| // 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/readalignment.proto |
| |
| package genomics |
| |
| import ( |
| reflect "reflect" |
| sync "sync" |
| |
| proto "github.com/golang/protobuf/proto" |
| _struct "github.com/golang/protobuf/ptypes/struct" |
| _ "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 |
| |
| // A linear alignment can be represented by one CIGAR string. Describes the |
| // mapped position and local alignment of the read to the reference. |
| type LinearAlignment struct { |
| state protoimpl.MessageState |
| sizeCache protoimpl.SizeCache |
| unknownFields protoimpl.UnknownFields |
| |
| // The position of this alignment. |
| Position *Position `protobuf:"bytes,1,opt,name=position,proto3" json:"position,omitempty"` |
| // The mapping quality of this alignment. Represents how likely |
| // the read maps to this position as opposed to other locations. |
| // |
| // Specifically, this is -10 log10 Pr(mapping position is wrong), rounded to |
| // the nearest integer. |
| MappingQuality int32 `protobuf:"varint,2,opt,name=mapping_quality,json=mappingQuality,proto3" json:"mapping_quality,omitempty"` |
| // Represents the local alignment of this sequence (alignment matches, indels, |
| // etc) against the reference. |
| Cigar []*CigarUnit `protobuf:"bytes,3,rep,name=cigar,proto3" json:"cigar,omitempty"` |
| } |
| |
| func (x *LinearAlignment) Reset() { |
| *x = LinearAlignment{} |
| if protoimpl.UnsafeEnabled { |
| mi := &file_google_genomics_v1_readalignment_proto_msgTypes[0] |
| ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) |
| ms.StoreMessageInfo(mi) |
| } |
| } |
| |
| func (x *LinearAlignment) String() string { |
| return protoimpl.X.MessageStringOf(x) |
| } |
| |
| func (*LinearAlignment) ProtoMessage() {} |
| |
| func (x *LinearAlignment) ProtoReflect() protoreflect.Message { |
| mi := &file_google_genomics_v1_readalignment_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 LinearAlignment.ProtoReflect.Descriptor instead. |
| func (*LinearAlignment) Descriptor() ([]byte, []int) { |
| return file_google_genomics_v1_readalignment_proto_rawDescGZIP(), []int{0} |
| } |
| |
| func (x *LinearAlignment) GetPosition() *Position { |
| if x != nil { |
| return x.Position |
| } |
| return nil |
| } |
| |
| func (x *LinearAlignment) GetMappingQuality() int32 { |
| if x != nil { |
| return x.MappingQuality |
| } |
| return 0 |
| } |
| |
| func (x *LinearAlignment) GetCigar() []*CigarUnit { |
| if x != nil { |
| return x.Cigar |
| } |
| return nil |
| } |
| |
| // A read alignment describes a linear alignment of a string of DNA to a |
| // [reference sequence][google.genomics.v1.Reference], in addition to metadata |
| // about the fragment (the molecule of DNA sequenced) and the read (the bases |
| // which were read by the sequencer). A read is equivalent to a line in a SAM |
| // file. A read belongs to exactly one read group and exactly one |
| // [read group set][google.genomics.v1.ReadGroupSet]. |
| // |
| // For more genomics resource definitions, see [Fundamentals of Google |
| // Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) |
| // |
| // ### Reverse-stranded reads |
| // |
| // Mapped reads (reads having a non-null `alignment`) can be aligned to either |
| // the forward or the reverse strand of their associated reference. Strandedness |
| // of a mapped read is encoded by `alignment.position.reverseStrand`. |
| // |
| // If we consider the reference to be a forward-stranded coordinate space of |
| // `[0, reference.length)` with `0` as the left-most position and |
| // `reference.length` as the right-most position, reads are always aligned left |
| // to right. That is, `alignment.position.position` always refers to the |
| // left-most reference coordinate and `alignment.cigar` describes the alignment |
| // of this read to the reference from left to right. All per-base fields such as |
| // `alignedSequence` and `alignedQuality` share this same left-to-right |
| // orientation; this is true of reads which are aligned to either strand. For |
| // reverse-stranded reads, this means that `alignedSequence` is the reverse |
| // complement of the bases that were originally reported by the sequencing |
| // machine. |
| // |
| // ### Generating a reference-aligned sequence string |
| // |
| // When interacting with mapped reads, it's often useful to produce a string |
| // representing the local alignment of the read to reference. The following |
| // pseudocode demonstrates one way of doing this: |
| // |
| // out = "" |
| // offset = 0 |
| // for c in read.alignment.cigar { |
| // switch c.operation { |
| // case "ALIGNMENT_MATCH", "SEQUENCE_MATCH", "SEQUENCE_MISMATCH": |
| // out += read.alignedSequence[offset:offset+c.operationLength] |
| // offset += c.operationLength |
| // break |
| // case "CLIP_SOFT", "INSERT": |
| // offset += c.operationLength |
| // break |
| // case "PAD": |
| // out += repeat("*", c.operationLength) |
| // break |
| // case "DELETE": |
| // out += repeat("-", c.operationLength) |
| // break |
| // case "SKIP": |
| // out += repeat(" ", c.operationLength) |
| // break |
| // case "CLIP_HARD": |
| // break |
| // } |
| // } |
| // return out |
| // |
| // ### Converting to SAM's CIGAR string |
| // |
| // The following pseudocode generates a SAM CIGAR string from the |
| // `cigar` field. Note that this is a lossy conversion |
| // (`cigar.referenceSequence` is lost). |
| // |
| // cigarMap = { |
| // "ALIGNMENT_MATCH": "M", |
| // "INSERT": "I", |
| // "DELETE": "D", |
| // "SKIP": "N", |
| // "CLIP_SOFT": "S", |
| // "CLIP_HARD": "H", |
| // "PAD": "P", |
| // "SEQUENCE_MATCH": "=", |
| // "SEQUENCE_MISMATCH": "X", |
| // } |
| // cigarStr = "" |
| // for c in read.alignment.cigar { |
| // cigarStr += c.operationLength + cigarMap[c.operation] |
| // } |
| // return cigarStr |
| type Read struct { |
| state protoimpl.MessageState |
| sizeCache protoimpl.SizeCache |
| unknownFields protoimpl.UnknownFields |
| |
| // The server-generated read ID, unique across all reads. This is different |
| // from the `fragmentName`. |
| Id string `protobuf:"bytes,1,opt,name=id,proto3" json:"id,omitempty"` |
| // The ID of the read group this read belongs to. A read belongs to exactly |
| // one read group. This is a server-generated ID which is distinct from SAM's |
| // RG tag (for that value, see |
| // [ReadGroup.name][google.genomics.v1.ReadGroup.name]). |
| ReadGroupId string `protobuf:"bytes,2,opt,name=read_group_id,json=readGroupId,proto3" json:"read_group_id,omitempty"` |
| // The ID of the read group set this read belongs to. A read belongs to |
| // exactly one read group set. |
| ReadGroupSetId string `protobuf:"bytes,3,opt,name=read_group_set_id,json=readGroupSetId,proto3" json:"read_group_set_id,omitempty"` |
| // The fragment name. Equivalent to QNAME (query template name) in SAM. |
| FragmentName string `protobuf:"bytes,4,opt,name=fragment_name,json=fragmentName,proto3" json:"fragment_name,omitempty"` |
| // The orientation and the distance between reads from the fragment are |
| // consistent with the sequencing protocol (SAM flag 0x2). |
| ProperPlacement bool `protobuf:"varint,5,opt,name=proper_placement,json=properPlacement,proto3" json:"proper_placement,omitempty"` |
| // The fragment is a PCR or optical duplicate (SAM flag 0x400). |
| DuplicateFragment bool `protobuf:"varint,6,opt,name=duplicate_fragment,json=duplicateFragment,proto3" json:"duplicate_fragment,omitempty"` |
| // The observed length of the fragment, equivalent to TLEN in SAM. |
| FragmentLength int32 `protobuf:"varint,7,opt,name=fragment_length,json=fragmentLength,proto3" json:"fragment_length,omitempty"` |
| // The read number in sequencing. 0-based and less than numberReads. This |
| // field replaces SAM flag 0x40 and 0x80. |
| ReadNumber int32 `protobuf:"varint,8,opt,name=read_number,json=readNumber,proto3" json:"read_number,omitempty"` |
| // The number of reads in the fragment (extension to SAM flag 0x1). |
| NumberReads int32 `protobuf:"varint,9,opt,name=number_reads,json=numberReads,proto3" json:"number_reads,omitempty"` |
| // Whether this read did not pass filters, such as platform or vendor quality |
| // controls (SAM flag 0x200). |
| FailedVendorQualityChecks bool `protobuf:"varint,10,opt,name=failed_vendor_quality_checks,json=failedVendorQualityChecks,proto3" json:"failed_vendor_quality_checks,omitempty"` |
| // The linear alignment for this alignment record. This field is null for |
| // unmapped reads. |
| Alignment *LinearAlignment `protobuf:"bytes,11,opt,name=alignment,proto3" json:"alignment,omitempty"` |
| // Whether this alignment is secondary. Equivalent to SAM flag 0x100. |
| // A secondary alignment represents an alternative to the primary alignment |
| // for this read. Aligners may return secondary alignments if a read can map |
| // ambiguously to multiple coordinates in the genome. By convention, each read |
| // has one and only one alignment where both `secondaryAlignment` |
| // and `supplementaryAlignment` are false. |
| SecondaryAlignment bool `protobuf:"varint,12,opt,name=secondary_alignment,json=secondaryAlignment,proto3" json:"secondary_alignment,omitempty"` |
| // Whether this alignment is supplementary. Equivalent to SAM flag 0x800. |
| // Supplementary alignments are used in the representation of a chimeric |
| // alignment. In a chimeric alignment, a read is split into multiple |
| // linear alignments that map to different reference contigs. The first |
| // linear alignment in the read will be designated as the representative |
| // alignment; the remaining linear alignments will be designated as |
| // supplementary alignments. These alignments may have different mapping |
| // quality scores. In each linear alignment in a chimeric alignment, the read |
| // will be hard clipped. The `alignedSequence` and |
| // `alignedQuality` fields in the alignment record will only |
| // represent the bases for its respective linear alignment. |
| SupplementaryAlignment bool `protobuf:"varint,13,opt,name=supplementary_alignment,json=supplementaryAlignment,proto3" json:"supplementary_alignment,omitempty"` |
| // The bases of the read sequence contained in this alignment record, |
| // **without CIGAR operations applied** (equivalent to SEQ in SAM). |
| // `alignedSequence` and `alignedQuality` may be |
| // shorter than the full read sequence and quality. This will occur if the |
| // alignment is part of a chimeric alignment, or if the read was trimmed. When |
| // this occurs, the CIGAR for this read will begin/end with a hard clip |
| // operator that will indicate the length of the excised sequence. |
| AlignedSequence string `protobuf:"bytes,14,opt,name=aligned_sequence,json=alignedSequence,proto3" json:"aligned_sequence,omitempty"` |
| // The quality of the read sequence contained in this alignment record |
| // (equivalent to QUAL in SAM). |
| // `alignedSequence` and `alignedQuality` may be shorter than the full read |
| // sequence and quality. This will occur if the alignment is part of a |
| // chimeric alignment, or if the read was trimmed. When this occurs, the CIGAR |
| // for this read will begin/end with a hard clip operator that will indicate |
| // the length of the excised sequence. |
| AlignedQuality []int32 `protobuf:"varint,15,rep,packed,name=aligned_quality,json=alignedQuality,proto3" json:"aligned_quality,omitempty"` |
| // The mapping of the primary alignment of the |
| // `(readNumber+1)%numberReads` read in the fragment. It replaces |
| // mate position and mate strand in SAM. |
| NextMatePosition *Position `protobuf:"bytes,16,opt,name=next_mate_position,json=nextMatePosition,proto3" json:"next_mate_position,omitempty"` |
| // A map of additional read alignment information. This must be of the form |
| // map<string, string[]> (string key mapping to a list of string values). |
| Info map[string]*_struct.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"` |
| } |
| |
| func (x *Read) Reset() { |
| *x = Read{} |
| if protoimpl.UnsafeEnabled { |
| mi := &file_google_genomics_v1_readalignment_proto_msgTypes[1] |
| ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) |
| ms.StoreMessageInfo(mi) |
| } |
| } |
| |
| func (x *Read) String() string { |
| return protoimpl.X.MessageStringOf(x) |
| } |
| |
| func (*Read) ProtoMessage() {} |
| |
| func (x *Read) ProtoReflect() protoreflect.Message { |
| mi := &file_google_genomics_v1_readalignment_proto_msgTypes[1] |
| 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 Read.ProtoReflect.Descriptor instead. |
| func (*Read) Descriptor() ([]byte, []int) { |
| return file_google_genomics_v1_readalignment_proto_rawDescGZIP(), []int{1} |
| } |
| |
| func (x *Read) GetId() string { |
| if x != nil { |
| return x.Id |
| } |
| return "" |
| } |
| |
| func (x *Read) GetReadGroupId() string { |
| if x != nil { |
| return x.ReadGroupId |
| } |
| return "" |
| } |
| |
| func (x *Read) GetReadGroupSetId() string { |
| if x != nil { |
| return x.ReadGroupSetId |
| } |
| return "" |
| } |
| |
| func (x *Read) GetFragmentName() string { |
| if x != nil { |
| return x.FragmentName |
| } |
| return "" |
| } |
| |
| func (x *Read) GetProperPlacement() bool { |
| if x != nil { |
| return x.ProperPlacement |
| } |
| return false |
| } |
| |
| func (x *Read) GetDuplicateFragment() bool { |
| if x != nil { |
| return x.DuplicateFragment |
| } |
| return false |
| } |
| |
| func (x *Read) GetFragmentLength() int32 { |
| if x != nil { |
| return x.FragmentLength |
| } |
| return 0 |
| } |
| |
| func (x *Read) GetReadNumber() int32 { |
| if x != nil { |
| return x.ReadNumber |
| } |
| return 0 |
| } |
| |
| func (x *Read) GetNumberReads() int32 { |
| if x != nil { |
| return x.NumberReads |
| } |
| return 0 |
| } |
| |
| func (x *Read) GetFailedVendorQualityChecks() bool { |
| if x != nil { |
| return x.FailedVendorQualityChecks |
| } |
| return false |
| } |
| |
| func (x *Read) GetAlignment() *LinearAlignment { |
| if x != nil { |
| return x.Alignment |
| } |
| return nil |
| } |
| |
| func (x *Read) GetSecondaryAlignment() bool { |
| if x != nil { |
| return x.SecondaryAlignment |
| } |
| return false |
| } |
| |
| func (x *Read) GetSupplementaryAlignment() bool { |
| if x != nil { |
| return x.SupplementaryAlignment |
| } |
| return false |
| } |
| |
| func (x *Read) GetAlignedSequence() string { |
| if x != nil { |
| return x.AlignedSequence |
| } |
| return "" |
| } |
| |
| func (x *Read) GetAlignedQuality() []int32 { |
| if x != nil { |
| return x.AlignedQuality |
| } |
| return nil |
| } |
| |
| func (x *Read) GetNextMatePosition() *Position { |
| if x != nil { |
| return x.NextMatePosition |
| } |
| return nil |
| } |
| |
| func (x *Read) GetInfo() map[string]*_struct.ListValue { |
| if x != nil { |
| return x.Info |
| } |
| return nil |
| } |
| |
| var File_google_genomics_v1_readalignment_proto protoreflect.FileDescriptor |
| |
| var file_google_genomics_v1_readalignment_proto_rawDesc = []byte{ |
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| } |
| |
| var ( |
| file_google_genomics_v1_readalignment_proto_rawDescOnce sync.Once |
| file_google_genomics_v1_readalignment_proto_rawDescData = file_google_genomics_v1_readalignment_proto_rawDesc |
| ) |
| |
| func file_google_genomics_v1_readalignment_proto_rawDescGZIP() []byte { |
| file_google_genomics_v1_readalignment_proto_rawDescOnce.Do(func() { |
| file_google_genomics_v1_readalignment_proto_rawDescData = protoimpl.X.CompressGZIP(file_google_genomics_v1_readalignment_proto_rawDescData) |
| }) |
| return file_google_genomics_v1_readalignment_proto_rawDescData |
| } |
| |
| var file_google_genomics_v1_readalignment_proto_msgTypes = make([]protoimpl.MessageInfo, 3) |
| var file_google_genomics_v1_readalignment_proto_goTypes = []interface{}{ |
| (*LinearAlignment)(nil), // 0: google.genomics.v1.LinearAlignment |
| (*Read)(nil), // 1: google.genomics.v1.Read |
| nil, // 2: google.genomics.v1.Read.InfoEntry |
| (*Position)(nil), // 3: google.genomics.v1.Position |
| (*CigarUnit)(nil), // 4: google.genomics.v1.CigarUnit |
| (*_struct.ListValue)(nil), // 5: google.protobuf.ListValue |
| } |
| var file_google_genomics_v1_readalignment_proto_depIdxs = []int32{ |
| 3, // 0: google.genomics.v1.LinearAlignment.position:type_name -> google.genomics.v1.Position |
| 4, // 1: google.genomics.v1.LinearAlignment.cigar:type_name -> google.genomics.v1.CigarUnit |
| 0, // 2: google.genomics.v1.Read.alignment:type_name -> google.genomics.v1.LinearAlignment |
| 3, // 3: google.genomics.v1.Read.next_mate_position:type_name -> google.genomics.v1.Position |
| 2, // 4: google.genomics.v1.Read.info:type_name -> google.genomics.v1.Read.InfoEntry |
| 5, // 5: google.genomics.v1.Read.InfoEntry.value:type_name -> google.protobuf.ListValue |
| 6, // [6:6] is the sub-list for method output_type |
| 6, // [6:6] is the sub-list for method input_type |
| 6, // [6:6] is the sub-list for extension type_name |
| 6, // [6:6] is the sub-list for extension extendee |
| 0, // [0:6] is the sub-list for field type_name |
| } |
| |
| func init() { file_google_genomics_v1_readalignment_proto_init() } |
| func file_google_genomics_v1_readalignment_proto_init() { |
| if File_google_genomics_v1_readalignment_proto != nil { |
| return |
| } |
| file_google_genomics_v1_cigar_proto_init() |
| file_google_genomics_v1_position_proto_init() |
| if !protoimpl.UnsafeEnabled { |
| file_google_genomics_v1_readalignment_proto_msgTypes[0].Exporter = func(v interface{}, i int) interface{} { |
| switch v := v.(*LinearAlignment); i { |
| case 0: |
| return &v.state |
| case 1: |
| return &v.sizeCache |
| case 2: |
| return &v.unknownFields |
| default: |
| return nil |
| } |
| } |
| file_google_genomics_v1_readalignment_proto_msgTypes[1].Exporter = func(v interface{}, i int) interface{} { |
| switch v := v.(*Read); 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_readalignment_proto_rawDesc, |
| NumEnums: 0, |
| NumMessages: 3, |
| NumExtensions: 0, |
| NumServices: 0, |
| }, |
| GoTypes: file_google_genomics_v1_readalignment_proto_goTypes, |
| DependencyIndexes: file_google_genomics_v1_readalignment_proto_depIdxs, |
| MessageInfos: file_google_genomics_v1_readalignment_proto_msgTypes, |
| }.Build() |
| File_google_genomics_v1_readalignment_proto = out.File |
| file_google_genomics_v1_readalignment_proto_rawDesc = nil |
| file_google_genomics_v1_readalignment_proto_goTypes = nil |
| file_google_genomics_v1_readalignment_proto_depIdxs = nil |
| } |