this linear
    74  	// alignment is part of a chimeric alignment, or if the read has been
    75  	// trimmed (for example, during error correction or to trim poly-A tails for
    76  	// RNA-seq). This operator is equivalent to SAM's `H`.
    77  	CigarUnit_CLIP_HARD CigarUnit_Operation = 6
    78  	// The pad operator indicates that there is padding in an alignment. This
    79  	// operator is equivalent to SAM's `P`.
    80  	CigarUnit_PAD CigarUnit_Operation = 7
    81  	// This operator indicates that this portion of the aligned sequence exactly
    82  	// matches the reference. This operator is equivalent to SAM's `=`.
    83  	CigarUnit_SEQUENCE_MATCH CigarUnit_Operation = 8
    84  	// This operator indicates that this portion of the aligned sequence is an
    85  	// alignment match to the reference, but a sequence mismatch. This can
    86  	// indicate a SNP or a read error. This operator is equivalent to SAM's
    87  	// `X`.
    88  	CigarUnit_SEQUENCE_MISMATCH CigarUnit_Operation = 9
    89  )
    90  
    91  // Enum value maps for CigarUnit_Operation.
    92  var (
    93  	CigarUnit_Operation_name = map[int32]string{
    94  		0: "OPERATION_UNSPECIFIED",
    95  		1: "ALIGNMENT_MATCH",
    96  		2: "INSERT",
    97  		3: "DELETE",
    98  		4: "SKIP",
    99  		5: "CLIP_SOFT",
   100  		6: "CLIP_HARD",
   101  		7: "PAD",
   102  		8: "SEQUENCE_MATCH",
   103  		9: "SEQUENCE_MISMATCH",
   104  	}
   105  	CigarUnit_Operation_value = map[string]int32{
   106  		"OPERATION_UNSPECIFIED": 0,
   107  		"ALIGNMENT_MATCH":       1,
   108  		"INSERT":                2,
   109  		"DELETE":                3,
   110  		"SKIP":                  4,
   111  		"CLIP_SOFT":             5,
   112  		"CLIP_HARD":             6,
   113  		"PAD":                   7,
   114  		"SEQUENCE_MATCH":        8,
   115  		"SEQUENCE_MISMATCH":     9,
   116  	}
   117  )
   118  
   119  func (x CigarUnit_Operation) Enum() *CigarUnit_Operation {
   120  	p := new(CigarUnit_Operation)
   121  	*p = x
   122  	return p
   123  }
   124  
   125  func (x CigarUnit_Operation) String() string {
   126  	return protoimpl.X.EnumStringOf(x.Descriptor(), protoreflect.EnumNumber(x))
   127  }
   128  
   129  func (CigarUnit_Operation) Descriptor() protoreflect.EnumDescriptor {
   130  	return file_google_genomics_v1_cigar_proto_enumTypes[0].Descriptor()
   131  }
   132  
   133  func (CigarUnit_Operation) Type() protoreflect.EnumType {
   134  	return &file_google_genomics_v1_cigar_proto_enumTypes[0]
   135  }
   136  
   137  func (x CigarUnit_Operation) Number() protoreflect.EnumNumber {
   138  	return protoreflect.EnumNumber(x)
   139  }
   140  
   141  // Deprecated: Use CigarUnit_Operation.Descriptor instead.
   142  func (CigarUnit_Operation) EnumDescriptor() ([]byte, []int) {
   143  	return file_google_genomics_v1_cigar_proto_rawDescGZIP(), []int{0, 0}
   144  }
   145  
   146  // A single CIGAR operation.
   147  type CigarUnit struct {
   148  	state         protoimpl.MessageState
   149  	sizeCache     protoimpl.SizeCache
   150  	unknownFields protoimpl.UnknownFields
   151  
   152  	Operation CigarUnit_Operation `protobuf:"varint,1,opt,name=operation,proto3,enum=google.genomics.v1.CigarUnit_Operation" json:"operation,omitempty"`
   153  	// The number of genomic bases that the operation runs for. Required.
   154  	OperationLength int64 `protobuf:"varint,2,opt,name=operation_length,json=operationLength,proto3" json:"operation_length,omitempty"`
   155  	// `referenceSequence` is only used at mismatches
   156  	// (`SEQUENCE_MISMATCH`) and deletions (`DELETE`).
   157  	// Filling this field replaces SAM's MD tag. If the relevant information is
   158  	// not available, this field is unset.
   159  	ReferenceSequence string `protobuf:"bytes,3,opt,name=reference_sequence,json=referenceSequence,proto3" json:"reference_sequence,omitempty"`
   160  }
   161  
   162  func (x *CigarUnit) Reset() {
   163  	*x = CigarUnit{}
   164  	if protoimpl.UnsafeEnabled {
   165  		mi := &file_google_genomics_v1_cigar_proto_msgTypes[0]
   166  		ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x))
   167  		ms.StoreMessageInfo(mi)
   168  	}
   169  }
   170  
   171  func (x *CigarUnit) String() string {
   172  	return protoimpl.X.MessageStringOf(x)
   173  }
   174  
   175  func (*CigarUnit) ProtoMessage() {}
   176  
   177  func (x *CigarUnit) ProtoReflect() protoreflect.Message {
   178  	mi := &file_google_genomics_v1_cigar_proto_msgTypes[0]
   179  	if protoimpl.UnsafeEnabled && x != nil {
   180  		ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x))
   181  		if ms.LoadMessageInfo() == nil {
   182  			ms.StoreMessageInfo(mi)
   183  		}
   184  		return ms
   185  	}
   186  	return mi.MessageOf(x)
   187  }
   188  
   189  // Deprecated: Use CigarUnit.ProtoReflect.Descriptor instead.
   190  func (*CigarUnit) Descriptor() ([]byte, []int) {
   191  	return file_google_genomics_v1_cigar_proto_rawDescGZIP(), []int{0}
   192  }
   193  
   194  func (x *CigarUnit) GetOperation() CigarUnit_Operation {
   195  	if x != nil {
   196  		return x.Operation
   197  	}
   198  	return CigarUnit_OPERATION_UNSPECIFIED
   199  }
   200  
   201  func (x *CigarUnit) GetOperationLength() int64 {
   202  	if x != nil {
   203  		return x.OperationLength
   204  	}
   205  	return 0
   206  }
   207  
   208  func (x *CigarUnit) GetReferenceSequence() string {
   209  	if x != nil {
   210  		return x.ReferenceSequence
   211  	}
   212  	return ""
   213  }
   214  
   215  var File_google_genomics_v1_cigar_proto protoreflect.FileDescriptor
   216  
   217  var file_google_genomics_v1_cigar_proto_rawDesc = []byte{
   218  	0x0a, 0x1e, 0x67, 0x6f, 0x6f, 0x67, 0x6c, 0x65, 0x2f, 0x67, 0x65, 0x6e, 0x6f, 0x6d, 0x69, 0x63,
   219  	0x73, 0x2f, 0x76, 0x31, 0x2f, 0x63, 0x69, 0x67, 0x61, 0x72, 0x2e, 0x70, 0x72, 0x6f, 0x74, 0x6f,
   220  	0x12, 0x12, 0x67, 0x6f, 0x6f, 0x67, 0x6c, 0x65, 0x2e, 0x67, 0x65, 0x6e, 0x6f, 0x6d, 0x69, 0x63,
   221  	0x73, 0x2e, 0x76, 0x31, 0x1a, 0x1c, 0x67, 0x6f, 0x6f, 0x67, 0x6c, 0x65, 0x2f, 0x61, 0x70, 0x69,
   222  	0x2f, 0x61, 0x6e, 0x6e, 0x6f, 0x74, 0x61, 0x74, 0x69, 0x6f, 0x6e, 0x73, 0x2e, 0x70, 0x72, 0x6f,
   223  	0x74, 0x6f, 0x22, 0xde, 0x02, 0x0a, 0x09, 0x43, 0x69, 0x67, 0x61, 0x72, 0x55, 0x6e, 0x69, 0x74,
   224  	0x12, 0x45, 0x0a, 0x09, 0x6f, 0x70, 0x65, 0x72, 0x61, 0x74, 0x69, 0x6f, 0x6e, 0x18, 0x01, 0x20,
   225  	0x01, 0x28, 0x0e, 0x32, 0x27, 0x2e, 0x67, 0x6f, 0x6f, 0x67, 0x6c, 0x65, 0x2e, 0x67, 0x65, 0x6e,
   226  	0x6f, 0x6d, 0x69, 0x63, 0x73, 0x2e, 0x76, 0x31, 0x2e, 0x43, 0x69, 0x67, 0x61, 0x72, 0x55, 0x6e,
   227  	0x69, 0x74, 0x2e, 0x4f, 0x70, 0x65, 0x72, 0x61, 0x74, 0x69, 0x6f, 0x6e, 0x52, 0x09, 0x6f, 0x70,
   228  	0x65, 0x72, 0x61, 0x74, 0x69, 0x6f, 0x6e, 0x12, 0x29, 0x0a, 0x10, 0x6f, 0x70, 0x65, 0x72, 0x61,
   229  	0x74, 0x69, 0x6f, 0x6e, 0x5f, 0x6c, 0x65, 0x6e, 0x67, 0x74, 0x68, 0x18, 0x02, 0x20, 0x01, 0x28,
   230  	0x03, 0x52, 0x0f, 0x6f, 0x70, 0x65, 0x72, 0x61, 0x74, 0x69, 0x6f, 0x6e, 0x4c, 0x65, 0x6e, 0x67,
   231  	0x74, 0x68, 0x12, 0x2d, 0x0a, 0x12, 0x72, 0x65, 0x66, 0x65, 0x72, 0x65, 0x6e, 0x63, 0x65, 0x5f,
   232  	0x73, 0x65, 0x71, 0x75, 0x65, 0x6e, 0x63, 0x65, 0x18, 0x03, 0x20, 0x01, 0x28, 0x09, 0x52, 0x11,
   233  	0x72, 0x65, 0x66, 0x65, 0x72, 0x65, 0x6e, 0x63, 0x65, 0x53, 0x65, 0x71, 0x75, 0x65, 0x6e, 0x63,
   234  	0x65, 0x22, 0xaf, 0x01, 0x0a, 0x09, 0x4f, 0x70, 0x65, 0x72, 0x61, 0x74, 0x69, 0x6f, 0x6e, 0x12,
   235  	0x19, 0x0a, 0x15, 0x4f, 0x50, 0x45, 0x52, 0x41, 0x54, 0x49, 0x4f, 0x4e, 0x5f, 0x55, 0x4e, 0x53,
   236  	0x50, 0x45, 0x43, 0x49, 0x46, 0x49, 0x45, 0x44, 0x10, 0x00, 0x12, 0x13, 0x0a, 0x0f, 0x41, 0x4c,
   237  	0x49, 0x47, 0x4e, 0x4d, 0x45, 0x4e, 0x54, 0x5f, 0x4d, 0x41, 0x54, 0x43, 0x48, 0x10, 0x01, 0x12,
   238  	0x0a, 0x0a, 0x06, 0x49, 0x4e, 0x53, 0x45, 0x52, 0x54, 0x10, 0x02, 0x12, 0x0a, 0x0a, 0x06, 0x44,
   239  	0x45, 0x4c, 0x45, 0x54, 0x45, 0x10, 0x03, 0x12, 0x08, 0x0a, 0x04, 0x53, 0x4b, 0x49, 0x50, 0x10,
   240  	0x04, 0x12, 0x0d, 0x0a, 0x09, 0x43, 0x4c, 0x49, 0x50, 0x5f, 0x53, 0x4f, 0x46, 0x54, 0x10, 0x05,
   241  	0x12, 0x0d, 0x0a, 0x09, 0x43, 0x4c, 0x49, 0x50, 0x5f, 0x48, 0x41, 0x52, 0x44, 0x10, 0x06, 0x12,
   242  	0x07, 0x0a, 0x03, 0x50, 0x41, 0x44, 0x10, 0x07, 0x12, 0x12, 0x0a, 0x0e, 0x53, 0x45, 0x51, 0x55,
   243  	0x45, 0x4e, 0x43, 0x45, 0x5f, 0x4d, 0x41, 0x54, 0x43, 0x48, 0x10, 0x08, 0x12, 0x15, 0x0a, 0x11,
   244  	0x53, 0x45, 0x51, 0x55, 0x45, 0x4e, 0x43, 0x45, 0x5f, 0x4d, 0x49, 0x53, 0x4d, 0x41, 0x54, 0x43,
   245  	0x48, 0x10, 0x09, 0x42, 0x65, 0x0a, 0x16, 0x63, 0x6f, 0x6d, 0x2e, 0x67, 0x6f, 0x6f, 0x67, 0x6c,
   246  	0x65, 0x2e, 0x67, 0x65, 0x6e, 0x6f, 0x6d, 0x69, 0x63, 0x73, 0x2e, 0x76, 0x31, 0x42, 0x0a, 0x43,
   247  	0x69, 0x67, 0x61, 0x72, 0x50, 0x72, 0x6f, 0x74, 0x6f, 0x50, 0x01, 0x5a, 0x3a, 0x67, 0x6f, 0x6f,
   248  	0x67, 0x6c, 0x65, 0x2e, 0x67, 0x6f, 0x6c, 0x61, 0x6e, 0x67, 0x2e, 0x6f, 0x72, 0x67, 0x2f, 0x67,
   249  	0x65, 0x6e, 0x70, 0x72, 0x6f, 0x74, 0x6f, 0x2f, 0x67, 0x6f, 0x6f, 0x67, 0x6c, 0x65, 0x61, 0x70,
   250  	0x69, 0x73, 0x2f, 0x67, 0x65, 0x6e, 0x6f, 0x6d, 0x69, 0x63, 0x73, 0x2f, 0x76, 0x31, 0x3b, 0x67,
   251  	0x65, 0x6e, 0x6f, 0x6d, 0x69, 0x63, 0x73, 0xf8, 0x01, 0x01, 0x62, 0x06, 0x70, 0x72, 0x6f, 0x74,
   252  	0x6f, 0x33,
   253  }
   254  
   255  var (
   256  	file_google_genomics_v1_cigar_proto_rawDescOnce sync.Once
   257  	file_google_genomics_v1_cigar_proto_rawDescData = file_google_genomics_v1_cigar_proto_rawDesc
   258  )
   259  
   260  func file_google_genomics_v1_cigar_proto_rawDescGZIP() []byte {
   261  	file_google_genomics_v1_cigar_proto_rawDescOnce.Do(func() {
   262  		file_google_genomics_v1_cigar_proto_rawDescData = protoimpl.X.CompressGZIP(file_google_genomics_v1_cigar_proto_rawDescData)
   263  	})
   264  	return file_google_genomics_v1_cigar_proto_rawDescData
   265  }
   266  
   267  var file_google_genomics_v1_cigar_proto_enumTypes = make([]protoimpl.EnumInfo, 1)
   268  var file_google_genomics_v1_cigar_proto_msgTypes = make([]protoimpl.MessageInfo, 1)
   269  var file_google_genomics_v1_cigar_proto_goTypes = []interface{}{
   270  	(CigarUnit_Operation)(0), // 0: google.genomics.v1.CigarUnit.Operation
   271  	(*CigarUnit)(nil),        // 1: google.genomics.v1.CigarUnit
   272  }
   273  var file_google_genomics_v1_cigar_proto_depIdxs = []int32{
   274  	0, // 0: google.genomics.v1.CigarUnit.operation:type_name -> google.genomics.v1.CigarUnit.Operation
   275  	1, // [1:1] is the sub-list for method output_type
   276  	1, // [1:1] is the sub-list for method input_type
   277  	1, // [1:1] is the sub-list for extension type_name
   278  	1, // [1:1] is the sub-list for extension extendee
   279  	0, // [0:1] is the sub-list for field type_name
   280  }
   281  
   282  func init() { file_google_genomics_v1_cigar_proto_init() }
   283  func file_google_genomics_v1_cigar_proto_init() {
   284  	if File_google_genomics_v1_cigar_proto != nil {
   285  		return
   286  	}
   287  	if !protoimpl.UnsafeEnabled {
   288  		file_google_genomics_v1_cigar_proto_msgTypes[0].Exporter = func(v interface{}, i int) interface{} {
   289  			switch v := v.(*CigarUnit); i {
   290  			case 0:
   291  				return &v.state
   292  			case 1:
   293  				return &v.sizeCache
   294  			case 2:
   295  				return &v.unknownFields
   296  			default:
   297  				return nil
   298  			}
   299  		}
   300  	}
   301  	type x struct{}
   302  	out := protoimpl.TypeBuilder{
   303  		File: protoimpl.DescBuilder{
   304  			GoPackagePath: reflect.TypeOf(x{}).PkgPath(),
   305  			RawDescriptor: file_google_genomics_v1_cigar_proto_rawDesc,
   306  			NumEnums:      1,
   307  			NumMessages:   1,
   308  			NumExtensions: 0,
   309  			NumServices:   0,
   310  		},
   311  		GoTypes:           file_google_genomics_v1_cigar_proto_goTypes,
   312  		DependencyIndexes: file_google_genomics_v1_cigar_proto_depIdxs,
   313  		EnumInfos:         file_google_genomics_v1_cigar_proto_enumTypes,
   314  		MessageInfos:      file_google_genomics_v1_cigar_proto_msgTypes,
   315  	}.Build()
   316  	File_google_genomics_v1_cigar_proto = out.File
   317  	file_google_genomics_v1_cigar_proto_rawDesc = nil
   318  	file_google_genomics_v1_cigar_proto_goTypes = nil
   319  	file_google_genomics_v1_cigar_proto_depIdxs = nil
   320  }
   321
View as plain text