readalignment.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/readalignment.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  	structpb "google.golang.org/protobuf/types/known/structpb"
    31  )
    32  
    33  const (
    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  // A linear alignment can be represented by one CIGAR string. Describes the
    41  // mapped position and local alignment of the read to the reference.
    42  type LinearAlignment struct {
    43  	state         protoimpl.MessageState
    44  	sizeCache     protoimpl.SizeCache
    45  	unknownFields protoimpl.UnknownFields
    46  
    47  	// The position of this alignment.
    48  	Position *Position `protobuf:"bytes,1,opt,name=position,proto3" json:"position,omitempty"`
    49  	// The mapping quality of this alignment. Represents how likely
    50  	// the read maps to this position as opposed to other locations.
    51  	//
    52  	// Specifically, this is -10 log10 Pr(mapping position is wrong), rounded to
    53  	// the nearest integer.
    54  	MappingQuality int32 `protobuf:"varint,2,opt,name=mapping_quality,json=mappingQuality,proto3" json:"mapping_quality,omitempty"`
    55  	// Represents the local alignment of this sequence (alignment matches, indels,
    56  	// etc) against the reference.
    57  	Cigar []*CigarUnit `protobuf:"bytes,3,rep,name=cigar,proto3" json:"cigar,omitempty"`
    58  }
    59  
    60  func (x *LinearAlignment) Reset() {
    61  	*x = LinearAlignment{}
    62  	if protoimpl.UnsafeEnabled {
    63  		mi := &file_google_genomics_v1_readalignment_proto_msgTypes[0]
    64  		ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x))
    65  		ms.StoreMessageInfo(mi)
    66  	}
    67  }
    68  
    69  func (x *LinearAlignment) String() string {
    70  	return protoimpl.X.MessageStringOf(x)
    71  }
    72  
    73  func (*LinearAlignment) ProtoMessage() {}
    74  
    75  func (x *LinearAlignment) ProtoReflect() protoreflect.Message {
    76  	mi := &file_google_genomics_v1_readalignment_proto_msgTypes[0]
    77  	if protoimpl.UnsafeEnabled && x != nil {
    78  		ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x))
    79  		if ms.LoadMessageInfo() == nil {
    80  			ms.StoreMessageInfo(mi)
    81  		}
    82  		return ms
    83  	}
    84  	return mi.MessageOf(x)
    85  }
    86  
    87  // Deprecated: Use LinearAlignment.ProtoReflect.Descriptor instead.
    88  func (*LinearAlignment) Descriptor() ([]byte, []int) {
    89  	return file_google_genomics_v1_readalignment_proto_rawDescGZIP(), []int{0}
    90  }
    91  
    92  func (x *LinearAlignment) GetPosition() *Position {
    93  	if x != nil {
    94  		return x.Position
    95  	}
    96  	return nil
    97  }
    98  
    99  func (x *LinearAlignment) GetMappingQuality() int32 {
   100  	if x != nil {
   101  		return x.MappingQuality
   102  	}
   103  	return 0
   104  }
   105  
   106  func (x *LinearAlignment) GetCigar() []*CigarUnit {
   107  	if x != nil {
   108  		return x.Cigar
   109  	}
   110  	return nil
   111  }
   112  
   113  // A read alignment describes a linear alignment of a string of DNA to a
   114  // [reference sequence][google.genomics.v1.Reference], in addition to metadata
   115  // about the fragment (the molecule of DNA sequenced) and the read (the bases
   116  // which were read by the sequencer). A read is equivalent to a line in a SAM
   117  // file. A read belongs to exactly one read group and exactly one
   118  // [read group set][google.genomics.v1.ReadGroupSet].
   119  //
   120  // For more genomics resource definitions, see [Fundamentals of Google
   121  // Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
   122  //
   123  // ### Reverse-stranded reads
   124  //
   125  // Mapped reads (reads having a non-null `alignment`) can be aligned to either
   126  // the forward or the reverse strand of their associated reference. Strandedness
   127  // of a mapped read is encoded by `alignment.position.reverseStrand`.
   128  //
   129  // If we consider the reference to be a forward-stranded coordinate space of
   130  // `[0, reference.length)` with `0` as the left-most position and
   131  // `reference.length` as the right-most position, reads are always aligned left
   132  // to right. That is, `alignment.position.position` always refers to the
   133  // left-most reference coordinate and `alignment.cigar` describes the alignment
   134  // of this read to the reference from left to right. All per-base fields such as
   135  // `alignedSequence` and `alignedQuality` share this same left-to-right
   136  // orientation; this is true of reads which are aligned to either strand. For
   137  // reverse-stranded reads, this means that `alignedSequence` is the reverse
   138  // complement of the bases that were originally reported by the sequencing
   139  // machine.
   140  //
   141  // ### Generating a reference-aligned sequence string
   142  //
   143  // When interacting with mapped reads, it's often useful to produce a string
   144  // representing the local alignment of the read to reference. The following
   145  // pseudocode demonstrates one way of doing this:
   146  //
   147  //	out = ""
   148  //	offset = 0
   149  //	for c in read.alignment.cigar {
   150  //	  switch c.operation {
   151  //	  case "ALIGNMENT_MATCH", "SEQUENCE_MATCH", "SEQUENCE_MISMATCH":
   152  //	    out += read.alignedSequence[offset:offset+c.operationLength]
   153  //	    offset += c.operationLength
   154  //	    break
   155  //	  case "CLIP_SOFT", "INSERT":
   156  //	    offset += c.operationLength
   157  //	    break
   158  //	  case "PAD":
   159  //	    out += repeat("*", c.operationLength)
   160  //	    break
   161  //	  case "DELETE":
   162  //	    out += repeat("-", c.operationLength)
   163  //	    break
   164  //	  case "SKIP":
   165  //	    out += repeat(" ", c.operationLength)
   166  //	    break
   167  //	  case "CLIP_HARD":
   168  //	    break
   169  //	  }
   170  //	}
   171  //	return out
   172  //
   173  // ### Converting to SAM's CIGAR string
   174  //
   175  // The following pseudocode generates a SAM CIGAR string from the
   176  // `cigar` field. Note that this is a lossy conversion
   177  // (`cigar.referenceSequence` is lost).
   178  //
   179  //	cigarMap = {
   180  //	  "ALIGNMENT_MATCH": "M",
   181  //	  "INSERT": "I",
   182  //	  "DELETE": "D",
   183  //	  "SKIP": "N",
   184  //	  "CLIP_SOFT": "S",
   185  //	  "CLIP_HARD": "H",
   186  //	  "PAD": "P",
   187  //	  "SEQUENCE_MATCH": "=",
   188  //	  "SEQUENCE_MISMATCH": "X",
   189  //	}
   190  //	cigarStr = ""
   191  //	for c in read.alignment.cigar {
   192  //	  cigarStr += c.operationLength + cigarMap[c.operation]
   193  //	}
   194  //	return cigarStr
   195  type Read struct {
   196  	state         protoimpl.MessageState
   197  	sizeCache     protoimpl.SizeCache
   198  	unknownFields protoimpl.UnknownFields
   199  
   200  	// The server-generated read ID, unique across all reads. This is different
   201  	// from the `fragmentName`.
   202  	Id string `protobuf:"bytes,1,opt,name=id,proto3" json:"id,omitempty"`
   203  	// The ID of the read group this read belongs to. A read belongs to exactly
   204  	// one read group. This is a server-generated ID which is distinct from SAM's
   205  	// RG tag (for that value, see
   206  	// [ReadGroup.name][google.genomics.v1.ReadGroup.name]).
   207  	ReadGroupId string `protobuf:"bytes,2,opt,name=read_group_id,json=readGroupId,proto3" json:"read_group_id,omitempty"`
   208  	// The ID of the read group set this read belongs to. A read belongs to
   209  	// exactly one read group set.
   210  	ReadGroupSetId string `protobuf:"bytes,3,opt,name=read_group_set_id,json=readGroupSetId,proto3" json:"read_group_set_id,omitempty"`
   211  	// The fragment name. Equivalent to QNAME (query template name) in SAM.
   212  	FragmentName string `protobuf:"bytes,4,opt,name=fragment_name,json=fragmentName,proto3" json:"fragment_name,omitempty"`
   213  	// The orientation and the distance between reads from the fragment are
   214  	// consistent with the sequencing protocol (SAM flag 0x2).
   215  	ProperPlacement bool `protobuf:"varint,5,opt,name=proper_placement,json=properPlacement,proto3" json:"proper_placement,omitempty"`
   216  	// The fragment is a PCR or optical duplicate (SAM flag 0x400).
   217  	DuplicateFragment bool `protobuf:"varint,6,opt,name=duplicate_fragment,json=duplicateFragment,proto3" json:"duplicate_fragment,omitempty"`
   218  	// The observed length of the fragment, equivalent to TLEN in SAM.
   219  	FragmentLength int32 `protobuf:"varint,7,opt,name=fragment_length,json=fragmentLength,proto3" json:"fragment_length,omitempty"`
   220  	// The read number in sequencing. 0-based and less than numberReads. This
   221  	// field replaces SAM flag 0x40 and 0x80.
   222  	ReadNumber int32 `protobuf:"varint,8,opt,name=read_number,json=readNumber,proto3" json:"read_number,omitempty"`
   223  	// The number of reads in the fragment (extension to SAM flag 0x1).
   224  	NumberReads int32 `protobuf:"varint,9,opt,name=number_reads,json=numberReads,proto3" json:"number_reads,omitempty"`
   225  	// Whether this read did not pass filters, such as platform or vendor quality
   226  	// controls (SAM flag 0x200).
   227  	FailedVendorQualityChecks bool `protobuf:"varint,10,opt,name=failed_vendor_quality_checks,json=failedVendorQualityChecks,proto3" json:"failed_vendor_quality_checks,omitempty"`
   228  	// The linear alignment for this alignment record. This field is null for
   229  	// unmapped reads.
   230  	Alignment *LinearAlignment `protobuf:"bytes,11,opt,name=alignment,proto3" json:"alignment,omitempty"`
   231  	// Whether this alignment is secondary. Equivalent to SAM flag 0x100.
   232  	// A secondary alignment represents an alternative to the primary alignment
   233  	// for this read. Aligners may return secondary alignments if a read can map
   234  	// ambiguously to multiple coordinates in the genome. By convention, each read
   235  	// has one and only one alignment where both `secondaryAlignment`
   236  	// and `supplementaryAlignment` are false.
   237  	SecondaryAlignment bool `protobuf:"varint,12,opt,name=secondary_alignment,json=secondaryAlignment,proto3" json:"secondary_alignment,omitempty"`
   238  	// Whether this alignment is supplementary. Equivalent to SAM flag 0x800.
   239  	// Supplementary alignments are used in the representation of a chimeric
   240  	// alignment. In a chimeric alignment, a read is split into multiple
   241  	// linear alignments that map to different reference contigs. The first
   242  	// linear alignment in the read will be designated as the representative
   243  	// alignment; the remaining linear alignments will be designated as
   244  	// supplementary alignments. These alignments may have different mapping
   245  	// quality scores. In each linear alignment in a chimeric alignment, the read
   246  	// will be hard clipped. The `alignedSequence` and
   247  	// `alignedQuality` fields in the alignment record will only
   248  	// represent the bases for its respective linear alignment.
   249  	SupplementaryAlignment bool `protobuf:"varint,13,opt,name=supplementary_alignment,json=supplementaryAlignment,proto3" json:"supplementary_alignment,omitempty"`
   250  	// The bases of the read sequence contained in this alignment record,
   251  	// **without CIGAR operations applied** (equivalent to SEQ in SAM).
   252  	// `alignedSequence` and `alignedQuality` may be
   253  	// shorter than the full read sequence and quality. This will occur if the
   254  	// alignment is part of a chimeric alignment, or if the read was trimmed. When
   255  	// this occurs, the CIGAR for this read will begin/end with a hard clip
   256  	// operator that will indicate the length of the excised sequence.
   257  	AlignedSequence string `protobuf:"bytes,14,opt,name=aligned_sequence,json=alignedSequence,proto3" json:"aligned_sequence,omitempty"`
   258  	// The quality of the read sequence contained in this alignment record
   259  	// (equivalent to QUAL in SAM).
   260  	// `alignedSequence` and `alignedQuality` may be shorter than the full read
   261  	// sequence and quality. This will occur if the alignment is part of a
   262  	// chimeric alignment, or if the read was trimmed. When this occurs, the CIGAR
   263  	// for this read will begin/end with a hard clip operator that will indicate
   264  	// the length of the excised sequence.
   265  	AlignedQuality []int32 `protobuf:"varint,15,rep,packed,name=aligned_quality,json=alignedQuality,proto3" json:"aligned_quality,omitempty"`
   266  	// The mapping of the primary alignment of the
   267  	// `(readNumber+1)%numberReads` read in the fragment. It replaces
   268  	// mate position and mate strand in SAM.
   269  	NextMatePosition *Position `protobuf:"bytes,16,opt,name=next_mate_position,json=nextMatePosition,proto3" json:"next_mate_position,omitempty"`
   270  	// A map of additional read alignment information. This must be of the form
   271  	// map<string, string[]> (string key mapping to a list of string values).
   272  	Info map[string]*structpb.ListValue `protobuf:"bytes,17,rep,name=info,proto3" json:"info,omitempty" protobuf_key:"bytes,1,opt,name=key,proto3" protobuf_val:"bytes,2,opt,name=value,proto3"`
   273  }
   274  
   275  func (x *Read) Reset() {
   276  	*x = Read{}
   277  	if protoimpl.UnsafeEnabled {
   278  		mi := &file_google_genomics_v1_readalignment_proto_msgTypes[1]
   279  		ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x))
   280  		ms.StoreMessageInfo(mi)
   281  	}
   282  }
   283  
   284  func (x *Read) String() string {
   285  	return protoimpl.X.MessageStringOf(x)
   286  }
   287  
   288  func (*Read) ProtoMessage() {}
   289  
   290  func (x *Read) ProtoReflect() protoreflect.Message {
   291  	mi := &file_google_genomics_v1_readalignment_proto_msgTypes[1]
   292  	if protoimpl.UnsafeEnabled && x != nil {
   293  		ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x))
   294  		if ms.LoadMessageInfo() == nil {
   295  			ms.StoreMessageInfo(mi)
   296  		}
   297  		return ms
   298  	}
   299  	return mi.MessageOf(x)
   300  }
   301  
   302  // Deprecated: Use Read.ProtoReflect.Descriptor instead.
   303  func (*Read) Descriptor() ([]byte, []int) {
   304  	return file_google_genomics_v1_readalignment_proto_rawDescGZIP(), []int{1}
   305  }
   306  
   307  func (x *Read) GetId() string {
   308  	if x != nil {
   309  		return x.Id
   310  	}
   311  	return ""
   312  }
   313  
   314  func (x *Read) GetReadGroupId() string {
   315  	if x != nil {
   316  		return x.ReadGroupId
   317  	}
   318  	return ""
   319  }
   320  
   321  func (x *Read) GetReadGroupSetId() string {
   322  	if x != nil {
   323  		return x.ReadGroupSetId
   324  	}
   325  	return ""
   326  }
   327  
   328  func (x *Read) GetFragmentName() string {
   329  	if x != nil {
   330  		return x.FragmentName
   331  	}
   332  	return ""
   333  }
   334  
   335  func (x *Read) GetProperPlacement() bool {
   336  	if x != nil {
   337  		return x.ProperPlacement
   338  	}
   339  	return false
   340  }
   341  
   342  func (x *Read) GetDuplicateFragment() bool {
   343  	if x != nil {
   344  		return x.DuplicateFragment
   345  	}
   346  	return false
   347  }
   348  
   349  func (x *Read) GetFragmentLength() int32 {
   350  	if x != nil {
   351  		return x.FragmentLength
   352  	}
   353  	return 0
   354  }
   355  
   356  func (x *Read) GetReadNumber() int32 {
   357  	if x != nil {
   358  		return x.ReadNumber
   359  	}
   360  	return 0
   361  }
   362  
   363  func (x *Read) GetNumberReads() int32 {
   364  	if x != nil {
   365  		return x.NumberReads
   366  	}
   367  	return 0
   368  }
   369  
   370  func (x *Read) GetFailedVendorQualityChecks() bool {
   371  	if x != nil {
   372  		return x.FailedVendorQualityChecks
   373  	}
   374  	return false
   375  }
   376  
   377  func (x *Read) GetAlignment() *LinearAlignment {
   378  	if x != nil {
   379  		return x.Alignment
   380  	}
   381  	return nil
   382  }
   383  
   384  func (x *Read) GetSecondaryAlignment() bool {
   385  	if x != nil {
   386  		return x.SecondaryAlignment
   387  	}
   388  	return false
   389  }
   390  
   391  func (x *Read) GetSupplementaryAlignment() bool {
   392  	if x != nil {
   393  		return x.SupplementaryAlignment
   394  	}
   395  	return false
   396  }
   397  
   398  func (x *Read) GetAlignedSequence() string {
   399  	if x != nil {
   400  		return x.AlignedSequence
   401  	}
   402  	return ""
   403  }
   404  
   405  func (x *Read) GetAlignedQuality() []int32 {
   406  	if x != nil {
   407  		return x.AlignedQuality
   408  	}
   409  	return nil
   410  }
   411  
   412  func (x *Read) GetNextMatePosition() *Position {
   413  	if x != nil {
   414  		return x.NextMatePosition
   415  	}
   416  	return nil
   417  }
   418  
   419  func (x *Read) GetInfo() map[string]*structpb.ListValue {
   420  	if x != nil {
   421  		return x.Info
   422  	}
   423  	return nil
   424  }
   425  
   426  var File_google_genomics_v1_readalignment_proto protoreflect.FileDescriptor
   427  
   428  var file_google_genomics_v1_readalignment_proto_rawDesc = []byte{
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   514  }
   515  
   516  var (
   517  	file_google_genomics_v1_readalignment_proto_rawDescOnce sync.Once
   518  	file_google_genomics_v1_readalignment_proto_rawDescData = file_google_genomics_v1_readalignment_proto_rawDesc
   519  )
   520  
   521  func file_google_genomics_v1_readalignment_proto_rawDescGZIP() []byte {
   522  	file_google_genomics_v1_readalignment_proto_rawDescOnce.Do(func() {
   523  		file_google_genomics_v1_readalignment_proto_rawDescData = protoimpl.X.CompressGZIP(file_google_genomics_v1_readalignment_proto_rawDescData)
   524  	})
   525  	return file_google_genomics_v1_readalignment_proto_rawDescData
   526  }
   527  
   528  var file_google_genomics_v1_readalignment_proto_msgTypes = make([]protoimpl.MessageInfo, 3)
   529  var file_google_genomics_v1_readalignment_proto_goTypes = []interface{}{
   530  	(*LinearAlignment)(nil),    // 0: google.genomics.v1.LinearAlignment
   531  	(*Read)(nil),               // 1: google.genomics.v1.Read
   532  	nil,                        // 2: google.genomics.v1.Read.InfoEntry
   533  	(*Position)(nil),           // 3: google.genomics.v1.Position
   534  	(*CigarUnit)(nil),          // 4: google.genomics.v1.CigarUnit
   535  	(*structpb.ListValue)(nil), // 5: google.protobuf.ListValue
   536  }
   537  var file_google_genomics_v1_readalignment_proto_depIdxs = []int32{
   538  	3, // 0: google.genomics.v1.LinearAlignment.position:type_name -> google.genomics.v1.Position
   539  	4, // 1: google.genomics.v1.LinearAlignment.cigar:type_name -> google.genomics.v1.CigarUnit
   540  	0, // 2: google.genomics.v1.Read.alignment:type_name -> google.genomics.v1.LinearAlignment
   541  	3, // 3: google.genomics.v1.Read.next_mate_position:type_name -> google.genomics.v1.Position
   542  	2, // 4: google.genomics.v1.Read.info:type_name -> google.genomics.v1.Read.InfoEntry
   543  	5, // 5: google.genomics.v1.Read.InfoEntry.value:type_name -> google.protobuf.ListValue
   544  	6, // [6:6] is the sub-list for method output_type
   545  	6, // [6:6] is the sub-list for method input_type
   546  	6, // [6:6] is the sub-list for extension type_name
   547  	6, // [6:6] is the sub-list for extension extendee
   548  	0, // [0:6] is the sub-list for field type_name
   549  }
   550  
   551  func init() { file_google_genomics_v1_readalignment_proto_init() }
   552  func file_google_genomics_v1_readalignment_proto_init() {
   553  	if File_google_genomics_v1_readalignment_proto != nil {
   554  		return
   555  	}
   556  	file_google_genomics_v1_cigar_proto_init()
   557  	file_google_genomics_v1_position_proto_init()
   558  	if !protoimpl.UnsafeEnabled {
   559  		file_google_genomics_v1_readalignment_proto_msgTypes[0].Exporter = func(v interface{}, i int) interface{} {
   560  			switch v := v.(*LinearAlignment); i {
   561  			case 0:
   562  				return &v.state
   563  			case 1:
   564  				return &v.sizeCache
   565  			case 2:
   566  				return &v.unknownFields
   567  			default:
   568  				return nil
   569  			}
   570  		}
   571  		file_google_genomics_v1_readalignment_proto_msgTypes[1].Exporter = func(v interface{}, i int) interface{} {
   572  			switch v := v.(*Read); i {
   573  			case 0:
   574  				return &v.state
   575  			case 1:
   576  				return &v.sizeCache
   577  			case 2:
   578  				return &v.unknownFields
   579  			default:
   580  				return nil
   581  			}
   582  		}
   583  	}
   584  	type x struct{}
   585  	out := protoimpl.TypeBuilder{
   586  		File: protoimpl.DescBuilder{
   587  			GoPackagePath: reflect.TypeOf(x{}).PkgPath(),
   588  			RawDescriptor: file_google_genomics_v1_readalignment_proto_rawDesc,
   589  			NumEnums:      0,
   590  			NumMessages:   3,
   591  			NumExtensions: 0,
   592  			NumServices:   0,
   593  		},
   594  		GoTypes:           file_google_genomics_v1_readalignment_proto_goTypes,
   595  		DependencyIndexes: file_google_genomics_v1_readalignment_proto_depIdxs,
   596  		MessageInfos:      file_google_genomics_v1_readalignment_proto_msgTypes,
   597  	}.Build()
   598  	File_google_genomics_v1_readalignment_proto = out.File
   599  	file_google_genomics_v1_readalignment_proto_rawDesc = nil
   600  	file_google_genomics_v1_readalignment_proto_goTypes = nil
   601  	file_google_genomics_v1_readalignment_proto_depIdxs = nil
   602  }
   603
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